A B C D E F G H I J K L M N O P Q R S T U V W X Z _

A

aa - Class in org.forester.applications

aa() - Constructor for class org.forester.applications.aa

AA_REGEXP - Static variable in interface org.forester.sequence.MolecularSequence

aaa - Class in org.forester.applications

aaa() - Constructor for class org.forester.applications.aaa

AbstractRenderer - Class in org.forester.development

AbstractRenderer() - Constructor for class org.forester.development.AbstractRenderer

ACCESSION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Accession - Class in org.forester.phylogeny.data

Accession(String) - Constructor for class org.forester.phylogeny.data.Accession

Accession(String, String) - Constructor for class org.forester.phylogeny.data.Accession

Accession(String, Accession.Source) - Constructor for class org.forester.phylogeny.data.Accession

Accession(String, String, String) - Constructor for class org.forester.phylogeny.data.Accession

Accession.Source - Enum in org.forester.phylogeny.data

ACCESSION_COMMENT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

ACCESSION_SOURCE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

AccessionParser - Class in org.forester.io.parsers.phyloxml.data

actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.ArchaeopteryxE

actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.FontChooser

actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.MainFrame

Action performed.

actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.MainFrameApplication

actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.tools.PhyloInferenceDialog

actionPerformed(ActionEvent) - Method in class org.forester.archaeopteryx.TreePanel

actionPerformed(ActionEvent) - Method in class org.forester.msa_compactor.Chart

activate() - Method in class org.forester.archaeopteryx.tools.PhyloInferenceDialog

addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains, SortedSet<BinaryDomainCombination>) - Static method in class org.forester.surfacing.SurfacingUtil

addAllDomainIdsToSet(GenomeWideCombinableDomains, SortedSet<String>) - Static method in class org.forester.surfacing.SurfacingUtil

addAnnotation(Annotation) - Method in class org.forester.phylogeny.data.Sequence

addAsChild(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny

Adds this Phylogeny to the list of child nodes of PhylogenyNode parent and sets the parent of this to parent.

addAsChild(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode

Adds PhylogenyNode n to the list of child nodes and sets the _parent of n to this.

addAsSibling(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny

addChildElement(XmlElement) - Method in class org.forester.io.parsers.phyloxml.XmlElement

addCombinableDomain(String) - Method in class org.forester.surfacing.BasicCombinableDomains

addCombinableDomain(String) - Method in interface org.forester.surfacing.CombinableDomains

To add a new combinable domain.

addConfidence(Confidence) - Method in class org.forester.phylogeny.data.BranchData

addCrossReference(Accession) - Method in class org.forester.phylogeny.data.Sequence

addDistribution(Distribution) - Method in class org.forester.phylogeny.data.NodeData

addDomain(ProteinDomain) - Method in class org.forester.phylogeny.data.DomainArchitecture

addDomainIdToIgnore(String) - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

addGainedCharacter(String) - Method in class org.forester.phylogeny.data.BinaryCharacters

addKeyDomainProtein(String) - Method in class org.forester.surfacing.BasicCombinableDomains

addKeyDomainProtein(String) - Method in interface org.forester.surfacing.CombinableDomains

addLength(Species, int) - Method in class org.forester.surfacing.DomainLengths

addLengths(List<Protein>) - Method in class org.forester.surfacing.DomainLengthsTable

addLostCharacter(String) - Method in class org.forester.phylogeny.data.BinaryCharacters

addMolecularSeqsToTree(Phylogeny, Msa) - Static method in class org.forester.phylogeny.PhylogenyMethods

addPairing(double, int, int) - Method in class org.forester.evoinference.distance.Sarray

addPairing(int, int, int) - Method in class org.forester.evoinference.distance.Sarray

addPairing(double, int, int) - Method in class org.forester.evoinference.distance.Sset

addPairing(int, int, int) - Method in class org.forester.evoinference.distance.Sset

addPhylogenyInNewTab(Phylogeny, Configuration, String, String) - Method in class org.forester.archaeopteryx.MainPanel

addPresentCharacter(String) - Method in class org.forester.phylogeny.data.BinaryCharacters

addProcess(String) - Method in class org.forester.archaeopteryx.tools.ProcessPool

addProperty(Property) - Method in class org.forester.phylogeny.data.PropertiesMap

addProteinDomain(Domain) - Method in class org.forester.protein.BasicProtein

addProteinDomain(Domain) - Method in interface org.forester.protein.Protein

addReference(Reference) - Method in class org.forester.phylogeny.data.NodeData

addSequence(Sequence) - Method in class org.forester.phylogeny.data.NodeData

addSequenceRelation(SequenceRelation) - Method in class org.forester.phylogeny.data.Sequence

addTaxonomy(Taxonomy) - Method in class org.forester.phylogeny.data.NodeData

addUri(Uri) - Method in class org.forester.phylogeny.data.Annotation

addUri(Uri) - Method in interface org.forester.phylogeny.data.MultipleUris

addUri(Uri) - Method in class org.forester.phylogeny.data.Sequence

addUri(Uri) - Method in class org.forester.phylogeny.data.Taxonomy

addValue(double) - Method in class org.forester.util.BasicDescriptiveStatistics

addValue(double) - Method in interface org.forester.util.DescriptiveStatistics

AdjactantDirectedBinaryDomainCombination - Class in org.forester.surfacing

AdjactantDirectedCombinableDomains - Class in org.forester.surfacing

AdjactantDirectedCombinableDomains(String, Species) - Constructor for class org.forester.surfacing.AdjactantDirectedCombinableDomains

ALL_PFAMS_ENCOUNTERED_SUFFIX - Static variable in class org.forester.application.surfacing

ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX - Static variable in class org.forester.application.surfacing

ALL_PFAMS_GAINED_AS_DC_SUFFIX - Static variable in class org.forester.application.surfacing

ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX - Static variable in class org.forester.application.surfacing

ALL_PFAMS_LOST_AS_DC_SUFFIX - Static variable in class org.forester.application.surfacing

ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX - Static variable in class org.forester.application.surfacing

ALLOW_DDBJ_BLAST - Static variable in class org.forester.archaeopteryx.Constants

ALLOW_MULTIPLE_PARENTS_DEFAULT - Static variable in class org.forester.phylogeny.Phylogeny

ALVEOLATA_COLOR - Static variable in class org.forester.util.TaxonomyColors

AMIGO_LINK - Static variable in class org.forester.surfacing.SurfacingConstants

AMOEBOZOA_COLOR - Static variable in class org.forester.util.TaxonomyColors

AncestralTaxonomyInference - Class in org.forester.analysis

AncestralTaxonomyInference() - Constructor for class org.forester.analysis.AncestralTaxonomyInference

AncestralTaxonomyInferenceException - Exception in org.forester.analysis

AncestralTaxonomyInferenceException() - Constructor for exception org.forester.analysis.AncestralTaxonomyInferenceException

AncestralTaxonomyInferenceException(String) - Constructor for exception org.forester.analysis.AncestralTaxonomyInferenceException

AncestralTaxonomyInferrer - Class in org.forester.archaeopteryx.tools

AncestralTaxonomyInferrer(MainFrame, TreePanel, Phylogeny) - Constructor for class org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer

ANNOTATION - Static variable in class org.forester.archaeopteryx.TreeColorSet

ANNOTATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Annotation - Class in org.forester.phylogeny.data

Annotation() - Constructor for class org.forester.phylogeny.data.Annotation

Annotation(String) - Constructor for class org.forester.phylogeny.data.Annotation

Annotation(String, String) - Constructor for class org.forester.phylogeny.data.Annotation

ANNOTATION_DESC - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

ANNOTATION_EVIDENCE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

ANNOTATION_REF_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

ANNOTATION_SOURCE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

ANNOTATION_TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

AnnotationParser - Class in org.forester.io.parsers.phyloxml.data

annotator - Class in org.forester.application

annotator() - Constructor for class org.forester.application.annotator

APACHE_FEATURES_VALIDATION_SCHEMA - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser

APACHE_FEATURES_VALIDATION_SCHEMA - Static variable in class org.forester.io.parsers.tol.TolParser

APACHE_FEATURES_VALIDATION_SCHEMA_FULL - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser

APACHE_FEATURES_VALIDATION_SCHEMA_FULL - Static variable in class org.forester.io.parsers.tol.TolParser

APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser

APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION - Static variable in class org.forester.io.parsers.tol.TolParser

appendClose(Writer, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendElement(Writer, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendElement(Writer, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendElement(Writer, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendElement(Writer, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendElement(Writer, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendElement(Writer, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendElement(Writer, String, String, String, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendElement(Writer, String, String, String, String, String, String, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendOpen(Writer, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendOpen(Writer, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendOpen(Writer, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendOpen(Writer, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendOpen(Writer, String, String, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendOpen(Writer, String, String, String, String, String, String, String, String, String, String, String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

appendSeparatorIfNotEmpty(StringBuffer, char) - Static method in class org.forester.util.ForesterUtil

appendValue(String) - Method in class org.forester.io.parsers.phyloxml.XmlElement

APTX_VISUALIZATION_REF - Static variable in class org.forester.phylogeny.data.NodeVisualData

AptxUtil - Class in org.forester.archaeopteryx

AptxUtil() - Constructor for class org.forester.archaeopteryx.AptxUtil

AptxUtil.GraphicsExportType - Enum in org.forester.archaeopteryx

APUSOZOA_COLOR - Static variable in class org.forester.util.TaxonomyColors

ARACYC_STR - Static variable in interface org.forester.go.GoXRef

ARCHAEA - Static variable in class org.forester.ws.seqdb.UniProtTaxonomy

ARCHAEA_COLOR - Static variable in class org.forester.util.TaxonomyColors

Archaeopteryx - Class in org.forester.archaeopteryx

Archaeopteryx() - Constructor for class org.forester.archaeopteryx.Archaeopteryx

ArchaeopteryxA - Class in org.forester.archaeopteryx

ArchaeopteryxA() - Constructor for class org.forester.archaeopteryx.ArchaeopteryxA

ArchaeopteryxE - Class in org.forester.archaeopteryx

ArchaeopteryxE() - Constructor for class org.forester.archaeopteryx.ArchaeopteryxE

arithmeticMean() - Method in class org.forester.util.BasicDescriptiveStatistics

arithmeticMean() - Method in interface org.forester.util.DescriptiveStatistics

AsciiHistogram - Class in org.forester.util

AsciiHistogram(DescriptiveStatistics) - Constructor for class org.forester.util.AsciiHistogram

AsciiHistogram(DescriptiveStatistics, String) - Constructor for class org.forester.util.AsciiHistogram

asSequenceList() - Method in class org.forester.msa.BasicMsa

asSequenceList() - Method in interface org.forester.msa.Msa

asSimpleText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

asSimpleText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

asSimpleText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

asSimpleText() - Method in class org.forester.go.BasicGoTerm

asSimpleText() - Method in class org.forester.phylogeny.data.Accession

asSimpleText() - Method in class org.forester.phylogeny.data.Annotation

asSimpleText() - Method in class org.forester.phylogeny.data.BinaryCharacters

asSimpleText() - Method in class org.forester.phylogeny.data.BranchColor

asSimpleText() - Method in class org.forester.phylogeny.data.BranchData

asSimpleText() - Method in class org.forester.phylogeny.data.BranchWidth

asSimpleText() - Method in class org.forester.phylogeny.data.Confidence

asSimpleText() - Method in class org.forester.phylogeny.data.Date

asSimpleText() - Method in class org.forester.phylogeny.data.Distribution

asSimpleText() - Method in class org.forester.phylogeny.data.DomainArchitecture

asSimpleText() - Method in class org.forester.phylogeny.data.Event

asSimpleText() - Method in class org.forester.phylogeny.data.Identifier

asSimpleText() - Method in class org.forester.phylogeny.data.NodeData

asSimpleText() - Method in class org.forester.phylogeny.data.NodeVisualData

asSimpleText() - Method in interface org.forester.phylogeny.data.PhylogenyData

asSimpleText() - Method in class org.forester.phylogeny.data.Point

asSimpleText() - Method in class org.forester.phylogeny.data.Polygon

asSimpleText() - Method in class org.forester.phylogeny.data.PropertiesMap

asSimpleText() - Method in class org.forester.phylogeny.data.Property

asSimpleText() - Method in class org.forester.phylogeny.data.ProteinDomain

asSimpleText() - Method in class org.forester.phylogeny.data.Reference

asSimpleText() - Method in class org.forester.phylogeny.data.Sequence

asSimpleText() - Method in class org.forester.phylogeny.data.SequenceRelation

asSimpleText() - Method in class org.forester.phylogeny.data.Taxonomy

asSimpleText() - Method in class org.forester.phylogeny.data.Uri

asString() - Method in interface org.forester.pccx.Coverage

asString() - Method in interface org.forester.pccx.CoverageCalculationOptions

asString() - Method in class org.forester.pccx.ExternalNodeBasedCoverage

asString() - Method in class org.forester.pccx.ExternalNodeBasedCoverageMethodOptions

asSummary() - Method in class org.forester.util.BasicDescriptiveStatistics

asSummary() - Method in interface org.forester.util.DescriptiveStatistics

asText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

asText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

asText() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

asText() - Method in class org.forester.go.BasicGoTerm

asText() - Method in class org.forester.phylogeny.data.Accession

asText() - Method in class org.forester.phylogeny.data.Annotation

asText() - Method in class org.forester.phylogeny.data.BinaryCharacters

asText() - Method in class org.forester.phylogeny.data.BranchColor

asText() - Method in class org.forester.phylogeny.data.BranchData

asText() - Method in class org.forester.phylogeny.data.BranchWidth

asText() - Method in class org.forester.phylogeny.data.Confidence

asText() - Method in class org.forester.phylogeny.data.Date

asText() - Method in class org.forester.phylogeny.data.Distribution

asText() - Method in class org.forester.phylogeny.data.DomainArchitecture

asText() - Method in class org.forester.phylogeny.data.Event

asText() - Method in class org.forester.phylogeny.data.Identifier

asText() - Method in class org.forester.phylogeny.data.NodeData

asText() - Method in class org.forester.phylogeny.data.NodeVisualData

asText() - Method in interface org.forester.phylogeny.data.PhylogenyData

asText() - Method in class org.forester.phylogeny.data.Point

asText() - Method in class org.forester.phylogeny.data.Polygon

asText() - Method in class org.forester.phylogeny.data.PropertiesMap

asText() - Method in class org.forester.phylogeny.data.Property

asText() - Method in class org.forester.phylogeny.data.ProteinDomain

asText() - Method in class org.forester.phylogeny.data.Reference

asText() - Method in class org.forester.phylogeny.data.Sequence

asText() - Method in class org.forester.phylogeny.data.SequenceRelation

asText() - Method in class org.forester.phylogeny.data.Taxonomy

asText() - Method in class org.forester.phylogeny.data.Uri

attributeEqualsValue(XmlElement, String, String) - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler

attributeEqualsValue(XmlElement, String, String) - Static method in class org.forester.io.parsers.tol.TolXmlHandler

AUTHDATE - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

AUTHORITY - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

B

BACKGROUND - Static variable in class org.forester.archaeopteryx.TreeColorSet

BACKGROUND_GRADIENT_BOTTOM - Static variable in class org.forester.archaeopteryx.TreeColorSet

BACTERIA - Static variable in class org.forester.ws.seqdb.UniProtTaxonomy

BACTERIA_COLOR - Static variable in class org.forester.util.TaxonomyColors

BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES - Static variable in class org.forester.application.surfacing

BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES - Static variable in class org.forester.application.surfacing

BASE_UNIPROT_URL - Static variable in class org.forester.ws.seqdb.SequenceDbWsTools

BasicBinaryDomainCombination - Class in org.forester.surfacing

BasicCharacterStateMatrix<S> - Class in org.forester.evoinference.matrix.character

BasicCharacterStateMatrix(int, int) - Constructor for class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

BasicCharacterStateMatrix(int, int, S) - Constructor for class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

BasicCharacterStateMatrix(List<List<S>>) - Constructor for class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

BasicCharacterStateMatrix(S[][]) - Constructor for class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

BasicCombinableDomains - Class in org.forester.surfacing

BasicCombinableDomains(String, Species) - Constructor for class org.forester.surfacing.BasicCombinableDomains

BasicDescriptiveStatistics - Class in org.forester.util

BasicDescriptiveStatistics() - Constructor for class org.forester.util.BasicDescriptiveStatistics

BasicDescriptiveStatistics(String) - Constructor for class org.forester.util.BasicDescriptiveStatistics

BasicDomain - Class in org.forester.protein

BasicDomain(String) - Constructor for class org.forester.protein.BasicDomain

BasicDomain(String, int, int, short, short, double, double) - Constructor for class org.forester.protein.BasicDomain

BasicDomainSimilarityCalculator - Class in org.forester.surfacing

BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField, boolean, boolean, boolean, boolean) - Constructor for class org.forester.surfacing.BasicDomainSimilarityCalculator

BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField, boolean, boolean, boolean) - Constructor for class org.forester.surfacing.BasicDomainSimilarityCalculator

BasicExternalNodeBasedCoverageExtender - Class in org.forester.pccx

BasicExternalNodeBasedCoverageExtender() - Constructor for class org.forester.pccx.BasicExternalNodeBasedCoverageExtender

BasicGenomeWideCombinableDomains - Class in org.forester.surfacing

BasicGoRelationship - Class in org.forester.go

BasicGoRelationship(String) - Constructor for class org.forester.go.BasicGoRelationship

BasicGoRelationship(String, String) - Constructor for class org.forester.go.BasicGoRelationship

BasicGoRelationship(GoRelationship.Type, GoId) - Constructor for class org.forester.go.BasicGoRelationship

BasicGoSubset - Class in org.forester.go

BasicGoSubset(String) - Constructor for class org.forester.go.BasicGoSubset

BasicGoSubset(GoSubset.Type) - Constructor for class org.forester.go.BasicGoSubset

BasicGoTerm - Class in org.forester.go

BasicGoTerm(GoId, String, GoNameSpace, boolean) - Constructor for class org.forester.go.BasicGoTerm

BasicGoTerm(String, String, String, boolean) - Constructor for class org.forester.go.BasicGoTerm

BasicGoXRef - Class in org.forester.go

BasicGoXRef(String) - Constructor for class org.forester.go.BasicGoXRef

BasicGoXRef(GoXRef.Type, String) - Constructor for class org.forester.go.BasicGoXRef

BasicMsa - Class in org.forester.msa

BasicMsa(int, int, MolecularSequence.TYPE) - Constructor for class org.forester.msa.BasicMsa

BasicPhylogeniesWebserviceClient - Class in org.forester.archaeopteryx.webservices

BasicPhylogeniesWebserviceClient(String, String, String, String, WebservicesManager.WsPhylogenyFormat, PhylogenyMethods.PhylogenyNodeField, String, boolean, String, Object) - Constructor for class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient

BasicProtein - Class in org.forester.protein

BasicProtein(String, String, int) - Constructor for class org.forester.protein.BasicProtein

BasicSequence - Class in org.forester.sequence

BasicSequence(String, String, MolecularSequence.TYPE) - Constructor for class org.forester.sequence.BasicSequence

Only use if you know what you are doing!

BasicSequence(String, char[], MolecularSequence.TYPE) - Constructor for class org.forester.sequence.BasicSequence

Only use if you know what you are doing!

BasicSpecies - Class in org.forester.species

BasicSpecies(String) - Constructor for class org.forester.species.BasicSpecies

BasicSymmetricalDistanceMatrix - Class in org.forester.evoinference.matrix.distance

BasicSymmetricalDistanceMatrix(int) - Constructor for class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

BasicTable<E> - Class in org.forester.util

BasicTable() - Constructor for class org.forester.util.BasicTable

BasicTableParser - Class in org.forester.util

BDC_PRESENT_NEXUS - Static variable in class org.forester.application.surfacing

BEGIN_CHARACTERS - Static variable in class org.forester.io.parsers.nexus.NexusConstants

BEGIN_DATA - Static variable in class org.forester.io.parsers.nexus.NexusConstants

BEGIN_TAXA - Static variable in class org.forester.io.parsers.nexus.NexusConstants

BEGIN_TREES - Static variable in class org.forester.io.parsers.nexus.NexusConstants

BINARY_CHARACTER - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

BINARY_CHARACTERS - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

BINARY_CHARACTERS_GAINED - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

BINARY_CHARACTERS_GAINED_COUNT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

BINARY_CHARACTERS_LOST - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

BINARY_CHARACTERS_LOST_COUNT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

BINARY_CHARACTERS_PRESENT - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

BINARY_CHARACTERS_PRESENT_COUNT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

BINARY_CHARACTERS_TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

BINARY_DOMAIN_COMBINATIONS - Static variable in class org.forester.archaeopteryx.TreeColorSet

BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO - Static variable in class org.forester.application.surfacing

BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH - Static variable in class org.forester.application.surfacing

BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED - Static variable in class org.forester.application.surfacing

BinaryCharacters - Class in org.forester.phylogeny.data

BinaryCharacters() - Constructor for class org.forester.phylogeny.data.BinaryCharacters

BinaryCharacters(SortedSet<String>, SortedSet<String>, SortedSet<String>, String) - Constructor for class org.forester.phylogeny.data.BinaryCharacters

BinaryCharacters(SortedSet<String>, SortedSet<String>, SortedSet<String>, String, int, int, int) - Constructor for class org.forester.phylogeny.data.BinaryCharacters

BinaryCharactersParser - Class in org.forester.io.parsers.phyloxml.data

BinaryDomainCombination - Interface in org.forester.protein

BinaryDomainCombination.DomainCombinationType - Enum in org.forester.protein

BinaryDomainCombination.OutputFormat - Enum in org.forester.protein

BindingDB_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

BIOLOGICAL_PROCESS_STR - Static variable in class org.forester.go.GoNameSpace

Blast - Class in org.forester.archaeopteryx.tools

Blast() - Constructor for class org.forester.archaeopteryx.tools.Blast

BootstrapResampler - Class in org.forester.evoinference.tools

BootstrapResampler() - Constructor for class org.forester.evoinference.tools.BootstrapResampler

BRANCH - Static variable in class org.forester.archaeopteryx.TreeColorSet

BRANCH_LENGTH - Static variable in class org.forester.archaeopteryx.TreeColorSet

BRANCH_LENGTH - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

BRANCH_LENGTH_DEFAULT - Static variable in class org.forester.phylogeny.data.PhylogenyDataUtil

Value of -99.0 is used as default value.

BRANCH_WIDTH_DEFAULT_VALUE - Static variable in class org.forester.phylogeny.data.BranchWidth

BranchColor - Class in org.forester.phylogeny.data

BranchColor() - Constructor for class org.forester.phylogeny.data.BranchColor

BranchColor(Color) - Constructor for class org.forester.phylogeny.data.BranchColor

BranchCountingBasedScoringMethod - Class in org.forester.pccx

BranchCountingBasedScoringMethod() - Constructor for class org.forester.pccx.BranchCountingBasedScoringMethod

BranchData - Class in org.forester.phylogeny.data

BranchData() - Constructor for class org.forester.phylogeny.data.BranchData

BranchLengthBasedScoringMethod - Class in org.forester.pccx

BranchLengthBasedScoringMethod() - Constructor for class org.forester.pccx.BranchLengthBasedScoringMethod

BranchWidth - Class in org.forester.phylogeny.data

BranchWidth() - Constructor for class org.forester.phylogeny.data.BranchWidth

BranchWidth(double) - Constructor for class org.forester.phylogeny.data.BranchWidth

BranchWidthParser - Class in org.forester.io.parsers.phyloxml.data

C

calcBasicGapinessStatistics(Msa) - Static method in class org.forester.msa.MsaMethods

calcColor(double, double, double, Color, Color) - Static method in class org.forester.util.ForesterUtil

This calculates a color.

calcColor(double, double, double, double, Color, Color, Color) - Static method in class org.forester.util.ForesterUtil

This calculates a color.

calcFractionalDissimilarities(Msa) - Static method in class org.forester.evoinference.distance.PairwiseDistanceCalculator

calcGappiness() - Method in class org.forester.msa.DeleteableMsa

calcGapRatio(Msa) - Static method in class org.forester.msa.MsaMethods

calcGapSumPerColumn(Msa, int) - Static method in class org.forester.msa.DeleteableMsa

calcGapSumPerColumn(Msa, int) - Static method in class org.forester.msa.MsaMethods

calcKimuraDistances(Msa) - Static method in class org.forester.evoinference.distance.PairwiseDistanceCalculator

calcKimuraDistances(Msa, double) - Static method in class org.forester.evoinference.distance.PairwiseDistanceCalculator

calcNormalizedShannonsEntropy(int, Msa) - Static method in class org.forester.msa.MsaMethods

calcNormalizedShannonsEntropy(int, Msa, int) - Static method in class org.forester.msa.MsaMethods

calcNumberOfGaps(MolecularSequence) - Static method in class org.forester.msa.MsaMethods

calcNumberOfGapsInMsa(Msa) - Static method in class org.forester.msa.MsaMethods

calcNumberOfGapsStats(Msa) - Static method in class org.forester.msa.MsaMethods

calcPoissonDistances(Msa) - Static method in class org.forester.evoinference.distance.PairwiseDistanceCalculator

calcTree() - Method in class org.forester.msa_compactor.MsaCompactor

calculateBranchLengthStatistics(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

calculateColorFromString(String, boolean) - Static method in class org.forester.archaeopteryx.AptxUtil

calculateConfidenceStatistics(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

calculateCopyNumberDifferences(List<GenomeWideCombinableDomains>, SortedMap<Species, List<Protein>>, List<String>, List<String>, List<String>, int, Double, File, File, File, Map<String, List<GoId>>, Map<GoId, GoTerm>, File, File, File) - Static method in class org.forester.surfacing.DomainCountsDifferenceUtil

calculateCoverage(List<Phylogeny>, List<String>, CoverageCalculationOptions, boolean) - Method in interface org.forester.pccx.CoverageCalculationMethod

calculateCoverage(List<Phylogeny>, List<String>, boolean) - Method in class org.forester.pccx.CoverageCalculator

calculateCoverage(List<Phylogeny>, List<String>, CoverageCalculationOptions, boolean) - Method in class org.forester.pccx.ExternalNodeBasedCoverageMethod

calculateDepth() - Method in class org.forester.phylogeny.PhylogenyNode

calculateDescriptiveStatisticsForMeanValues(Set<DomainSimilarity>) - Static method in class org.forester.surfacing.SurfacingUtil

calculateDistance(PhylogenyNode, PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Calculates the distance between PhylogenyNodes node1 and node2.

calculateDistanceToRoot() - Method in class org.forester.phylogeny.PhylogenyNode

calculateEffectiveLengthStatistics(Msa) - Static method in class org.forester.msa.MsaMethods

calculateIdentityRatio(int, int, Msa) - Static method in class org.forester.msa.MsaMethods

calculateIdentityRatio(Msa, int) - Static method in class org.forester.msa.MsaMethods

calculateLCA(PhylogenyNode, PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Returns the LCA of PhylogenyNodes node1 and node2.

calculateLCAonTreeWithIdsInPreOrder(PhylogenyNode, PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Returns the LCA of PhylogenyNodes node1 and node2.

calculateMaxBranchesToLeaf(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

calculateMaxDepth(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

calculateMaxDistanceToRoot(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

calculateMeanBasedStatistics() - Method in class org.forester.surfacing.DomainLengths

Returns descriptive statistics based on the arithmetic means for each species.

calculateMeanBasedStatisticsForAllSpecies() - Method in class org.forester.surfacing.DomainLengthsTable

calculateMeanBasedStatisticsForDomain(String) - Method in class org.forester.surfacing.DomainLengthsTable

calculateMeanBasedStatisticsForSpecies(Species) - Method in class org.forester.surfacing.DomainLengthsTable

calculateNodeWithMaxDistanceToRoot(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

calculateNumberOfDescendantsPerNodeStatistics(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

calculateNumberOfExternalNodesWithoutTaxonomy(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

calculateOrthologTable(Phylogeny[], boolean) - Static method in class org.forester.rio.RIO

calculateOverlap(Domain, List<Boolean>) - Static method in class org.forester.util.ForesterUtil

calculateResidueDestributionPerColumn(Msa, int) - Static method in class org.forester.msa.MsaMethods

calculateScoreForExternalNode(SortedMap<PhylogenyNode, Double>, Phylogeny, PhylogenyNode, CoverageCalculationOptions) - Method in class org.forester.pccx.BranchCountingBasedScoringMethod

calculateScoreForExternalNode(SortedMap<PhylogenyNode, Double>, Phylogeny, PhylogenyNode, CoverageCalculationOptions) - Method in interface org.forester.pccx.ScoringMethodForExternalNode

This calculates the coverage score for one external node.

calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

This returns a score between 0.0 (no binary domain combination in common) and 1.0 (all binary domain combinations in common) measuring the similarity between two genomes based on the number of shared binary domain combinations: t: sum of (distinct) binary domain combinations s: sum of shared (distinct) binary domain combinations 1 - ( ( t - s ) / t )

calculateSharedDomainsBasedGenomeSimilarityScore() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

This returns a score between 0.0 (no domains in common) and 1.0 (all domains in common) measuring the similarity between two genomes based on the number of shared domains: t: sum of (distinct) domains s: sum of shared (distinct) domains 1 - ( ( t - s ) / t )

calculateSimilarities(PairwiseDomainSimilarityCalculator, List<GenomeWideCombinableDomains>, boolean, boolean) - Method in class org.forester.surfacing.BasicDomainSimilarityCalculator

calculateSimilarities(PairwiseDomainSimilarityCalculator, List<GenomeWideCombinableDomains>, boolean, boolean) - Method in interface org.forester.surfacing.DomainSimilarityCalculator

calculateSimilarity(CombinableDomains, CombinableDomains) - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator

calculateSimilarity(CombinableDomains, CombinableDomains) - Method in class org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator

calculateSimilarity(CombinableDomains, CombinableDomains) - Method in interface org.forester.surfacing.PairwiseDomainSimilarityCalculator

calculateSimilarity(CombinableDomains, CombinableDomains) - Method in class org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator

calculateSubtreeHeight(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny

This calculates the height of the subtree emanating at n for rooted, tree-shaped phylogenies

calculateZScoreForSpecies(Species) - Method in class org.forester.surfacing.DomainLengths

Note.

canDoMsa() - Method in class org.forester.archaeopteryx.tools.InferenceManager

CELLULAR_COMPONENT_STR - Static variable in class org.forester.go.GoNameSpace

CELLULAR_ORGANISMS - Static variable in class org.forester.ws.seqdb.UniProtTaxonomy

characters(char[], int, int) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler

characters(char[], int, int) - Method in class org.forester.io.parsers.tol.TolXmlHandler

CharacterStateMatrix<S> - Interface in org.forester.evoinference.matrix.character

CharacterStateMatrix.BinaryStates - Enum in org.forester.evoinference.matrix.character

It is crucial that the order ABSENT, UNKNOWN, PRESENT not be changes since this determines the sort order.

CharacterStateMatrix.Format - Enum in org.forester.evoinference.matrix.character

CharacterStateMatrix.GainLossStates - Enum in org.forester.evoinference.matrix.character

CharacterStateMatrix.NucleotideStates - Enum in org.forester.evoinference.matrix.character

CHARSTATELABELS - Static variable in class org.forester.io.parsers.nexus.NexusConstants

Chart - Class in org.forester.msa_compactor

chart(int, boolean, boolean) - Method in class org.forester.msa_compactor.MsaCompactor

check_fasta - Class in org.forester.application

check_fasta() - Constructor for class org.forester.application.check_fasta

checkForOutputFileWriteability(File) - Static method in class org.forester.surfacing.SurfacingUtil

checkWriteabilityForPairwiseComparisons(DomainSimilarity.PRINT_OPTION, String[][], String, File) - Static method in class org.forester.surfacing.SurfacingUtil

CHLOROPHYTA_COLOR - Static variable in class org.forester.util.TaxonomyColors

CHOANOFLAGELLIDA - Static variable in class org.forester.util.TaxonomyColors

CLADE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

CLADE - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

CLADE_DATE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

CLADE_DATE_DESC - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

CLADE_DATE_MAX - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

CLADE_DATE_MIN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

CLADE_DATE_UNIT - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

CLADE_DATE_VALUE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

clear() - Method in class org.forester.datastructures.Queue

Removes all elements from this queue.

clearHashIdToNodeMap() - Method in class org.forester.phylogeny.Phylogeny

clone() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

clone() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

clone() - Method in class org.forester.archaeopteryx.webservices.WebservicesManager

clone() - Method in class org.forester.evoinference.distance.PairwiseDistanceCalculator

clone() - Method in class org.forester.msa.MsaInferrer

clone() - Method in class org.forester.msa.MsaMethods

clone() - Method in class org.forester.phylogeny.factories.ParserBasedPhylogenyFactory

clone() - Method in class org.forester.phylogeny.PhylogenyMethods

clone() - Method in class org.forester.ws.seqdb.EbiDbEntry

clone() - Method in class org.forester.ws.seqdb.UniProtEntry

ClustalOmega - Class in org.forester.msa

CNIDARIA_COLOR - Static variable in class org.forester.util.TaxonomyColors

coefficientOfVariation() - Method in class org.forester.util.BasicDescriptiveStatistics

coefficientOfVariation() - Method in interface org.forester.util.DescriptiveStatistics

Computes the coefficient of variation.

COLLAPSED - Static variable in class org.forester.archaeopteryx.TreeColorSet

collapseSubtreeStructure(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

collapseWhiteSpace(String) - Static method in class org.forester.util.ForesterUtil

collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates>, BinaryDomainCombination.DomainCombinationType, List<BinaryDomainCombination>, boolean) - Static method in class org.forester.surfacing.SurfacingUtil

collection2file(File, Collection<?>, String) - Static method in class org.forester.util.ForesterUtil

collection2writer(Writer, Collection<?>, String) - Static method in class org.forester.util.ForesterUtil

COLOR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

COLOR_BLUE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

COLOR_GREEN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

COLOR_RED - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

ColorParser - Class in org.forester.io.parsers.phyloxml.data

colorToHex(Color) - Static method in class org.forester.util.ForesterUtil

CombinableDomains - Interface in org.forester.surfacing

CombinationsBasedPairwiseDomainSimilarity - Class in org.forester.surfacing

CombinationsBasedPairwiseDomainSimilarity(int, int, int) - Constructor for class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity

CombinationsBasedPairwiseDomainSimilarityCalculator - Class in org.forester.surfacing

CombinationsBasedPairwiseDomainSimilarityCalculator() - Constructor for class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator

CommandLineArguments - Class in org.forester.util

CommandLineArguments(String[]) - Constructor for class org.forester.util.CommandLineArguments

CommandProcessBuilder - Class in org.forester.util

CommandProcessBuilder() - Constructor for class org.forester.util.CommandProcessBuilder

compare(Phylogeny, Phylogeny, boolean, boolean, boolean) - Static method in class org.forester.tools.SupportCount

compare(StringInt, StringInt) - Method in class org.forester.util.StringInt.DescendingIntComparator

compareTo(GoRelationship) - Method in class org.forester.go.BasicGoRelationship

compareTo(GoSubset) - Method in class org.forester.go.BasicGoSubset

compareTo(GoTerm) - Method in class org.forester.go.BasicGoTerm

Compares based on GO id.

compareTo(GoXRef) - Method in class org.forester.go.BasicGoXRef

compareTo(OntologizerResult) - Method in class org.forester.go.etc.OntologizerResult

compareTo(GoId) - Method in class org.forester.go.GoId

compareTo(Mapping) - Method in class org.forester.go.PfamToGoMapping

compareTo(GapContribution) - Method in class org.forester.msa_compactor.GapContribution

compareTo(Accession) - Method in class org.forester.phylogeny.data.Accession

compareTo(Annotation) - Method in class org.forester.phylogeny.data.Annotation

compareTo(Confidence) - Method in class org.forester.phylogeny.data.Confidence

compareTo(Sequence) - Method in class org.forester.phylogeny.data.Sequence

compareTo(Taxonomy) - Method in class org.forester.phylogeny.data.Taxonomy

compareTo(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode

compareTo(Domain) - Method in class org.forester.protein.BasicDomain

Basic domains are compared/sorted based upon their identifiers (case insensitive) and their numbers.

compareTo(ProteinId) - Method in class org.forester.protein.ProteinId

compareTo(Species) - Method in class org.forester.species.BasicSpecies

compareTo(BinaryDomainCombination) - Method in class org.forester.surfacing.BasicBinaryDomainCombination

compareTo(DomainSimilarity) - Method in class org.forester.surfacing.DomainSimilarity

compareTo(Domain) - Method in class org.forester.surfacing.SimpleDomain

componentHidden(ComponentEvent) - Method in class org.forester.archaeopteryx.MainPanel

componentMoved(ComponentEvent) - Method in class org.forester.archaeopteryx.MainPanel

componentResized(ComponentEvent) - Method in class org.forester.archaeopteryx.MainPanel

componentShown(ComponentEvent) - Method in class org.forester.archaeopteryx.MainPanel

computeMappingCostL() - Method in class org.forester.sdi.SDI

Computes the cost of mapping the gene tree gene_tree onto the species tree species_tree.

confadd - Class in org.forester.application

confadd() - Constructor for class org.forester.application.confadd

CONFIDENCE - Static variable in class org.forester.archaeopteryx.TreeColorSet

CONFIDENCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Confidence - Class in org.forester.phylogeny.data

Confidence() - Constructor for class org.forester.phylogeny.data.Confidence

Confidence(double, String) - Constructor for class org.forester.phylogeny.data.Confidence

Confidence(double, String, double) - Constructor for class org.forester.phylogeny.data.Confidence

CONFIDENCE_DEFAULT - Static variable in class org.forester.phylogeny.data.ProteinDomain

CONFIDENCE_DEFAULT_VALUE - Static variable in class org.forester.phylogeny.data.Confidence

CONFIDENCE_SD_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

CONFIDENCE_TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

ConfidenceAssessor - Class in org.forester.tools

ConfidenceParser - Class in org.forester.io.parsers.phyloxml.data

Configuration - Class in org.forester.archaeopteryx

Configuration() - Constructor for class org.forester.archaeopteryx.Configuration

Configuration(String, boolean, boolean, boolean) - Constructor for class org.forester.archaeopteryx.Configuration

Configuration.EXT_NODE_DATA_RETURN_ON - Enum in org.forester.archaeopteryx

Configuration.UI - Enum in org.forester.archaeopteryx

Constants - Class in org.forester.archaeopteryx

Constants() - Constructor for class org.forester.archaeopteryx.Constants

contains(List<String>, boolean) - Method in class org.forester.protein.BasicProtein

contains(List<String>, boolean) - Method in interface org.forester.protein.Protein

If in_nc_order is set to true, this should return true only and only if the order in List 'domains' and this protein (as determined by the start positions of the domains of this proteins, _not_ by their index) are the same (interspersing, 'other', domains in this are ignored).

contains(String) - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

contains(String) - Method in interface org.forester.surfacing.GenomeWideCombinableDomains

containsCharacter(String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

containsCharacter(String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

containsIdentifier(String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

containsIdentifier(String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

copy() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

copy() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

copy() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

copy() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

copy() - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

copy() - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

copy() - Method in class org.forester.go.BasicGoTerm

Makes a shallow copy.

copy() - Method in class org.forester.phylogeny.data.Accession

copy() - Method in class org.forester.phylogeny.data.Annotation

copy() - Method in class org.forester.phylogeny.data.BinaryCharacters

copy() - Method in class org.forester.phylogeny.data.BranchColor

copy() - Method in class org.forester.phylogeny.data.BranchData

copy() - Method in class org.forester.phylogeny.data.BranchWidth

copy() - Method in class org.forester.phylogeny.data.Confidence

copy() - Method in class org.forester.phylogeny.data.Date

copy() - Method in class org.forester.phylogeny.data.Distribution

copy() - Method in class org.forester.phylogeny.data.DomainArchitecture

copy() - Method in class org.forester.phylogeny.data.Event

copy() - Method in class org.forester.phylogeny.data.Identifier

copy() - Method in class org.forester.phylogeny.data.NodeData

copy() - Method in class org.forester.phylogeny.data.NodeVisualData

copy() - Method in interface org.forester.phylogeny.data.PhylogenyData

Creates a new PhylogenyData object with identical values as this PhylogenyData.

copy(ArrayList<PhylogenyData>) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

Creates a deep copy of ArrayList of PhylogenyData objects.

copy() - Method in class org.forester.phylogeny.data.Point

copy() - Method in class org.forester.phylogeny.data.Polygon

copy() - Method in class org.forester.phylogeny.data.PropertiesMap

copy() - Method in class org.forester.phylogeny.data.Property

copy() - Method in class org.forester.phylogeny.data.ProteinDomain

copy() - Method in class org.forester.phylogeny.data.Reference

copy() - Method in class org.forester.phylogeny.data.Sequence

Not a deep copy.

copy() - Method in class org.forester.phylogeny.data.SequenceRelation

copy() - Method in class org.forester.phylogeny.data.Taxonomy

copy() - Method in class org.forester.phylogeny.data.Uri

copy() - Method in class org.forester.phylogeny.Phylogeny

Returns a deep copy of this Phylogeny.

copy(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny

Returns a deep copy of this Phylogeny.

copy() - Method in class org.forester.ws.seqdb.UniProtTaxonomy

Creates deep copy for all fields, except lineage.

copyFile(File, File) - Static method in class org.forester.util.ForesterUtil

copyNodeData() - Method in class org.forester.phylogeny.PhylogenyNode

Returns a new PhylogenyNode which has its data copied from this PhylogenyNode.

copyNodeDataShallow() - Method in class org.forester.phylogeny.PhylogenyNode

Returns a new PhylogenyNode which has the same data as this PhylogenyNode.

copySequence(MolecularSequence) - Static method in class org.forester.sequence.BasicSequence

copyShallow() - Method in class org.forester.phylogeny.Phylogeny

Returns a shallow copy of this Phylogeny.

copyShallow(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny

core_chars - Class in org.forester.applications

core_chars() - Constructor for class org.forester.applications.core_chars

CORUM_STR - Static variable in interface org.forester.go.GoXRef

count(Phylogeny, Phylogeny[], boolean, boolean) - Static method in class org.forester.tools.SupportCount

count(Phylogeny, Phylogeny[], boolean, double, boolean) - Static method in class org.forester.tools.SupportCount

This counts the support of topology phylogeny by the topologies in phylogenies.

COUNT_DEFAULT - Static variable in class org.forester.phylogeny.data.BinaryCharacters

count_support - Class in org.forester.application

count_support() - Constructor for class org.forester.application.count_support

countCategories(List<GoTerm>, List<GoTerm>, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils

This is for counting the how many times each GO term in 'categories' is a (direct or indirect) super term of the GO terms in 'experiment_set'.

countCategoriesId(List<GoId>, List<GoId>, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils

countChars(String, char) - Static method in class org.forester.util.ForesterUtil

countNumberOfOneDescendantNodes(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

countNumberOfPolytomies(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

CountsBasedPairwiseDomainSimilarity - Class in org.forester.surfacing

CountsBasedPairwiseDomainSimilarity(short, short) - Constructor for class org.forester.surfacing.CountsBasedPairwiseDomainSimilarity

counts_difference: (counts for domain 1) minus (counts for domain 2).

Coverage - Interface in org.forester.pccx

CoverageCalculationMethod - Interface in org.forester.pccx

CoverageCalculationOptions - Interface in org.forester.pccx

CoverageCalculator - Class in org.forester.pccx

CoverageExtender - Interface in org.forester.pccx

create(Object, Object) - Method in class org.forester.phylogeny.factories.ParserBasedPhylogenyFactory

create(Object, Object, String) - Method in class org.forester.phylogeny.factories.ParserBasedPhylogenyFactory

create(Object, Object) - Method in interface org.forester.phylogeny.factories.PhylogenyFactory

This must create a Phylogeny from source (e.g.

createAaSequence(String, String) - Static method in class org.forester.sequence.BasicSequence

createApplication(Phylogeny) - Static method in class org.forester.archaeopteryx.Archaeopteryx

createApplication(Phylogeny, Configuration, String) - Static method in class org.forester.archaeopteryx.Archaeopteryx

createApplication(Phylogeny[]) - Static method in class org.forester.archaeopteryx.Archaeopteryx

createApplication(Phylogeny[], String, String) - Static method in class org.forester.archaeopteryx.Archaeopteryx

createBalancedPhylogeny(int, int) - Static method in class org.forester.development.DevelopmentTools

Creates a completely balanced rooted phylogeny with a given number of levels and children per node.

createBiologicalProcess() - Static method in class org.forester.go.GoNameSpace

createBufferedWriter(File) - Static method in class org.forester.util.ForesterUtil

createBufferedWriter(String) - Static method in class org.forester.util.ForesterUtil

createCellularComponent() - Static method in class org.forester.go.GoNameSpace

createDefaultClients() - Static method in class org.forester.archaeopteryx.webservices.WebserviceUtil

createDnaSequence(String, String) - Static method in class org.forester.sequence.BasicSequence

createDomainIdToGoIdMap(List<PfamToGoMapping>) - Static method in class org.forester.surfacing.SurfacingUtil

createDomainIdToSecondaryFeaturesMap(File) - Static method in class org.forester.surfacing.SurfacingUtil

createEasyWriter(File) - Static method in class org.forester.util.ForesterUtil

createEasyWriter(String) - Static method in class org.forester.util.ForesterUtil

createFileForWriting(String) - Static method in class org.forester.util.ForesterUtil

createFromNhxString(String) - Static method in class org.forester.phylogeny.data.Property

createGoIdToGoTermMap(List<GoTerm>) - Static method in class org.forester.go.GoUtils

createInstance(Phylogeny[], Configuration) - Static method in class org.forester.archaeopteryx.MainFrameApplication

createInstance(Phylogeny[], Configuration, String, File) - Static method in class org.forester.archaeopteryx.MainFrameApplication

createInstance(Configuration) - Static method in class org.forester.archaeopteryx.Options

createInstance(String, String, Configuration) - Static method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

createInstance(List<Double>, DescriptiveStatistics, Configuration) - Static method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

createInstance(Configuration) - Static method in class org.forester.archaeopteryx.tools.InferenceManager

createInstance(Configuration) - Static method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

createInstance() - Static method in class org.forester.archaeopteryx.tools.ProcessPool

createInstance() - Static method in class org.forester.evoinference.distance.NeighborJoining

createInstance(boolean, int) - Static method in class org.forester.evoinference.distance.NeighborJoining

createInstance() - Static method in class org.forester.evoinference.distance.NeighborJoiningF

createInstance(boolean, int) - Static method in class org.forester.evoinference.distance.NeighborJoiningF

createInstance() - Static method in class org.forester.evoinference.distance.NeighborJoiningR

createInstance(boolean, int) - Static method in class org.forester.evoinference.distance.NeighborJoiningR

createInstance() - Static method in class org.forester.evoinference.parsimony.DolloParsimony

createInstance() - Static method in class org.forester.io.parsers.SymmetricalDistanceMatrixParser

createInstance(List<MolecularSequence>) - Static method in class org.forester.msa.BasicMsa

createInstance(String) - Static method in class org.forester.msa.ClustalOmega

createInstance(List<MolecularSequence>) - Static method in class org.forester.msa.DeleteableMsa

createInstance(Msa) - Static method in class org.forester.msa.DeleteableMsa

createInstance(String) - Static method in class org.forester.msa.Mafft

createInstance() - Static method in class org.forester.msa.MsaMethods

createInstance(List<Protein>, boolean, Species) - Static method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

createInstance(List<Protein>, boolean, Species, BinaryDomainCombination.DomainCombinationType) - Static method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

createInstance(List<Protein>, boolean, Species, Map<String, List<GoId>>, BinaryDomainCombination.DomainCombinationType, Map<String, DescriptiveStatistics>, Map<String, DescriptiveStatistics>) - Static method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

createInstance(Phylogeny) - Static method in class org.forester.surfacing.DomainParsimonyCalculator

createInstance(Phylogeny, List<GenomeWideCombinableDomains>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator

createInstance(Phylogeny, List<GenomeWideCombinableDomains>, Map<String, Set<String>>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator

createInstanceFromNhxString(String) - Static method in class org.forester.phylogeny.Phylogeny

createInstanceFromNhxString(String) - Static method in class org.forester.phylogeny.PhylogenyNode

createInstanceFromNhxString(String, NHXParser.TAXONOMY_EXTRACTION) - Static method in class org.forester.phylogeny.PhylogenyNode

createInstanceFromNhxString(String, NHXParser.TAXONOMY_EXTRACTION, boolean) - Static method in class org.forester.phylogeny.PhylogenyNode

createInstanceFromPlainText(List<String>) - Static method in class org.forester.ws.seqdb.UniProtEntry

createInstanceFromPlainTextForRefSeq(List<String>) - Static method in class org.forester.ws.seqdb.EbiDbEntry

createMaskFormatter(String) - Static method in class org.forester.archaeopteryx.AptxUtil

createMatrixOfBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator

createMatrixOfDomainPresenceOrAbsence(List<GenomeWideCombinableDomains>, SortedSet<String>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator

createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains>, Map<String, String>) - Static method in class org.forester.surfacing.DomainParsimonyCalculator

createMeanBasedStatisticsPerSpeciesTable() - Method in class org.forester.surfacing.DomainLengthsTable

createMolecularFunction() - Static method in class org.forester.go.GoNameSpace

createNameToExtNodeMap(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

createNjTreeBasedOnMatrixToFile(File, DistanceMatrix) - Static method in class org.forester.surfacing.SurfacingUtil

createParametersAsString(boolean, double, double, int, boolean, File, BinaryDomainCombination.DomainCombinationType) - Static method in class org.forester.surfacing.SurfacingUtil

createParserDependingFileContents(File, boolean) - Static method in class org.forester.io.parsers.util.ParserUtils

createParserDependingOnFileType(File, boolean) - Static method in class org.forester.io.parsers.util.ParserUtils

createParserDependingOnUrlContents(URL, boolean) - Static method in class org.forester.io.parsers.util.ParserUtils

createPhylogenyWriter() - Static method in class org.forester.io.writers.PhylogenyWriter

createPhyloXmlParser() - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

createPhyloXmlParserXsdValidating() - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

createReader(Object) - Static method in class org.forester.io.parsers.util.ParserUtils

createResampledColumnPositions(int, int, long) - Static method in class org.forester.evoinference.tools.BootstrapResampler

createRnaSequence(String, String) - Static method in class org.forester.sequence.BasicSequence

createSingleDuplicationEvent() - Static method in class org.forester.phylogeny.data.Event

createSingleSpeciationEvent() - Static method in class org.forester.phylogeny.data.Event

createSingleSpeciationOrDuplicationEvent() - Static method in class org.forester.phylogeny.data.Event

createSpecialFromScientificName(String) - Static method in class org.forester.ws.seqdb.UniProtTaxonomy

createSplitWriters(File, String, Map<Character, Writer>) - Static method in class org.forester.surfacing.SurfacingUtil

createTaxCodeToIdMap(Phylogeny) - Static method in class org.forester.surfacing.SurfacingUtil

createUnassigned() - Static method in class org.forester.go.GoNameSpace

createUriForSeqWeb(PhylogenyNode, Configuration, TreePanel) - Static method in class org.forester.archaeopteryx.TreePanelUtil

createUrisForPdbWeb(PhylogenyNode, List<Accession>, Configuration, TreePanel) - Static method in class org.forester.archaeopteryx.TreePanelUtil

CTD_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

CTENOPHORA_COLOR - Static variable in class org.forester.util.TaxonomyColors

D

D_PROMISCUITY_FILE_SUFFIX - Static variable in class org.forester.application.surfacing

DATATYPE - Static variable in class org.forester.io.parsers.nexus.NexusConstants

Date - Class in org.forester.phylogeny.data

Date() - Constructor for class org.forester.phylogeny.data.Date

Date(String) - Constructor for class org.forester.phylogeny.data.Date

Date(String, BigDecimal, BigDecimal, BigDecimal, String) - Constructor for class org.forester.phylogeny.data.Date

DateParser - Class in org.forester.io.parsers.phyloxml.data

ddbjBlast(String) - Method in class org.forester.archaeopteryx.tools.Blast

DEBUG - Static variable in class org.forester.applications.get_shared_chars

DEBUG - Static variable in class org.forester.archaeopteryx.tools.SequenceDataRetriver

DEBUG - Static variable in class org.forester.io.parsers.phyloxml.XmlElement

decorate(Phylogeny, Map<String, Map<String, String>>, boolean) - Static method in class org.forester.tools.PhylogenyDecorator

decorate(Phylogeny, Map<String, String>, PhylogenyDecorator.FIELD, boolean, boolean, boolean, boolean, boolean, boolean) - Static method in class org.forester.tools.PhylogenyDecorator

decorate(Phylogeny, Map<String, String>, PhylogenyDecorator.FIELD, boolean, boolean, boolean, Map<String, String>, boolean, boolean, boolean) - Static method in class org.forester.tools.PhylogenyDecorator

decoratePrintableDomainSimilarities(SortedSet<DomainSimilarity>, DomainSimilarityCalculator.Detailedness) - Static method in class org.forester.surfacing.SurfacingUtil

decorator - Class in org.forester.application

decorator() - Constructor for class org.forester.application.decorator

decoratorX - Class in org.forester.application

decoratorX() - Constructor for class org.forester.application.decoratorX

DEFAULT_LINES_TO_RETURN - Static variable in class org.forester.ws.seqdb.SequenceDbWsTools

DEFAULT_RANGE - Static variable in class org.forester.rio.RIO

DEFAULT_SIZE - Static variable in class org.forester.phylogeny.data.NodeVisualData

DEFAULT_VALUE - Static variable in class org.forester.phylogeny.data.Event

DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA - Static variable in class org.forester.evoinference.distance.PairwiseDistanceCalculator

DEFAULT_WIDTH - Static variable in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

DeleteableMsa - Class in org.forester.msa

deleteAllDomainIdsToIgnore() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

deleteExternalNodesNegativeSelection(Set<Long>, Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

deleteExternalNodesNegativeSelection(String[], Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

deleteExternalNodesPositiveSelection(String[], Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

deleteExternalNodesPositiveSelectionT(List<Taxonomy>, Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

deleteGapColumns(double) - Method in class org.forester.msa.DeleteableMsa

deleteGapColumns(double, int, Msa) - Method in class org.forester.msa.MsaMethods

deleteGapColumns(double) - Method in class org.forester.msa_compactor.MsaCompactor

deleteGapOnlyColumns() - Method in class org.forester.msa.DeleteableMsa

deleteInternalNodesWithOnlyOneDescendent(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

deleteNonOrthologousExternalNodes(Phylogeny, PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

deleteRow(String, boolean) - Method in class org.forester.msa.DeleteableMsa

deleteSubtree(PhylogenyNode, boolean) - Method in class org.forester.phylogeny.Phylogeny

Need to call clearHashIdToNodeMap() afterwards (not done automatically to allow client multiple deletions in linear time).

dequeue() - Method in class org.forester.datastructures.Queue

Dequeues one element from this queue.

DescendingIntComparator() - Constructor for class org.forester.util.StringInt.DescendingIntComparator

DescriptiveStatistics - Interface in org.forester.util

destroy() - Method in class org.forester.archaeopteryx.ArchaeopteryxA

destroy() - Method in class org.forester.archaeopteryx.ArchaeopteryxE

determineMaxIdLength() - Method in class org.forester.msa.DeleteableMsa

determineTaxonomyComparisonBase(Phylogeny) - Static method in class org.forester.sdi.SDIutil

DEUTEROSTOMIA_COLOR - Static variable in class org.forester.util.TaxonomyColors

DevelopmentTools - Class in org.forester.development

DIKARYA_COLOR - Static variable in class org.forester.util.TaxonomyColors

DIMENSIONS - Static variable in class org.forester.io.parsers.nexus.NexusConstants

DirectedBinaryDomainCombination - Class in org.forester.surfacing

DirectedCombinableDomains - Class in org.forester.surfacing

DirectedCombinableDomains(String, Species) - Constructor for class org.forester.surfacing.DirectedCombinableDomains

display(List<MsaProperties>, int, boolean, String) - Static method in class org.forester.msa_compactor.Chart

displayTree(Phylogeny) - Method in class org.forester.msa_compactor.MsaCompactor

DistanceMatrix - Interface in org.forester.evoinference.matrix.distance

DistanceMatrix.Format - Enum in org.forester.evoinference.matrix.distance

DISTRIBUTION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Distribution - Class in org.forester.phylogeny.data

Distribution(String) - Constructor for class org.forester.phylogeny.data.Distribution

Distribution(String, List<Point>) - Constructor for class org.forester.phylogeny.data.Distribution

Distribution(String, List<Point>, List<Polygon>) - Constructor for class org.forester.phylogeny.data.Distribution

DISTRIBUTION_DESC - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

DistributionParser - Class in org.forester.io.parsers.phyloxml.data

divideIntoSubTrees(Phylogeny, double) - Static method in class org.forester.phylogeny.PhylogenyMethods

DNA_REGEXP - Static variable in interface org.forester.sequence.MolecularSequence

doit(List<Protein>, List<String>, Writer, String, String, Map<String, List<Integer>>) - Static method in class org.forester.surfacing.SurfacingUtil

DolloParsimony - Class in org.forester.evoinference.parsimony

dom_dup - Class in org.forester.application

dom_dup() - Constructor for class org.forester.application.dom_dup

Domain - Interface in org.forester.protein

DOMAIN_BASE - Static variable in class org.forester.archaeopteryx.TreeColorSet

DOMAIN_BASE_COLOR_FOR_PDF - Static variable in class org.forester.archaeopteryx.Constants

DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX - Static variable in class org.forester.application.surfacing

DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION - Static variable in class org.forester.application.surfacing

DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS - Static variable in class org.forester.application.surfacing

DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS - Static variable in class org.forester.application.surfacing

DOMAIN_LABEL - Static variable in class org.forester.archaeopteryx.TreeColorSet

DOMAIN_LABEL_COLOR_FOR_PDF - Static variable in class org.forester.archaeopteryx.Constants

DOMAIN_STRUCTURE - Static variable in class org.forester.io.parsers.nhx.NHXtags

DomainArchitecture - Class in org.forester.phylogeny.data

DomainArchitecture() - Constructor for class org.forester.phylogeny.data.DomainArchitecture

DomainArchitecture(List<PhylogenyData>, int) - Constructor for class org.forester.phylogeny.data.DomainArchitecture

DomainArchitecture(String) - Constructor for class org.forester.phylogeny.data.DomainArchitecture

DomainArchitectureBasedGenomeSimilarityCalculator - Class in org.forester.surfacing

DomainArchitectureBasedGenomeSimilarityCalculator(GenomeWideCombinableDomains, GenomeWideCombinableDomains) - Constructor for class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

DomainArchitectureParser - Class in org.forester.io.parsers.phyloxml.data

DomainCountsBasedPairwiseSimilarityCalculator - Class in org.forester.surfacing

DomainCountsBasedPairwiseSimilarityCalculator() - Constructor for class org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator

DomainCountsDifferenceUtil - Class in org.forester.surfacing

DomainCountsDifferenceUtil() - Constructor for class org.forester.surfacing.DomainCountsDifferenceUtil

DomainCountsDifferenceUtil.COPY_CALCULATION_MODE - Enum in org.forester.surfacing

DomainLengths - Class in org.forester.surfacing

DomainLengths(String) - Constructor for class org.forester.surfacing.DomainLengths

DomainLengthsTable - Class in org.forester.surfacing

DomainLengthsTable() - Constructor for class org.forester.surfacing.DomainLengthsTable

domainloss_replacement - Class in org.forester.applications

domainloss_replacement() - Constructor for class org.forester.applications.domainloss_replacement

DomainMidPositionComparator - Static variable in class org.forester.protein.BasicProtein

DomainParsimonyCalculator - Class in org.forester.surfacing

DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO - Static variable in class org.forester.application.surfacing

DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH - Static variable in class org.forester.application.surfacing

DOMAINS_PRESENT_NEXUS - Static variable in class org.forester.application.surfacing

DomainSimilarity - Class in org.forester.surfacing

DomainSimilarity(CombinableDomains, double, double, double, double, double, int, int, int, SortedMap<Species, SpeciesSpecificDcData>, boolean, boolean) - Constructor for class org.forester.surfacing.DomainSimilarity

DomainSimilarity(CombinableDomains, int, int, SortedMap<Species, SpeciesSpecificDcData>, boolean, boolean) - Constructor for class org.forester.surfacing.DomainSimilarity

DomainSimilarity.DomainSimilarityScoring - Enum in org.forester.surfacing

DomainSimilarity.DomainSimilaritySortField - Enum in org.forester.surfacing

DomainSimilarity.PRINT_OPTION - Enum in org.forester.surfacing

DomainSimilarityCalculator - Interface in org.forester.surfacing

DomainSimilarityCalculator.Detailedness - Enum in org.forester.surfacing

DomainSimilarityCalculator.GoAnnotationOutput - Enum in org.forester.surfacing

domainsPerProteinsStatistics(String, List<Protein>, DescriptiveStatistics, SortedMap<Integer, Integer>, SortedSet<String>, SortedSet<String>, SortedSet<String>, Writer) - Static method in class org.forester.surfacing.SurfacingUtil

drawLine(double, double, double, double, Graphics) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

DrugBank_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

DUPLICATION - Static variable in class org.forester.archaeopteryx.TreeColorSet

DUPLICATION_OR_SPECATION - Static variable in class org.forester.archaeopteryx.TreeColorSet

E

EasyWriter - Class in org.forester.util

EasyWriter(BufferedWriter) - Constructor for class org.forester.util.EasyWriter

EbiDbEntry - Class in org.forester.ws.seqdb

EC_STR - Static variable in interface org.forester.go.GoXRef

EMBL_DBS_REFSEQ_N - Static variable in class org.forester.ws.seqdb.SequenceDbWsTools

EMBL_DBS_REFSEQ_P - Static variable in class org.forester.ws.seqdb.SequenceDbWsTools

EMBL_EMBL - Static variable in class org.forester.ws.seqdb.SequenceDbWsTools

EMBL_GENBANK - Static variable in class org.forester.ws.seqdb.SequenceDbWsTools

EMBL_REFSEQ - Static variable in class org.forester.ws.seqdb.SequenceDbWsTools

EMBRYOPHYTA_COLOR - Static variable in class org.forester.util.TaxonomyColors

ENCOUNTERED_PFAMS_SUMMARY_SUFFIX - Static variable in class org.forester.application.surfacing

end() - Method in class org.forester.archaeopteryx.MainFrameApplication

end(MainFrame) - Method in class org.forester.archaeopteryx.tools.RunnableProcess

END - Static variable in class org.forester.io.parsers.nexus.NexusConstants

endElement(String, String, String) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler

endElement(String, String, String) - Method in class org.forester.io.parsers.tol.TolXmlHandler

enqueue(Object) - Method in class org.forester.datastructures.Queue

Adds Object element to thisqueue.

ENSEMBL_PATTERN - Static variable in class org.forester.util.SequenceAccessionTools

ensurePresenceOfDate(PhylogenyNode) - Static method in class org.forester.util.ForesterUtil

ensurePresenceOfDistribution(PhylogenyNode) - Static method in class org.forester.util.ForesterUtil

ensurePresenceOfSequence(PhylogenyNode) - Static method in class org.forester.util.ForesterUtil

ensurePresenceOfTaxonomy(PhylogenyNode) - Static method in class org.forester.util.ForesterUtil

EOL_LINK - Static variable in class org.forester.surfacing.SurfacingConstants

equals(Object) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

equals(Object) - Method in class org.forester.go.BasicGoRelationship

Based on value and type.

equals(Object) - Method in class org.forester.go.BasicGoSubset

equals(Object) - Method in class org.forester.go.BasicGoTerm

Return true if both GO id and namespace are equal.

equals(Object) - Method in class org.forester.go.BasicGoXRef

Based on value and type.

equals(Object) - Method in class org.forester.go.GoId

equals(Object) - Method in class org.forester.go.GoNameSpace

equals(Object) - Method in class org.forester.go.PfamToGoMapping

Based on key and value.

equals(Object) - Method in class org.forester.phylogeny.data.Accession

equals(Object) - Method in class org.forester.phylogeny.data.Annotation

equals(Object) - Method in class org.forester.phylogeny.data.Identifier

equals(Object) - Method in class org.forester.phylogeny.data.Sequence

equals(Object) - Method in class org.forester.phylogeny.data.Taxonomy

equals(Object) - Method in class org.forester.phylogeny.PhylogenyBranch

equals(Object) - Method in class org.forester.phylogeny.PhylogenyNode

equals(Object) - Method in class org.forester.protein.BasicDomain

Basic domains are considered equal if they have the same identifier (case sensitive).

equals(Object) - Method in class org.forester.protein.ProteinId

equals(Object) - Method in class org.forester.sequence.BasicSequence

equals(Object) - Method in class org.forester.species.BasicSpecies

equals(Object) - Method in class org.forester.surfacing.BasicBinaryDomainCombination

EUKARYOTA - Static variable in class org.forester.ws.seqdb.UniProtTaxonomy

evaluate(String, Phylogeny[], Phylogeny, boolean, double) - Static method in class org.forester.tools.ConfidenceAssessor

evaluate(String, Phylogeny[], Phylogeny, boolean, double, int, int) - Static method in class org.forester.tools.ConfidenceAssessor

Event - Class in org.forester.phylogeny.data

Event() - Constructor for class org.forester.phylogeny.data.Event

Event(Event.EventType) - Constructor for class org.forester.phylogeny.data.Event

Event(int, int, int) - Constructor for class org.forester.phylogeny.data.Event

Event(int, int, int, String) - Constructor for class org.forester.phylogeny.data.Event

Event(String) - Constructor for class org.forester.phylogeny.data.Event

Event.EventType - Enum in org.forester.phylogeny.data

EVENT_DUPLICATIONS - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

EVENT_LOSSES - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

EVENT_SPECIATIONS - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

EVENT_TYPE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

EventParser - Class in org.forester.io.parsers.phyloxml.data

EVENTS - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Example1 - Class in org.forester.test.examples

Example1() - Constructor for class org.forester.test.examples.Example1

Example2 - Class in org.forester.test.examples

Example2() - Constructor for class org.forester.test.examples.Example2

Example3 - Class in org.forester.test.examples

Example3() - Constructor for class org.forester.test.examples.Example3

Example4 - Class in org.forester.test.examples

Example4() - Constructor for class org.forester.test.examples.Example4

Example5 - Class in org.forester.test.examples

Example5() - Constructor for class org.forester.test.examples.Example5

EXCAVATA_COLOR - Static variable in class org.forester.util.TaxonomyColors

execute(BasicSymmetricalDistanceMatrix) - Method in class org.forester.evoinference.distance.NeighborJoining

execute(List<BasicSymmetricalDistanceMatrix>) - Method in class org.forester.evoinference.distance.NeighborJoining

execute(BasicSymmetricalDistanceMatrix) - Method in class org.forester.evoinference.distance.NeighborJoiningF

execute(List<BasicSymmetricalDistanceMatrix>) - Method in class org.forester.evoinference.distance.NeighborJoiningF

execute(BasicSymmetricalDistanceMatrix) - Method in class org.forester.evoinference.distance.NeighborJoiningR

execute(List<BasicSymmetricalDistanceMatrix>) - Method in class org.forester.evoinference.distance.NeighborJoiningR

execute(Phylogeny, CharacterStateMatrix<CharacterStateMatrix.BinaryStates>) - Method in class org.forester.evoinference.parsimony.DolloParsimony

execute(Phylogeny, CharacterStateMatrix<STATE_TYPE>) - Method in class org.forester.evoinference.parsimony.FitchParsimony

execute(Phylogeny, CharacterStateMatrix<STATE_TYPE>, boolean) - Method in class org.forester.evoinference.parsimony.FitchParsimony

execute(Phylogeny, CharacterStateMatrix<STATE_TYPE>) - Method in class org.forester.evoinference.parsimony.SankoffParsimony

execute(List<String>, File) - Static method in class org.forester.util.CommandProcessBuilder

executeAnalysis(File, File, SDIutil.ALGORITHM, RIO.REROOTING, String, int, int, boolean, boolean, boolean) - Static method in class org.forester.rio.RIO

executeAnalysis(File, Phylogeny, SDIutil.ALGORITHM, RIO.REROOTING, String, boolean, boolean, boolean) - Static method in class org.forester.rio.RIO

executeAnalysis(File, Phylogeny, SDIutil.ALGORITHM, RIO.REROOTING, String, int, int, boolean, boolean, boolean) - Static method in class org.forester.rio.RIO

executeAnalysis(IteratingPhylogenyParser, File, SDIutil.ALGORITHM, RIO.REROOTING, String, int, int, boolean, boolean, boolean) - Static method in class org.forester.rio.RIO

executeAnalysis(IteratingPhylogenyParser, Phylogeny, SDIutil.ALGORITHM, RIO.REROOTING, String, boolean, boolean, boolean) - Static method in class org.forester.rio.RIO

executeAnalysis(IteratingPhylogenyParser, Phylogeny, SDIutil.ALGORITHM, RIO.REROOTING, String, int, int, boolean, boolean, boolean) - Static method in class org.forester.rio.RIO

executeAnalysis(Phylogeny[], Phylogeny) - Static method in class org.forester.rio.RIO

executeAnalysis(Phylogeny[], Phylogeny, SDIutil.ALGORITHM, RIO.REROOTING, String, boolean, boolean, boolean) - Static method in class org.forester.rio.RIO

executeAnalysis(Phylogeny[], Phylogeny, SDIutil.ALGORITHM, RIO.REROOTING, String, int, int, boolean, boolean, boolean) - Static method in class org.forester.rio.RIO

executeCommand() - Method in class org.forester.util.SystemCommandExecutor

executeDolloParsimonyOnBinaryDomainCombintionPresence() - Method in class org.forester.surfacing.DomainParsimonyCalculator

executeDolloParsimonyOnDomainPresence() - Method in class org.forester.surfacing.DomainParsimonyCalculator

executeDolloParsimonyOnDomainPresence(SortedSet<String>) - Method in class org.forester.surfacing.DomainParsimonyCalculator

executeDolloParsimonyOnSecondaryFeatures(Map<Species, MappingResults>) - Method in class org.forester.surfacing.DomainParsimonyCalculator

executeDomainLengthAnalysis(String[][], int, DomainLengthsTable, File) - Static method in class org.forester.surfacing.SurfacingUtil

executeFitchGainsAnalysis(File, List<BinaryDomainCombination>, int, SortedSet<BinaryDomainCombination>, boolean) - Static method in class org.forester.surfacing.SurfacingUtil

Warning: This side-effects 'all_bin_domain_combinations_encountered'!

executeFitchParsimonyOnBinaryDomainCombintion(boolean) - Method in class org.forester.surfacing.DomainParsimonyCalculator

executeFitchParsimonyOnBinaryDomainCombintion(long) - Method in class org.forester.surfacing.DomainParsimonyCalculator

executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures(boolean) - Method in class org.forester.surfacing.DomainParsimonyCalculator

executeFitchParsimonyOnDomainPresence(boolean) - Method in class org.forester.surfacing.DomainParsimonyCalculator

executeFitchParsimonyOnDomainPresence(long) - Method in class org.forester.surfacing.DomainParsimonyCalculator

executeOnGivenBinaryStatesMatrix(CharacterStateMatrix<CharacterStateMatrix.BinaryStates>, String[]) - Method in class org.forester.surfacing.DomainParsimonyCalculator

executeParsimonyAnalysis(long, boolean, String, DomainParsimonyCalculator, Phylogeny, Map<String, List<GoId>>, Map<GoId, GoTerm>, GoNameSpace, String, Map<String, Set<String>>[], SortedSet<String>, boolean, List<BinaryDomainCombination>, List<BinaryDomainCombination>, BinaryDomainCombination.DomainCombinationType, Map<String, DescriptiveStatistics>, Map<String, DescriptiveStatistics>, Map<String, DescriptiveStatistics>, Map<String, Integer>, boolean, boolean, boolean) - Static method in class org.forester.surfacing.SurfacingUtil

executeParsimonyAnalysisForSecondaryFeatures(String, DomainParsimonyCalculator, Phylogeny, String, Map<Species, MappingResults>, boolean) - Static method in class org.forester.surfacing.SurfacingUtil

executePlusMinusAnalysis(File, List<String>, List<String>, List<String>, List<GenomeWideCombinableDomains>, SortedMap<Species, List<Protein>>, Map<String, List<GoId>>, Map<GoId, GoTerm>, List<Object>) - Static method in class org.forester.surfacing.SurfacingUtil

ExternalForwardIterator - Class in org.forester.phylogeny.iterators

ExternalForwardIterator(Phylogeny) - Constructor for class org.forester.phylogeny.iterators.ExternalForwardIterator

Constructor for ExternalForwardIterator.

ExternalNodeBasedCoverage - Class in org.forester.pccx

ExternalNodeBasedCoverage(DescriptiveStatistics, double, CoverageCalculationOptions) - Constructor for class org.forester.pccx.ExternalNodeBasedCoverage

ExternalNodeBasedCoverageMethod - Class in org.forester.pccx

ExternalNodeBasedCoverageMethod() - Constructor for class org.forester.pccx.ExternalNodeBasedCoverageMethod

ExternalNodeBasedCoverageMethodOptions - Class in org.forester.pccx

ExternalNodeBasedCoverageMethodOptions(String) - Constructor for class org.forester.pccx.ExternalNodeBasedCoverageMethodOptions

This constructor sets the class name for the scoring method e.g.

externalNodesHaveChanged() - Method in class org.forester.phylogeny.Phylogeny

ExternalProgram - Class in org.forester.util

ExternalProgram(String) - Constructor for class org.forester.util.ExternalProgram

extractFastaInformation(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

extractProteinNames(List<Protein>, List<String>, Writer, String, String) - Static method in class org.forester.surfacing.SurfacingUtil

extractProteinNames(SortedMap<Species, List<Protein>>, String, Writer, String, String, double) - Static method in class org.forester.surfacing.SurfacingUtil

extractScientificNameFromNodeName(String) - Static method in class org.forester.io.parsers.util.ParserUtils

extractTaxonomyCodeFromNodeName(String, NHXParser.TAXONOMY_EXTRACTION) - Static method in class org.forester.io.parsers.util.ParserUtils

extractTaxonomyDataFromNodeName(PhylogenyNode, NHXParser.TAXONOMY_EXTRACTION) - Static method in class org.forester.io.parsers.util.ParserUtils

extractUniprotTaxonomyIdFromNodeName(String, NHXParser.TAXONOMY_EXTRACTION) - Static method in class org.forester.io.parsers.util.ParserUtils

F

FACTOR - Static variable in class org.forester.evoinference.distance.Sarray

FACTOR - Static variable in class org.forester.evoinference.distance.Sset

FailedConditionCheckException - Exception in org.forester.util

FailedConditionCheckException() - Constructor for exception org.forester.util.FailedConditionCheckException

FailedConditionCheckException(String) - Constructor for exception org.forester.util.FailedConditionCheckException

FASTA_DESC_LINE - Static variable in class org.forester.io.parsers.FastaParser

fasta_split - Class in org.forester.application

fasta_split() - Constructor for class org.forester.application.fasta_split

FastaParser - Class in org.forester.io.parsers

FastaParser() - Constructor for class org.forester.io.parsers.FastaParser

fatalError(String) - Static method in class org.forester.util.ForesterUtil

fatalError(String, String) - Static method in class org.forester.util.ForesterUtil

fatalErrorIfFileNotReadable(File) - Static method in class org.forester.util.ForesterUtil

fatalErrorIfFileNotReadable(String, File) - Static method in class org.forester.util.ForesterUtil

file22dArray(File) - Static method in class org.forester.util.ForesterUtil

file2array(File) - Static method in class org.forester.util.ForesterUtil

file2list(File) - Static method in class org.forester.util.ForesterUtil

file2set(File) - Static method in class org.forester.util.ForesterUtil

FILE_SEPARATOR - Static variable in class org.forester.util.ForesterUtil

find(List<Phylogeny>, List<String>, int, CoverageCalculationOptions, PrintStream) - Method in class org.forester.pccx.BasicExternalNodeBasedCoverageExtender

find(List<Phylogeny>, List<String>, int, CoverageCalculationOptions, PrintStream) - Method in interface org.forester.pccx.CoverageExtender

findRow(String) - Method in class org.forester.util.BasicTable

FitchParsimony<STATE_TYPE> - Class in org.forester.evoinference.parsimony

FitchParsimony() - Constructor for class org.forester.evoinference.parsimony.FitchParsimony

FONT_COLOR_REF - Static variable in class org.forester.phylogeny.data.NodeVisualData

FONT_COLOR_TYPE - Static variable in class org.forester.phylogeny.data.NodeVisualData

FONT_REF - Static variable in class org.forester.phylogeny.data.NodeVisualData

FONT_SIZE_REF - Static variable in class org.forester.phylogeny.data.NodeVisualData

FONT_SIZE_TYPE - Static variable in class org.forester.phylogeny.data.NodeVisualData

FONT_STYLE_BOLD - Static variable in class org.forester.phylogeny.data.NodeVisualData

FONT_STYLE_BOLD_ITALIC - Static variable in class org.forester.phylogeny.data.NodeVisualData

FONT_STYLE_ITALIC - Static variable in class org.forester.phylogeny.data.NodeVisualData

FONT_STYLE_PLAIN - Static variable in class org.forester.phylogeny.data.NodeVisualData

FONT_STYLE_REF - Static variable in class org.forester.phylogeny.data.NodeVisualData

FONT_STYLE_TYPE - Static variable in class org.forester.phylogeny.data.NodeVisualData

FONT_TYPE - Static variable in class org.forester.phylogeny.data.NodeVisualData

FontChooser - Class in org.forester.archaeopteryx

FontChooser() - Constructor for class org.forester.archaeopteryx.FontChooser

FontChooser(Font) - Constructor for class org.forester.archaeopteryx.FontChooser

FontChooser(String, int, int) - Constructor for class org.forester.archaeopteryx.FontChooser

FORESTER_DATE - Static variable in class org.forester.util.ForesterConstants

FORESTER_VERSION - Static variable in class org.forester.util.ForesterConstants

ForesterConstants - Class in org.forester.util

ForesterConstants() - Constructor for class org.forester.util.ForesterConstants

ForesterConstants.PhylogeneticTreeFormats - Enum in org.forester.util

ForesterUtil - Class in org.forester.util

FORMAT - Static variable in class org.forester.io.parsers.nexus.NexusConstants

FORMATTER - Static variable in class org.forester.phylogeny.data.Confidence

FORMATTER_06 - Static variable in class org.forester.util.ForesterUtil

FORMATTER_3 - Static variable in class org.forester.util.ForesterUtil

FORMATTER_6 - Static variable in class org.forester.util.ForesterUtil

FORMATTER_9 - Static variable in class org.forester.util.ForesterUtil

G

GAP - Static variable in interface org.forester.sequence.MolecularSequence

GAP_STR - Static variable in interface org.forester.sequence.MolecularSequence

GapContribution - Class in org.forester.msa_compactor

GENBANK_NUC_PATTERN_1 - Static variable in class org.forester.util.SequenceAccessionTools

GENBANK_NUC_PATTERN_2 - Static variable in class org.forester.util.SequenceAccessionTools

GENBANK_PROT_PATTERN - Static variable in class org.forester.util.SequenceAccessionTools

GENE_NAME - Static variable in class org.forester.io.parsers.nhx.NHXtags

gene_tree_preprocess - Class in org.forester.application

gene_tree_preprocess() - Constructor for class org.forester.application.gene_tree_preprocess

GeneralMsaParser - Class in org.forester.io.parsers

GeneralMsaParser() - Constructor for class org.forester.io.parsers.GeneralMsaParser

GeneralTable<IDENTIFIER_TYPE,VALUE_TYPE> - Class in org.forester.util

GeneralTable() - Constructor for class org.forester.util.GeneralTable

genome_counts_for_once_appearing_dcs - Class in org.forester.applications

genome_counts_for_once_appearing_dcs() - Constructor for class org.forester.applications.genome_counts_for_once_appearing_dcs

GenomeWideCombinableDomains - Interface in org.forester.surfacing

GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder - Enum in org.forester.surfacing

get(int, int) - Method in class org.forester.datastructures.IntMatrix

get(String) - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

get(String) - Method in interface org.forester.surfacing.GenomeWideCombinableDomains

get_distances - Class in org.forester.applications

get_distances() - Constructor for class org.forester.applications.get_distances

get_genome_counts_per_char - Class in org.forester.applications

get_genome_counts_per_char() - Constructor for class org.forester.applications.get_genome_counts_per_char

get_loss_nodes - Class in org.forester.applications

get_loss_nodes() - Constructor for class org.forester.applications.get_loss_nodes

get_shared_chars - Class in org.forester.applications

get_shared_chars() - Constructor for class org.forester.applications.get_shared_chars

get_subtree_specific_chars - Class in org.forester.applications

get_subtree_specific_chars() - Constructor for class org.forester.applications.get_subtree_specific_chars

getAbstractRenderer(int, int) - Method in class org.forester.development.MsaRenderer

getAccession() - Method in class org.forester.phylogeny.data.Sequence

getAccession() - Method in class org.forester.protein.BasicProtein

getAccession() - Method in interface org.forester.protein.Protein

getAccession() - Method in class org.forester.ws.seqdb.EbiDbEntry

getAccession() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getAccession() - Method in class org.forester.ws.seqdb.UniProtEntry

getAllBinaryDomainCombinations() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

Does not return binary combinations which contain one or two domains to be ignored -- if ignoring is allowed.

getAllCombinableDomainsIds() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

getAllCombinableDomainsIds() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains

getAllDescendants(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

getAllDescendants() - Method in class org.forester.phylogeny.PhylogenyNode

getAllDomainIds() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

getAllDomainIds() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains

This should return all domains ids present in the genome.

getAllDomainIds(List<GenomeWideCombinableDomains>) - Static method in class org.forester.surfacing.SurfacingUtil

getAllDomains() - Method in class org.forester.surfacing.BasicCombinableDomains

getAllDomains() - Method in interface org.forester.surfacing.CombinableDomains

This must return all domains in this set of combinable domains (i.e.

getAllDomains() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

Does not return domains which are to be ignored -- if ignoring is allowed.

getAllExternalDescendants() - Method in class org.forester.phylogeny.PhylogenyNode

Returns a List containing references to all external children of this PhylogenyNode.

getAllExternalDescendantsNames() - Method in class org.forester.phylogeny.PhylogenyNode

Returns a List containing references to all names of the external children of this PhylogenyNode.

getAllExternalNodeNames() - Method in class org.forester.phylogeny.Phylogeny

getAllSuperGoIds(GoId, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils

getAllSuperGoTerms(GoId, List<GoTerm>) - Static method in class org.forester.go.GoUtils

getAllSuperGoTerms(GoId, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils

getAllSuperGoTerms(GoTerm, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils

getAltIds() - Method in class org.forester.go.BasicGoTerm

getAltIds() - Method in interface org.forester.go.GoTerm

getAltitude() - Method in class org.forester.phylogeny.data.Point

getAltiudeUnit() - Method in class org.forester.phylogeny.data.Point

getAnalyzedGeneTrees() - Method in class org.forester.rio.RIO

getAnnotation(int) - Method in class org.forester.phylogeny.data.Sequence

getAnnotations() - Method in class org.forester.phylogeny.data.Sequence

getAnnotations() - Method in class org.forester.ws.seqdb.EbiDbEntry

getAnnotations() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getAnnotations() - Method in class org.forester.ws.seqdb.UniProtEntry

getAppliesTo() - Method in class org.forester.phylogeny.data.Property

getAttribute(String) - Method in class org.forester.io.parsers.phyloxml.XmlElement

getAttributes() - Method in class org.forester.io.parsers.phyloxml.XmlElement

getAtttributeValue(XmlElement, String) - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler

getAtttributeValue(XmlElement, String) - Static method in class org.forester.io.parsers.tol.TolXmlHandler

getAuthority() - Method in class org.forester.phylogeny.data.Taxonomy

getAvailablePhylogeniesWebserviceClient(int) - Method in class org.forester.archaeopteryx.webservices.WebservicesManager

getAvailablePhylogeniesWebserviceClients() - Method in class org.forester.archaeopteryx.webservices.WebservicesManager

getAvarageNormalizedScore() - Method in class org.forester.pccx.ExternalNodeBasedCoverage

getAvarageRawScore() - Method in class org.forester.pccx.ExternalNodeBasedCoverage

getAvgNumberOfGaps() - Method in class org.forester.msa_compactor.MsaProperties

getBaseFontFamilyName() - Method in class org.forester.archaeopteryx.Configuration

getBaseUrl() - Static method in class org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer

getBinaryCharacters() - Method in class org.forester.phylogeny.data.NodeData

getBinaryDomainCombinationsSpecificToGenome0() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

getBinaryDomainCombinationsSpecificToGenome1() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

getBootstrapSamples() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

getBranchColor() - Method in class org.forester.phylogeny.data.BranchData

getBranchColorValue(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Convenience method

getBranchData() - Method in class org.forester.phylogeny.PhylogenyNode

getBranchesInPreorder(Phylogeny) - Static method in class org.forester.sdi.SDIR

getBranchWidth() - Method in class org.forester.phylogeny.data.BranchData

getBranchWidthValue(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Convenience method

getCharacter(int) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

getCharacter(int) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

getCharacterIndex(String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

getCharacterIndex(String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

getCharStateLabels() - Method in class org.forester.io.parsers.nexus.NexusCharactersParser

getChildElement(int) - Method in class org.forester.io.parsers.phyloxml.XmlElement

getChildNode(int) - Method in class org.forester.phylogeny.PhylogenyNode

This return child node n of this node.

getChildNode1() - Method in class org.forester.phylogeny.PhylogenyNode

Convenience method.

getChildNode2() - Method in class org.forester.phylogeny.PhylogenyNode

Convenience method.

getChildNodeIndex() - Method in class org.forester.phylogeny.PhylogenyNode

This gets the child node index of this node.

getChildNodeIndex(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode

This gets the child node index of this node, given that parent is its parent

getChromosome() - Method in class org.forester.ws.seqdb.EbiDbEntry

getChromosome() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getChromosome() - Method in class org.forester.ws.seqdb.UniProtEntry

getCode() - Method in class org.forester.ws.seqdb.UniProtTaxonomy

getColumnAt(int) - Method in class org.forester.msa.BasicMsa

getColumnAt(int) - Method in interface org.forester.msa.Msa

getColumnIdentifiers() - Method in class org.forester.util.GeneralTable

getColumns() - Method in class org.forester.development.MsaRenderer

getColumnsAsMap(int, int) - Method in class org.forester.util.BasicTable

getColumnsAsMapDouble(int, int) - Method in class org.forester.util.BasicTable

getCombinableDomainIds(Species) - Method in class org.forester.surfacing.DomainSimilarity

getCombinableDomains() - Method in class org.forester.surfacing.BasicCombinableDomains

getCombinableDomains() - Method in interface org.forester.surfacing.CombinableDomains

getCombinableDomainsIds() - Method in class org.forester.surfacing.BasicCombinableDomains

getCombinableDomainsIds() - Method in interface org.forester.surfacing.CombinableDomains

Returns the combinable domain identifiers sorted in alphabetical manner: - keys are the combinable domain identifiers - values are the counts of proteins exhibiting a particular combination

getCombiningDomainIdsAsStringBuilder() - Method in class org.forester.surfacing.BasicCombinableDomains

getCombiningDomainIdsAsStringBuilder() - Method in interface org.forester.surfacing.CombinableDomains

getCombiningDomains() - Method in class org.forester.surfacing.BasicCombinableDomains

getCommandLineArgsAsString() - Method in class org.forester.util.CommandLineArguments

getComment() - Method in class org.forester.go.BasicGoTerm

getComment() - Method in interface org.forester.go.GoTerm

getComment() - Method in class org.forester.phylogeny.data.Accession

getCommonName() - Method in class org.forester.phylogeny.data.Taxonomy

getCommonName() - Method in class org.forester.ws.seqdb.UniProtTaxonomy

getConfidence() - Method in class org.forester.phylogeny.data.Annotation

getConfidence(int) - Method in class org.forester.phylogeny.data.BranchData

getConfidence() - Method in class org.forester.phylogeny.data.Event

getConfidence() - Method in class org.forester.phylogeny.data.ProteinDomain

getConfidence() - Method in class org.forester.phylogeny.data.SequenceRelation

getConfidence() - Method in class org.forester.phylogeny.Phylogeny

getConfidences() - Method in class org.forester.phylogeny.data.BranchData

getConfidenceValue(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Convenience method

getConfidenceValuesAsArray(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Convenience method

getConfiguration() - Method in class org.forester.archaeopteryx.MainFrame

getConnectedNode(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyBranch

getControlPanel() - Method in class org.forester.archaeopteryx.MainPanel

getCopiedAndPastedNodes() - Method in class org.forester.archaeopteryx.MainPanel

getCost() - Method in class org.forester.evoinference.parsimony.DolloParsimony

getCost() - Method in class org.forester.evoinference.parsimony.FitchParsimony

getCost() - Method in class org.forester.evoinference.parsimony.SankoffParsimony

getCost() - Method in class org.forester.surfacing.DomainParsimonyCalculator

getCount() - Method in class org.forester.sdi.SDIR

Returns the number of differently rooted trees which minimize the (rooting) "criterion" - as determined by method "infer".

getCrossReferences() - Method in class org.forester.phylogeny.data.Sequence

getCrossReferences() - Method in class org.forester.ws.seqdb.EbiDbEntry

getCrossReferences() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getCrossReferences() - Method in class org.forester.ws.seqdb.UniProtEntry

getCurrentDateTime() - Static method in class org.forester.util.ForesterUtil

getCurrentExternalNodesDataBuffer() - Method in class org.forester.archaeopteryx.ArchaeopteryxA

This method returns the current external node data which has been selected by the user by clicking the "Return ..." menu item.

getCurrentExternalNodesDataBuffer() - Method in class org.forester.archaeopteryx.ArchaeopteryxE

This method returns the current external node data which has been selected by the user by clicking the "Return ..." menu item.

getCurrentExternalNodesDataBuffer() - Method in class org.forester.archaeopteryx.MainFrame

This method returns the current external node data which has been selected by the user by clicking the "Return ..." menu item.

getCurrentExternalNodesDataBufferChangeCounter() - Method in class org.forester.archaeopteryx.ArchaeopteryxA

getCurrentExternalNodesDataBufferChangeCounter() - Method in class org.forester.archaeopteryx.ArchaeopteryxE

getCurrentExternalNodesDataBufferChangeCounter() - Method in class org.forester.archaeopteryx.MainFrame

getCurrentExternalNodesDataBufferLength() - Method in class org.forester.archaeopteryx.ArchaeopteryxA

getCurrentExternalNodesDataBufferLength() - Method in class org.forester.archaeopteryx.ArchaeopteryxE

getCurrentExternalNodesDataBufferLength() - Method in class org.forester.archaeopteryx.MainFrame

getCurrentPhylogeny(String) - Method in class org.forester.archaeopteryx.ArchaeopteryxE

This method returns the current phylogeny as a string in the chosen format

getCurrentPhylogenyGraphicsAsBase64EncodedString(String) - Method in class org.forester.archaeopteryx.ArchaeopteryxE

This method returns a view of the current phylogeny in a chosen graphics format, base64-encoded in a string so that in can be used from javascript.

getCurrentTreePanel() - Method in class org.forester.archaeopteryx.MainPanel

getCurrentUserDesktopPath() - Static method in class org.forester.util.WindowsUtils

getData() - Method in class org.forester.phylogeny.PhylogenyBranch

getData() - Method in class org.forester.util.BasicDescriptiveStatistics

getData() - Method in interface org.forester.util.DescriptiveStatistics

getDataAsDoubleArray() - Method in class org.forester.util.BasicDescriptiveStatistics

getDataAsDoubleArray() - Method in interface org.forester.util.DescriptiveStatistics

getDataType() - Method in class org.forester.phylogeny.data.Property

getDataValue() - Method in class org.forester.development.ResidueRenderer

getDate() - Method in class org.forester.phylogeny.data.NodeData

getDefaultBootstrapSamples() - Method in class org.forester.archaeopteryx.Configuration

getDefaultNodeFill() - Method in class org.forester.archaeopteryx.Configuration

getDefaultNodeShape() - Method in class org.forester.archaeopteryx.Configuration

getDefaultNodeShapeSize() - Method in class org.forester.archaeopteryx.Configuration

getDefaultParameters() - Static method in class org.forester.msa.ClustalOmega

getDefaultParameters() - Static method in class org.forester.msa.Mafft

getDefinition() - Method in class org.forester.go.BasicGoTerm

getDefinition() - Method in interface org.forester.go.GoTerm

getDesc() - Method in class org.forester.phylogeny.data.Annotation

getDesc() - Method in class org.forester.phylogeny.data.Date

getDesc() - Method in class org.forester.phylogeny.data.Distribution

getDescendants() - Method in class org.forester.phylogeny.PhylogenyNode

getDesciption() - Method in class org.forester.pccx.BranchCountingBasedScoringMethod

getDesciption() - Method in class org.forester.pccx.BranchLengthBasedScoringMethod

getDesciption() - Method in class org.forester.pccx.LogBranchLengthBasedScoringMethod

getDesciption() - Method in interface org.forester.pccx.ScoringMethodForExternalNode

This returns a short description of this scoring method

getDescription() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient

getDescription() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient

A short description of the webservice (~20 characters).

getDescription() - Method in class org.forester.phylogeny.data.Reference

getDescription() - Method in class org.forester.phylogeny.data.Uri

getDescription() - Method in class org.forester.phylogeny.Phylogeny

getDescription() - Method in class org.forester.protein.BasicProtein

getDescription() - Method in interface org.forester.protein.Protein

getDescription() - Method in class org.forester.surfacing.MappingResults

getDescription() - Method in class org.forester.util.BasicDescriptiveStatistics

getDescription() - Method in interface org.forester.util.DescriptiveStatistics

getDifferenceInCounts() - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity

getDifferenceInCounts() - Method in class org.forester.surfacing.CountsBasedPairwiseDomainSimilarity

Returns (counts for domain 1) minus (counts for domain 2).

getDifferenceInCounts() - Method in interface org.forester.surfacing.PairwiseDomainSimilarity

This should return the -- not normalized, not absolute -- difference in counts (for example domain counts) for the two domains.

getDistance() - Method in class org.forester.phylogeny.data.SequenceRelation

getDistanceToParent() - Method in class org.forester.phylogeny.PhylogenyNode

Returns the length of the branch leading to the _parent of this PhylogenyNode (double).

getDistanceUnit() - Method in class org.forester.phylogeny.Phylogeny

getDistribution() - Method in class org.forester.phylogeny.data.NodeData

Convenience method -- always returns the first Distribution.

getDistribution(int) - Method in class org.forester.phylogeny.data.NodeData

getDistributions() - Method in class org.forester.phylogeny.data.NodeData

getDoi() - Method in class org.forester.phylogeny.data.Reference

getDomain(int) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

getDomain(int) - Method in class org.forester.phylogeny.data.DomainArchitecture

getDomainArchitecture() - Method in class org.forester.phylogeny.data.Sequence

getDomainBaseColor() - Method in class org.forester.archaeopteryx.TreeColorSet

getDomainCombinationType() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

getDomainCombinationType() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains

getDomainCounts(List<Protein>) - Static method in class org.forester.surfacing.SurfacingUtil

getDomainDistanceScoresMeans() - Method in class org.forester.surfacing.PairwiseGenomeComparator

getDomainId() - Method in class org.forester.protein.BasicDomain

getDomainId() - Method in interface org.forester.protein.Domain

getDomainId() - Method in class org.forester.surfacing.DomainLengths

getDomainId() - Method in class org.forester.surfacing.DomainSimilarity

getDomainId() - Method in class org.forester.surfacing.SimpleDomain

getDomainLabelColor() - Method in class org.forester.archaeopteryx.TreeColorSet

getDomainLengths(String) - Method in class org.forester.surfacing.DomainLengthsTable

getDomainLengthsList() - Method in class org.forester.surfacing.DomainLengthsTable

getDomains() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

getDomains() - Method in class org.forester.phylogeny.data.DomainArchitecture

getDomainsEncountered() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getDomainsEncountered() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getDomainsIgnoredDueToDuf() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getDomainsIgnoredDueToDuf() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getDomainsIgnoredDueToEval() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getDomainsIgnoredDueToFsEval() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getDomainsIgnoredDueToIEval() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getDomainsIgnoredDueToIndividualScoreCutoff() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getDomainsIgnoredDueToIndividualScoreCutoff() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getDomainsIgnoredDueToNegativeDomainFilter() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getDomainsIgnoredDueToNegativeDomainFilter() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getDomainsIgnoredDueToNegativeDomainFilterCountsMap() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getDomainsIgnoredDueToNegativeDomainFilterCountsMap() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getDomainsIgnoredDueToOverlap() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getDomainsIgnoredDueToOverlap() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getDomainsIgnoredDueToVirusLikeIdCountsMap() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getDomainsIgnoredDueToVirusLikeIdCountsMap() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getDomainsIgnoredDueToVirusLikeIds() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getDomainsIgnoredDueToVirusLikeIds() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getDomainsSortedByPosition() - Method in class org.forester.protein.BasicProtein

getDomainsSortedByPosition() - Method in interface org.forester.protein.Protein

getDomainsSpecificToGenome0() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

getDomainsSpecificToGenome1() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

getDomainsStored() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getDomainsStored() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getDomainsStoredSet() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getDomainsStoredSet() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getDuplicationsStatistics() - Method in class org.forester.rio.RIO

getDuplicationsSum() - Method in class org.forester.sdi.GSDI

getDuplicationsSum() - Method in class org.forester.sdi.SDI

Returns the number of duplications.

getDuplicationsSumStats() - Method in class org.forester.sdi.GSDIR

getEntropy21() - Method in class org.forester.msa_compactor.MsaProperties

getEntropy7() - Method in class org.forester.msa_compactor.MsaProperties

getErrorCount() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

getErrorCount() - Method in class org.forester.io.parsers.tol.TolParser

getErrorDescription() - Method in class org.forester.msa.ClustalOmega

getErrorDescription() - Method in class org.forester.msa.Mafft

getErrorDescription() - Method in class org.forester.msa.MsaInferrer

getErrorMessages() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

getErrorMessages() - Method in class org.forester.io.parsers.tol.TolParser

getErrorStream() - Method in class org.forester.util.ExternalProgram

getEvent() - Method in class org.forester.phylogeny.data.NodeData

getEventAtLCA(PhylogenyNode, PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

getEventType() - Method in class org.forester.phylogeny.data.Event

getEvidence() - Method in class org.forester.phylogeny.data.Annotation

getExitCode() - Method in class org.forester.msa.ClustalOmega

getExitCode() - Method in class org.forester.msa.Mafft

getExitCode() - Method in class org.forester.msa.MsaInferrer

getExtDescNodeDataToReturn() - Method in class org.forester.archaeopteryx.Configuration

getExtDescNodeDataToReturn() - Method in class org.forester.archaeopteryx.Options

getExternalDescendantsTaxonomy(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Returns taxonomy t if all external descendants have the same taxonomy t, null otherwise.

getExternalNodes() - Method in class org.forester.phylogeny.Phylogeny

Warning.

getExtNodeDataReturnOn() - Method in class org.forester.archaeopteryx.Configuration

getExtNodesOfAnalyzedGeneTrees() - Method in class org.forester.rio.RIO

Returns the numbers of number of ext nodes in gene trees analyzed (after stripping).

getFile(int) - Method in class org.forester.util.CommandLineArguments

getFileSeparator() - Static method in class org.forester.util.ForesterUtil

getFillType() - Method in class org.forester.phylogeny.data.NodeVisualData

getFirstChildNode() - Method in class org.forester.phylogeny.PhylogenyNode

Convenience method.

getFirstExternalNode() - Method in class org.forester.phylogeny.Phylogeny

Returns the first external PhylogenyNode.

getFirstLine(Object) - Static method in class org.forester.util.ForesterUtil

getFirstNode() - Method in class org.forester.phylogeny.PhylogenyBranch

getFont() - Method in class org.forester.archaeopteryx.FontChooser

getFont() - Method in class org.forester.phylogeny.data.NodeVisualData

getFontColor() - Method in class org.forester.phylogeny.data.NodeVisualData

getFontMetricsLarge() - Method in class org.forester.archaeopteryx.TreeFontSet

getFontMetricsSmall() - Method in class org.forester.archaeopteryx.TreeFontSet

getFontName() - Method in class org.forester.archaeopteryx.FontChooser

getFontName() - Method in class org.forester.phylogeny.data.NodeVisualData

getFontSize() - Method in class org.forester.archaeopteryx.FontChooser

getFontSize() - Method in class org.forester.phylogeny.data.NodeVisualData

getFontStyle() - Method in class org.forester.archaeopteryx.FontChooser

getFontStyle() - Method in class org.forester.phylogeny.data.NodeVisualData

getFontStyleInt() - Method in class org.forester.phylogeny.data.NodeVisualData

getForesterLibraryInformation() - Static method in class org.forester.util.ForesterUtil

getFrameXSize() - Method in class org.forester.archaeopteryx.Configuration

getFrameYSize() - Method in class org.forester.archaeopteryx.Configuration

getFrom() - Method in class org.forester.phylogeny.data.ProteinDomain

getFrom() - Method in class org.forester.protein.BasicDomain

getFrom() - Method in interface org.forester.protein.Domain

getFrom() - Method in class org.forester.surfacing.SimpleDomain

getFurthestDescendant(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

getGainedCharacters() - Method in class org.forester.phylogeny.data.BinaryCharacters

getGainedCharactersAsStringArray() - Method in class org.forester.phylogeny.data.BinaryCharacters

getGainedCharactersAsStringBuffer() - Method in class org.forester.phylogeny.data.BinaryCharacters

getGainedCount() - Method in class org.forester.phylogeny.data.BinaryCharacters

getGainLossCountsMatrix() - Method in class org.forester.surfacing.DomainParsimonyCalculator

getGainLossMatrix() - Method in class org.forester.evoinference.parsimony.DolloParsimony

getGainLossMatrix() - Method in class org.forester.evoinference.parsimony.FitchParsimony

getGainLossMatrix() - Method in class org.forester.evoinference.parsimony.SankoffParsimony

getGainLossMatrix() - Method in class org.forester.surfacing.DomainParsimonyCalculator

getGapRatio() - Method in class org.forester.msa_compactor.MsaProperties

getGeneName() - Method in class org.forester.phylogeny.data.Sequence

getGeneName() - Method in class org.forester.ws.seqdb.EbiDbEntry

getGeneName() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getGeneName() - Method in class org.forester.ws.seqdb.UniProtEntry

getGeneTree() - Method in class org.forester.sdi.SDI

Returns the gene tree.

getGeodeticDatum() - Method in class org.forester.phylogeny.data.Point

getGoId() - Method in class org.forester.go.BasicGoRelationship

getGoId() - Method in class org.forester.go.BasicGoTerm

getGoId() - Method in class org.forester.go.etc.OntologizerResult

getGoId() - Method in interface org.forester.go.GoRelationship

getGoId() - Method in interface org.forester.go.GoTerm

getGoNameSpace() - Method in class org.forester.go.BasicGoTerm

getGoNameSpace() - Method in interface org.forester.go.GoTerm

getGoRelationships() - Method in class org.forester.go.BasicGoTerm

getGoRelationships() - Method in interface org.forester.go.GoTerm

getGoSubsets() - Method in class org.forester.go.BasicGoTerm

getGoSubsets() - Method in interface org.forester.go.GoTerm

getGoTermCount() - Method in class org.forester.go.OBOparser

getGoTerms() - Method in class org.forester.ws.seqdb.EbiDbEntry

getGoTerms() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getGoTerms() - Method in class org.forester.ws.seqdb.UniProtEntry

getGoXRefs() - Method in class org.forester.go.BasicGoTerm

getGoXRefs() - Method in interface org.forester.go.GoTerm

getGSDIRtaxCompBase() - Method in class org.forester.rio.RIO

getHeight() - Method in class org.forester.phylogeny.Phylogeny

This calculates the height for rooted, tree-shaped phylogenies.

getId() - Method in class org.forester.archaeopteryx.tools.ProcessRunning

getId() - Method in class org.forester.go.GoId

getId() - Method in class org.forester.phylogeny.data.ProteinDomain

getId() - Method in class org.forester.phylogeny.PhylogenyNode

Returns the ID (int) of this PhylogenyNode.

getId() - Method in class org.forester.protein.ProteinId

getId() - Method in class org.forester.ws.seqdb.UniProtTaxonomy

getId0() - Method in interface org.forester.protein.BinaryDomainCombination

getId0() - Method in class org.forester.surfacing.BasicBinaryDomainCombination

getId0Code() - Method in interface org.forester.protein.BinaryDomainCombination

getId0Code() - Method in class org.forester.surfacing.BasicBinaryDomainCombination

getId1() - Method in interface org.forester.protein.BinaryDomainCombination

getId1() - Method in class org.forester.surfacing.BasicBinaryDomainCombination

getId1Code() - Method in interface org.forester.protein.BinaryDomainCombination

getId1Code() - Method in class org.forester.surfacing.BasicBinaryDomainCombination

getIdentifier(int) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

getIdentifier(int) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

getIdentifier(int) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

getIdentifier(int) - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix

getIdentifier(int) - Method in class org.forester.msa.BasicMsa

getIdentifier(int) - Method in class org.forester.msa.DeleteableMsa

getIdentifier(int) - Method in interface org.forester.msa.Msa

getIdentifier() - Method in class org.forester.phylogeny.data.Taxonomy

getIdentifier() - Method in class org.forester.phylogeny.Phylogeny

getIdentifier() - Method in class org.forester.sequence.BasicSequence

getIdentifier() - Method in interface org.forester.sequence.MolecularSequence

getIdentifierIndex(String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

getIdentifierIndex(String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

getIdRef() - Method in class org.forester.phylogeny.data.Property

getIgnoredSequenceIds() - Method in class org.forester.msa.MsaMethods

getImageMap() - Method in class org.forester.archaeopteryx.TreePanel

getIndex(String) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

getIndex(String) - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix

getIndexesOfShortestTree(List<Phylogeny>) - Static method in class org.forester.sdi.GSDIR

getIndicator() - Method in class org.forester.phylogeny.PhylogenyNode

Returns the _indicator value of this PhylogenyNode.

getIndividualCutoffAppliesTo() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getInferenceManager() - Method in class org.forester.archaeopteryx.MainFrame

getInputStream() - Method in class org.forester.util.ExternalProgram

getInstance() - Static method in class org.forester.archaeopteryx.webservices.WebservicesManager

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.AccessionParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.AnnotationParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.BinaryCharactersParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.BranchWidthParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.ColorParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.ConfidenceParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.DateParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.DistributionParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.DomainArchitectureParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.EventParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.IdentifierParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.PointParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.PolygonParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.PropertyParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.ProteinDomainParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.ReferenceParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.SequenceParser

getInstance(Phylogeny) - Static method in class org.forester.io.parsers.phyloxml.data.SequenceRelationParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.TaxonomyParser

getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.UriParser

getInstance(CoverageCalculationMethod, CoverageCalculationOptions) - Static method in class org.forester.pccx.CoverageCalculator

getInstance() - Static method in class org.forester.phylogeny.factories.ParserBasedPhylogenyFactory

getInstructions() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient

getInstructions() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient

Instructions (and examples) on how to use the webservice.

getInt() - Method in class org.forester.util.StringInt

getIntermediateFilesBase() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

getInternalStatesMatrix() - Method in class org.forester.evoinference.parsimony.DolloParsimony

getInternalStatesMatrix() - Method in class org.forester.evoinference.parsimony.FitchParsimony

getInternalStatesMatrix() - Method in class org.forester.evoinference.parsimony.SankoffParsimony

getInternalStatesMatrix() - Method in class org.forester.surfacing.DomainParsimonyCalculator

getInternalStatesMatrixPriorToTraceback() - Method in class org.forester.evoinference.parsimony.FitchParsimony

Returns a view of the internal states prior to trace-back.

getInternalStatesMatrixPriorToTraceback() - Method in class org.forester.evoinference.parsimony.SankoffParsimony

Returns a view of the internal states prior to trace-back.

getIntNodesOfAnalyzedGeneTrees() - Method in class org.forester.rio.RIO

Returns the numbers of number of int nodes in gene trees analyzed (after stripping).

getKey() - Method in interface org.forester.go.Mapping

getKey() - Method in class org.forester.go.PfamToGoMapping

getKeyDomain() - Method in class org.forester.surfacing.BasicCombinableDomains

getKeyDomain() - Method in interface org.forester.surfacing.CombinableDomains

Returns the domain whose combinable domains are in stored in this combinable domains.

getKeyDomainCount() - Method in class org.forester.surfacing.BasicCombinableDomains

getKeyDomainCount() - Method in interface org.forester.surfacing.CombinableDomains

Returns how many times the key domain is present in a given species genome.

getKeyDomainProteins() - Method in class org.forester.surfacing.BasicCombinableDomains

getKeyDomainProteins() - Method in interface org.forester.surfacing.CombinableDomains

getKeyDomainProteinsCount() - Method in class org.forester.surfacing.BasicCombinableDomains

getKeyDomainProteinsCount() - Method in interface org.forester.surfacing.CombinableDomains

Returns how many proteins with the key domain are present in a given species genome.

getLabel(int) - Method in class org.forester.datastructures.IntMatrix

getLabelForGetExtDescendentsData() - Method in class org.forester.archaeopteryx.Configuration

getLastChildNode() - Method in class org.forester.phylogeny.PhylogenyNode

Convenience method.

getLatitude() - Method in class org.forester.phylogeny.data.Point

getLength() - Method in class org.forester.msa.BasicMsa

getLength() - Method in class org.forester.msa.DeleteableMsa

getLength() - Method in interface org.forester.msa.Msa

getLength() - Method in class org.forester.msa_compactor.MsaProperties

getLength() - Method in class org.forester.phylogeny.data.ProteinDomain

getLength() - Method in class org.forester.protein.BasicDomain

getLength() - Method in class org.forester.protein.BasicProtein

getLength() - Method in interface org.forester.protein.Domain

getLength() - Method in interface org.forester.protein.Protein

getLength() - Method in class org.forester.sequence.BasicSequence

getLength() - Method in interface org.forester.sequence.MolecularSequence

getLength() - Method in class org.forester.surfacing.SimpleDomain

getLengthStatistic(Species) - Method in class org.forester.surfacing.DomainLengths

getLengthStatistic(String, Species) - Method in class org.forester.surfacing.DomainLengthsTable

getLengthStatisticsList() - Method in class org.forester.surfacing.DomainLengths

getLineage() - Method in class org.forester.phylogeny.data.Taxonomy

getLineage() - Method in class org.forester.ws.seqdb.UniProtTaxonomy

getLineage(String) - Static method in class org.forester.ws.wabi.TxSearch

getLineageToRankMap() - Static method in class org.forester.archaeopteryx.MainPanel

getLineSeparator() - Static method in class org.forester.util.ForesterUtil

getLink() - Method in class org.forester.phylogeny.PhylogenyNode

Returns a refernce to the linked PhylogenyNode of this PhylogenyNode.

getLocation() - Method in class org.forester.phylogeny.data.Sequence

getLog() - Method in class org.forester.rio.RIO

getLongitude() - Method in class org.forester.phylogeny.data.Point

getLostCharacters() - Method in class org.forester.phylogeny.data.BinaryCharacters

getLostCharactersAsStringArray() - Method in class org.forester.phylogeny.data.BinaryCharacters

getLostCharactersAsStringBuffer() - Method in class org.forester.phylogeny.data.BinaryCharacters

getLostCount() - Method in class org.forester.phylogeny.data.BinaryCharacters

getMainPanel() - Method in class org.forester.archaeopteryx.MainFrame

getMainPanel() - Method in class org.forester.archaeopteryx.MainFrameApplet

getMainPanel() - Method in class org.forester.archaeopteryx.MainFrameApplication

getMainPanel() - Method in class org.forester.archaeopteryx.TreePanel

getMap() - Method in class org.forester.ws.seqdb.EbiDbEntry

getMap() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getMap() - Method in class org.forester.ws.seqdb.UniProtEntry

getMappedExternalSpeciesTreeNodes() - Method in class org.forester.sdi.GSDI

getMappedExternalSpeciesTreeNodes() - Method in interface org.forester.sdi.GSDII

getMappedExternalSpeciesTreeNodes() - Method in class org.forester.sdi.GSDIR

getMappingCount() - Method in class org.forester.go.PfamToGoParser

getMatrix() - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser

getMax() - Method in class org.forester.pccx.ExternalNodeBasedCoverage

getMax() - Method in class org.forester.phylogeny.data.Date

getMax() - Method in class org.forester.util.BasicDescriptiveStatistics

getMax() - Method in interface org.forester.util.DescriptiveStatistics

getMaximalDifference() - Method in class org.forester.surfacing.DomainSimilarity

For pairwise similarities, this should return the "difference"; for example the difference in counts for copy number based features (the same as getMaximalDifferenceInCounts(), or the number of actually different domain combinations.

getMaximalDifferenceInCounts() - Method in class org.forester.surfacing.DomainSimilarity

For pairwise similarities, this should return the difference in counts, while for comparisons of more than two domains, this should return the maximal difference in counts

getMaximalSimilarityScore() - Method in class org.forester.surfacing.DomainSimilarity

getMaximumConfidenceValue(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

Returns the largest confidence value found on phy.

getMeanBasedOutlierSpecies(double) - Method in class org.forester.surfacing.DomainLengths

getMeanSimilarityScore() - Method in class org.forester.surfacing.DomainSimilarity

getMenuName() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient

getMenuName() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient

A name/description which can appear on a menu.

getMin() - Method in class org.forester.pccx.ExternalNodeBasedCoverage

getMin() - Method in class org.forester.phylogeny.data.Date

getMin() - Method in class org.forester.util.BasicDescriptiveStatistics

getMin() - Method in interface org.forester.util.DescriptiveStatistics

getMinDuplicationsGeneTree() - Method in class org.forester.rio.RIO

getMinDuplicationsSum() - Method in class org.forester.sdi.GSDIR

getMinDuplicationsSumGeneTree() - Method in class org.forester.sdi.GSDIR

getMinimalDiffInSubTreeHeights() - Method in class org.forester.sdi.SDIR

Returns the (absolue value of the) minimal difference in tree heights of the two subtrees at the root (of the (re)rooted gene tree) - as determined by method "infer" - if minimize_height is set to true.

getMinimalDuplications() - Method in class org.forester.sdi.SDIR

Returns the minimal number of duplications - as determined by method "infer".

getMinimalMappingCost() - Method in class org.forester.sdi.SDIR

Returns the minimal mapping cost L - as determined by method "infer" - if minimize_mapping_cost is set to true.

getMinimalSimilarityScore() - Method in class org.forester.surfacing.DomainSimilarity

getMinimalTreeHeight() - Method in class org.forester.sdi.SDIR

Returns the minimal tree height - as determined by method "infer" - if minimize_height is set to true.

getMinimumDescendentsPerInternalNodes(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

getMolecularSequence() - Method in class org.forester.phylogeny.data.Sequence

getMolecularSequence() - Method in class org.forester.sequence.BasicSequence

getMolecularSequence() - Method in interface org.forester.sequence.MolecularSequence

getMolecularSequence() - Method in class org.forester.ws.seqdb.EbiDbEntry

getMolecularSequence() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getMolecularSequence() - Method in class org.forester.ws.seqdb.UniProtEntry

getMolecularSequenceAsString() - Method in class org.forester.sequence.BasicSequence

getMolecularSequenceAsString() - Method in interface org.forester.sequence.MolecularSequence

getMostPromiscuosDomain() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

getMostPromiscuosDomain() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains

getMsa() - Method in class org.forester.archaeopteryx.MainFrameApplication

getMsa() - Method in class org.forester.msa_compactor.MsaCompactor

getMsaFile() - Method in class org.forester.archaeopteryx.MainFrameApplication

getMsaPrg() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

getMsaPrgParameters() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

getMsaProcessingMaxAllowedGapRatio() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

getMsaProcessingMinAllowedLength() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

getN() - Method in class org.forester.pccx.ExternalNodeBasedCoverage

getN() - Method in class org.forester.surfacing.DomainSimilarity

This should return the number of pairwise distances used to calculate this similarity score

getN() - Method in class org.forester.util.BasicDescriptiveStatistics

getN() - Method in interface org.forester.util.DescriptiveStatistics

getName() - Method in class org.forester.archaeopteryx.tools.ProcessRunning

getName() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient

getName() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient

The name of the webservice.

getName() - Method in class org.forester.go.BasicGoTerm

getName() - Method in interface org.forester.go.GoTerm

getName() - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser

getName() - Method in class org.forester.io.parsers.nhx.NHXParser

getName() - Method in interface org.forester.io.parsers.PhylogenyParser

getName() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

getName() - Method in class org.forester.io.parsers.tol.TolParser

getName() - Method in class org.forester.phylogeny.data.ProteinDomain

getName() - Method in class org.forester.phylogeny.data.Sequence

getName() - Method in class org.forester.phylogeny.Phylogeny

Returns the name of this Phylogeny.

getName() - Method in class org.forester.phylogeny.PhylogenyNode

getName() - Method in class org.forester.protein.BasicProtein

getName() - Method in interface org.forester.protein.Protein

getName(int) - Method in class org.forester.util.CommandLineArguments

getNames() - Method in class org.forester.util.CommandLineArguments

getNChar() - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser

getNetGainsOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator

getNextExternalNode() - Method in class org.forester.phylogeny.PhylogenyNode

Returns a refernce to the next external PhylogenyNode of this PhylogenyNode.

getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() - Method in class org.forester.phylogeny.PhylogenyNode

getNode() - Method in class org.forester.phylogeny.iterators.PostOrderStackObject

getNode(long) - Method in class org.forester.phylogeny.Phylogeny

Finds the PhylogenyNode of this Phylogeny which has a matching ID number.

getNode(String) - Method in class org.forester.phylogeny.Phylogeny

Returns a PhylogenyNode of this Phylogeny which has a matching name.

getNodeColor() - Method in class org.forester.phylogeny.data.NodeVisualData

getNodeCount() - Method in class org.forester.phylogeny.Phylogeny

This is time-inefficient since it runs a iterator each time it is called.

getNodeCount() - Static method in class org.forester.phylogeny.PhylogenyNode

Returns the total number of all Nodes created so far.

getNodeData() - Method in class org.forester.phylogeny.PhylogenyNode

getNodeField() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient

getNodeField() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient

The node data field in which to place node names from simple unannotated formats (such as Newick).

getNodeName() - Method in class org.forester.phylogeny.data.NodeData

getNodes(String) - Method in class org.forester.phylogeny.Phylogeny

Returns a List with references to all Nodes of this Phylogeny which have a matching name.

getNodesViaGeneName(String) - Method in class org.forester.phylogeny.Phylogeny

getNodesViaSequenceName(String) - Method in class org.forester.phylogeny.Phylogeny

getNodesViaSequenceSymbol(String) - Method in class org.forester.phylogeny.Phylogeny

getNodesViaTaxonomyCode(String) - Method in class org.forester.phylogeny.Phylogeny

getNodesWithMatchingSpecies(String) - Method in class org.forester.phylogeny.Phylogeny

Returns a Vector with references to all Nodes of this Phylogeny which have a matching species name.

getNodeViaSequenceName(String) - Method in class org.forester.phylogeny.Phylogeny

getNodeViaTaxonomyCode(String) - Method in class org.forester.phylogeny.Phylogeny

getNodeVisualData() - Method in class org.forester.phylogeny.data.NodeData

getNormalizationFactor(Phylogeny) - Method in class org.forester.pccx.BranchCountingBasedScoringMethod

getNormalizationFactor(Phylogeny) - Method in class org.forester.pccx.BranchLengthBasedScoringMethod

getNormalizationFactor(Phylogeny) - Method in class org.forester.pccx.LogBranchLengthBasedScoringMethod

getNormalizationFactor(Phylogeny) - Method in interface org.forester.pccx.ScoringMethodForExternalNode

This calculates a normalization factor, so that a normalized score of 1.0 means complete coverage.

getNParents() - Method in class org.forester.go.etc.OntologizerResult

getNTax() - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser

getNumber() - Method in class org.forester.protein.BasicDomain

getNumber() - Method in interface org.forester.protein.Domain

getNumber() - Method in class org.forester.surfacing.SimpleDomain

getNumberOfBranches() - Method in class org.forester.phylogeny.Phylogeny

getNumberOfCharacters() - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

getNumberOfCharacters() - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

getNumberOfChildElements() - Method in class org.forester.io.parsers.phyloxml.XmlElement

getNumberOfColumns() - Method in class org.forester.util.BasicTable

getNumberOfCombinableDomains() - Method in class org.forester.surfacing.BasicCombinableDomains

getNumberOfCombinableDomains() - Method in interface org.forester.surfacing.CombinableDomains

getNumberOfConfidences() - Method in class org.forester.phylogeny.data.BranchData

getNumberOfDescendants() - Method in class org.forester.phylogeny.PhylogenyNode

getNumberOfDifferentDomains() - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity

getNumberOfDomains() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

getNumberOfDomains() - Method in class org.forester.phylogeny.data.DomainArchitecture

getNumberOfDuplications() - Method in class org.forester.phylogeny.data.Event

getNumberOfExternalNodes() - Method in class org.forester.phylogeny.Phylogeny

Returns the sum of external Nodes of this Phylogeny (int).

getNumberOfExternalNodes() - Method in class org.forester.phylogeny.PhylogenyNode

Returns the total number of external Nodes originating from this PhylogenyNode (int).

getNumberOfGapResidues() - Method in class org.forester.sequence.BasicSequence

getNumberOfGapResidues() - Method in interface org.forester.sequence.MolecularSequence

getNumberOfGeneLosses() - Method in class org.forester.phylogeny.data.Event

getNumberOfIdentifiers() - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

getNumberOfIdentifiers() - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

getNumberOfInternalNodes() - Method in class org.forester.phylogeny.Phylogeny

getNumberOfNames() - Method in class org.forester.util.CommandLineArguments

getNumberOfNodesLackingName(Phylogeny, StringBuilder) - Static method in class org.forester.surfacing.SurfacingUtil

getNumberOfParents() - Method in class org.forester.phylogeny.PhylogenyNode

getNumberOfProteinDomains() - Method in class org.forester.protein.BasicProtein

getNumberOfProteinDomains() - Method in interface org.forester.protein.Protein

getNumberOfProteinsExhibitingCombination(String) - Method in class org.forester.surfacing.BasicCombinableDomains

getNumberOfProteinsExhibitingCombination(String) - Method in interface org.forester.surfacing.CombinableDomains

getNumberOfRows() - Method in class org.forester.util.BasicTable

getNumberOfSameDomains() - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity

getNumberOfSequences() - Method in class org.forester.msa.BasicMsa

getNumberOfSequences() - Method in class org.forester.msa.DeleteableMsa

getNumberOfSequences() - Method in interface org.forester.msa.Msa

getNumberOfSequences() - Method in class org.forester.msa_compactor.MsaProperties

getNumberOfSpeciations() - Method in class org.forester.phylogeny.data.Event

getOptions() - Method in class org.forester.archaeopteryx.ArchaeopteryxE

getOptions() - Method in class org.forester.archaeopteryx.MainFrame

getOptions() - Method in class org.forester.archaeopteryx.MainPanel

getOptionValue(String) - Method in class org.forester.util.CommandLineArguments

getOptionValueAsChar(String) - Method in class org.forester.util.CommandLineArguments

getOptionValueAsCleanString(String) - Method in class org.forester.util.CommandLineArguments

Removes quotes

getOptionValueAsDouble(String) - Method in class org.forester.util.CommandLineArguments

getOptionValueAsInt(String) - Method in class org.forester.util.CommandLineArguments

getOptionValueAsLong(String) - Method in class org.forester.util.CommandLineArguments

getOriginalSize() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

getOriginalSize() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

getOriginalSize() - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData

getOriginalSize() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

getOrthologTable() - Method in class org.forester.rio.RIO

getOutputStream() - Method in class org.forester.util.ExternalProgram

getP() - Method in class org.forester.go.etc.OntologizerResult

getPAdjusted() - Method in class org.forester.go.etc.OntologizerResult

getParalogousNodes(PhylogenyNode, String[]) - Method in class org.forester.phylogeny.Phylogeny

Returns all paralogs of the external PhylogenyNode n of this Phylogeny.

getParameter() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

getParameter() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

getParameter() - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData

getParameter() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

getParent() - Method in class org.forester.io.parsers.phyloxml.XmlElement

getParent() - Method in class org.forester.phylogeny.PhylogenyNode

Returns a refernce to the parent PhylogenyNode of this PhylogenyNode.

getParentPlateRenderer() - Method in class org.forester.development.ResidueRenderer

getPathToLocalFastme() - Method in class org.forester.archaeopteryx.Configuration

getPathToLocalFastme() - Method in class org.forester.archaeopteryx.tools.InferenceManager

getPathToLocalMafft() - Method in class org.forester.archaeopteryx.Configuration

getPathToLocalMafft() - Method in class org.forester.archaeopteryx.tools.InferenceManager

getPathToLocalRaxml() - Method in class org.forester.archaeopteryx.Configuration

getPathToLocalRaxml() - Method in class org.forester.archaeopteryx.tools.InferenceManager

getPenultimateGoTerm(GoTerm, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils

getPerDomainEvalue() - Method in class org.forester.protein.BasicDomain

getPerDomainEvalue() - Method in interface org.forester.protein.Domain

getPerDomainEvalue() - Method in class org.forester.surfacing.SimpleDomain

getPerDomainScore() - Method in class org.forester.protein.BasicDomain

getPerDomainScore() - Method in interface org.forester.protein.Domain

getPerDomainScore() - Method in class org.forester.surfacing.SimpleDomain

getPerGenomeDomainPromiscuityStatistics() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

getPerGenomeDomainPromiscuityStatistics() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains

This should return a statistic for per domain promiscuity in a genome.

getPhase() - Method in class org.forester.phylogeny.iterators.PostOrderStackObject

getPhylogeneticInferenceOptions() - Method in class org.forester.archaeopteryx.tools.PhyloInferenceDialog

getPhylogeny() - Method in class org.forester.archaeopteryx.TreePanel

Get a pointer to the phylogeny

getPMin() - Method in class org.forester.go.etc.OntologizerResult

getPoints() - Method in class org.forester.phylogeny.data.Distribution

getPoints() - Method in class org.forester.phylogeny.data.Polygon

getPolygons() - Method in class org.forester.phylogeny.data.Distribution

getPopFamily() - Method in class org.forester.go.etc.OntologizerResult

getPopTerm() - Method in class org.forester.go.etc.OntologizerResult

getPopTotal() - Method in class org.forester.go.etc.OntologizerResult

getPreferredSize() - Method in class org.forester.development.MsaRenderer

getPresentCharacters() - Method in class org.forester.phylogeny.data.BinaryCharacters

getPresentCharactersAsStringArray() - Method in class org.forester.phylogeny.data.BinaryCharacters

getPresentCharactersAsStringBuffer() - Method in class org.forester.phylogeny.data.BinaryCharacters

getPresentCount() - Method in class org.forester.phylogeny.data.BinaryCharacters

getPreviousExternalNode() - Method in class org.forester.phylogeny.PhylogenyNode

Returns a refernce to the next external PhylogenyNode of this PhylogenyNode.

getPrintableNameByType(SequenceRelation.SEQUENCE_RELATION_TYPE) - Static method in class org.forester.phylogeny.data.SequenceRelation

getProcessById(long) - Method in class org.forester.archaeopteryx.tools.ProcessPool

getProcessByIndex(int) - Method in class org.forester.archaeopteryx.tools.ProcessPool

getProcessingInstructions() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient

getProcessingInstructions() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient

This is used to indicate any kind of special processing.

getProcessPool() - Method in class org.forester.archaeopteryx.MainFrame

getProperties() - Method in class org.forester.phylogeny.data.Annotation

getProperties() - Method in class org.forester.phylogeny.data.NodeData

getProperties() - Method in class org.forester.phylogeny.data.PropertiesMap

getPropertiesArray() - Method in class org.forester.phylogeny.data.PropertiesMap

getPropertiesWithGivenReferencePrefix(String) - Method in class org.forester.phylogeny.data.PropertiesMap

getProperty(String) - Method in class org.forester.phylogeny.data.PropertiesMap

getPropertyRefs() - Method in class org.forester.phylogeny.data.PropertiesMap

Returns all property refs of this PhylogenyNode as String array.

getProteinDomain(int) - Method in class org.forester.protein.BasicProtein

getProteinDomain(int) - Method in interface org.forester.protein.Protein

getProteinDomainCount(String) - Method in class org.forester.protein.BasicProtein

getProteinDomainCount(String) - Method in interface org.forester.protein.Protein

getProteinDomains() - Method in class org.forester.protein.BasicProtein

getProteinDomains(String) - Method in class org.forester.protein.BasicProtein

getProteinDomains() - Method in interface org.forester.protein.Protein

getProteinDomains(String) - Method in interface org.forester.protein.Protein

getProteinId() - Method in class org.forester.protein.BasicProtein

getProteinId() - Method in interface org.forester.protein.Protein

getProteinsEncountered() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getProteinsEncountered() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getProteinsIgnoredDueToFilter() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getProteinsIgnoredDueToFilter() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getProteinsStored() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getProteinsStored() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getProvider() - Method in class org.forester.phylogeny.data.Identifier

getProvider() - Method in class org.forester.ws.seqdb.EbiDbEntry

getProvider() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getProvider() - Method in class org.forester.ws.seqdb.UniProtEntry

getPwdDistanceMethod() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

getQualifiedName() - Method in class org.forester.io.parsers.phyloxml.XmlElement

getRandomNumberGeneratorSeed() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

getRank() - Method in class org.forester.phylogeny.data.Taxonomy

getRank() - Method in class org.forester.ws.seqdb.UniProtTaxonomy

getRef() - Method in class org.forester.phylogeny.data.Annotation

getRef() - Method in class org.forester.phylogeny.data.Property

getRef0() - Method in class org.forester.phylogeny.data.SequenceRelation

getRef1() - Method in class org.forester.phylogeny.data.SequenceRelation

getReference() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient

getReference() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient

To get a type of reference for the webservice (an URL or citation, for example).

getReference() - Method in class org.forester.phylogeny.data.NodeData

Convenience method -- always returns the first Reference.

getReference(int) - Method in class org.forester.phylogeny.data.NodeData

getReferences() - Method in class org.forester.phylogeny.data.NodeData

getRefSource() - Method in class org.forester.phylogeny.data.Annotation

getRefValue() - Method in class org.forester.phylogeny.data.Annotation

getRelevantSequenceRelationTypes() - Method in class org.forester.phylogeny.Phylogeny

getReMappedScientificNamesFromGeneTree() - Method in class org.forester.sdi.GSDI

getReMappedScientificNamesFromGeneTree() - Method in interface org.forester.sdi.GSDII

getReMappedScientificNamesFromGeneTree() - Method in class org.forester.sdi.GSDIR

getRemovedGeneTreeNodes() - Method in class org.forester.rio.RIO

getRemovedSeq() - Method in class org.forester.msa_compactor.MsaProperties

getRenderingFactorWidth() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

getRenderingFactorWidth() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

getRenderingFactorWidth() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

getRenderingSize() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

getRenderingSize() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

getRenderingSize() - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData

getRenderingSize() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

getResidueAt(int, int) - Method in class org.forester.msa.BasicMsa

getResidueAt(int, int) - Method in class org.forester.msa.DeleteableMsa

getResidueAt(int, int) - Method in interface org.forester.msa.Msa

getResidueAt(int, int) - Method in class org.forester.msa.ResampleableMsa

getResidueAt(int) - Method in class org.forester.sequence.BasicSequence

getResidueAt(int) - Method in interface org.forester.sequence.MolecularSequence

getResult(String, String) - Static method in class org.forester.development.HmmerRest

getResult(String) - Static method in class org.forester.development.HmmerRest

getResult(String) - Static method in class org.forester.ws.wabi.RestUtil

Method for access REST

getResult(String, String, String) - Static method in class org.forester.ws.wabi.RestUtil

getReturnFormat() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient

getReturnFormat() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient

The expected format of the response.

getRoot() - Method in class org.forester.phylogeny.Phylogeny

Returns the root PhylogenyNode of this Phylogeny.

getRowAsString(int, char) - Method in class org.forester.datastructures.IntMatrix

getRowAsString(int, String) - Method in class org.forester.util.BasicTable

getRowIdentifiers() - Method in class org.forester.util.GeneralTable

getRows() - Method in class org.forester.development.MsaRenderer

getS(int) - Method in class org.forester.evoinference.distance.Sarray

getS(int) - Method in class org.forester.evoinference.distance.Sset

getScientificName() - Method in class org.forester.phylogeny.data.Taxonomy

getScientificName() - Method in class org.forester.ws.seqdb.UniProtTaxonomy

getScore() - Method in interface org.forester.pccx.Coverage

getScore() - Method in class org.forester.pccx.ExternalNodeBasedCoverage

getScoringMethod() - Method in class org.forester.pccx.ExternalNodeBasedCoverageMethodOptions

getSD() - Method in class org.forester.pccx.ExternalNodeBasedCoverage

getSecondNode() - Method in class org.forester.phylogeny.PhylogenyBranch

getSeqs() - Method in class org.forester.archaeopteryx.MainFrameApplication

getSeqsFile() - Method in class org.forester.archaeopteryx.MainFrameApplication

getSequence(int) - Method in class org.forester.msa.BasicMsa

getSequence(String) - Method in class org.forester.msa.BasicMsa

getSequence(int) - Method in class org.forester.msa.DeleteableMsa

getSequence(String) - Method in interface org.forester.msa.Msa

getSequence(int) - Method in interface org.forester.msa.Msa

getSequence(int) - Method in class org.forester.msa.ResampleableMsa

getSequence() - Method in class org.forester.phylogeny.data.NodeData

Convenience method -- always returns the first Sequence.

getSequence(int) - Method in class org.forester.phylogeny.data.NodeData

getSequenceAsString(int) - Method in class org.forester.msa.BasicMsa

getSequenceAsString(int) - Method in interface org.forester.msa.Msa

getSequenceMapByIdForPhylogeny(Phylogeny) - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler

getSequenceName() - Method in class org.forester.ws.seqdb.EbiDbEntry

getSequenceName() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getSequenceName() - Method in class org.forester.ws.seqdb.UniProtEntry

getSequenceRelationQueries() - Method in class org.forester.phylogeny.Phylogeny

getSequenceRelations() - Method in class org.forester.phylogeny.data.Sequence

getSequences() - Method in class org.forester.phylogeny.data.NodeData

getSequenceSymbol() - Method in class org.forester.ws.seqdb.EbiDbEntry

getSequenceSymbol() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getSequenceSymbol() - Method in class org.forester.ws.seqdb.UniProtEntry

getShape() - Method in class org.forester.phylogeny.data.NodeVisualData

getSharedBinaryCombinationsBasedDistances() - Method in class org.forester.surfacing.PairwiseGenomeComparator

getSharedBinaryDomainCombinations() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

getSharedDomains() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

getSharedDomainsBasedDistances() - Method in class org.forester.surfacing.PairwiseGenomeComparator

getSimilarityScore() - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity

getSimilarityScore() - Method in class org.forester.surfacing.CountsBasedPairwiseDomainSimilarity

getSimilarityScore() - Method in interface org.forester.surfacing.PairwiseDomainSimilarity

getSize() - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

getSize() - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix

getSize() - Method in class org.forester.phylogeny.data.NodeVisualData

getSize() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

getSize() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains

getSmallFont() - Method in class org.forester.archaeopteryx.TreeFontSet

getSmallMaxAscent() - Method in class org.forester.archaeopteryx.TreeFontSet

getSmallMaxDescent() - Method in class org.forester.archaeopteryx.TreeFontSet

getSource() - Method in class org.forester.phylogeny.data.Accession

getSource() - Method in class org.forester.phylogeny.data.Annotation

getSourceId() - Method in class org.forester.phylogeny.data.Sequence

getSpeciationOrDuplicationEventsSum() - Method in class org.forester.sdi.GSDI

getSpeciationsSum() - Method in class org.forester.sdi.GSDI

getSpeciationsSum() - Method in interface org.forester.sdi.GSDII

getSpeciationsSum() - Method in class org.forester.sdi.GSDIR

getSpecies(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Convenience method for display purposes.

getSpecies() - Method in class org.forester.protein.BasicProtein

getSpecies() - Method in interface org.forester.protein.Protein

getSpecies() - Method in class org.forester.surfacing.BasicCombinableDomains

getSpecies() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

getSpecies() - Method in interface org.forester.surfacing.CombinableDomains

Returns the species of this combinable domains.

getSpecies() - Method in class org.forester.surfacing.DomainLengthsTable

getSpecies() - Method in class org.forester.surfacing.DomainSimilarity

getSpecies() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains

getSpeciesCustomOrder() - Method in class org.forester.surfacing.DomainSimilarity

getSpeciesData() - Method in class org.forester.surfacing.DomainSimilarity

This should return a map, which maps species names to SpeciesSpecificDomainSimilariyData

getSpeciesId() - Method in class org.forester.species.BasicSpecies

getSpeciesId() - Method in interface org.forester.species.Species

getSpeciesList() - Method in class org.forester.surfacing.DomainLengths

getSpeciesTree() - Method in class org.forester.rio.RIO

getSpeciesTree() - Method in class org.forester.sdi.SDI

Returns the species tree.

getSpeciesTreeUrlStr() - Method in class org.forester.archaeopteryx.ArchaeopteryxA

getStandardDeviation() - Method in class org.forester.phylogeny.data.Confidence

getStandardDeviationOfSimilarityScore() - Method in class org.forester.surfacing.DomainSimilarity

getStandardErrorFromCommand() - Method in class org.forester.util.SystemCommandExecutor

Get the standard error (stderr) from the command you just exec'd.

getStandardOutputFromCommand() - Method in class org.forester.util.SystemCommandExecutor

Get the standard output (stdout) from the command you just exec'd.

getStart() - Method in class org.forester.archaeopteryx.tools.ProcessRunning

getState(int, int) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

getState(String, int) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

getState(String, String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

getState(int, int) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

getState(String, int) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

getState(String, String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

getString() - Method in class org.forester.util.StringInt

getStrippedExternalGeneTreeNodes() - Method in class org.forester.sdi.GSDI

getStrippedExternalGeneTreeNodes() - Method in interface org.forester.sdi.GSDII

getStrippedExternalGeneTreeNodes() - Method in class org.forester.sdi.GSDIR

getStrippedSpeciesTreeNodes() - Method in class org.forester.sdi.GSDI

getStrippedSpeciesTreeNodes() - Method in interface org.forester.sdi.GSDII

getStrippedSpeciesTreeNodes() - Method in class org.forester.sdi.GSDIR

getStudyFamily() - Method in class org.forester.go.etc.OntologizerResult

getStudyTerm() - Method in class org.forester.go.etc.OntologizerResult

getStudyTotal() - Method in class org.forester.go.etc.OntologizerResult

getSum() - Method in class org.forester.util.BasicDescriptiveStatistics

getSum() - Method in interface org.forester.util.DescriptiveStatistics

getSummaryAsString() - Method in class org.forester.util.BasicDescriptiveStatistics

getSummaryAsString() - Method in interface org.forester.util.DescriptiveStatistics

getSumOfFailures() - Method in class org.forester.surfacing.MappingResults

getSumOfGainsOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator

getSumOfLossesOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator

getSumOfPresentOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator

getSumOfSuccesses() - Method in class org.forester.surfacing.MappingResults

getSuperGoIds() - Method in class org.forester.go.BasicGoTerm

getSuperGoIds() - Method in interface org.forester.go.GoTerm

getSymbol() - Method in class org.forester.phylogeny.data.Sequence

getSynonym() - Method in class org.forester.ws.seqdb.UniProtTaxonomy

getSynonyms() - Method in class org.forester.phylogeny.data.Taxonomy

getTabbedPane() - Method in class org.forester.archaeopteryx.MainPanel

getTaxCompBase() - Method in class org.forester.sdi.GSDI

getTaxCompBase() - Method in interface org.forester.sdi.GSDII

getTaxCompBase() - Method in class org.forester.sdi.GSDIR

getTaxGroupByTaxCode(String) - Static method in class org.forester.util.TaxonomyUtil

getTaxIdFromFakeTaxCode(String) - Static method in class org.forester.util.TaxonomyUtil

getTaxonomicRank(String) - Static method in class org.forester.ws.wabi.TxSearch

getTaxonomies() - Method in class org.forester.phylogeny.data.NodeData

getTaxonomiesFromCommonNameStrict(String, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

getTaxonomiesFromId(String, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

getTaxonomiesFromScientificNameStrict(String, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

Does not return "sub-types".

getTaxonomiesFromTaxonomyCode(String, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

getTaxonomy() - Method in class org.forester.phylogeny.data.NodeData

Convenience method -- always returns the first Taxonomy.

getTaxonomy(int) - Method in class org.forester.phylogeny.data.NodeData

getTaxonomyCode() - Method in class org.forester.phylogeny.data.Taxonomy

getTaxonomyExtraction() - Method in class org.forester.io.parsers.nhx.NHXParser

getTaxonomyIdentifier(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Convenience method for display purposes.

getTaxonomyIdentifier() - Method in class org.forester.ws.seqdb.EbiDbEntry

getTaxonomyIdentifier() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getTaxonomyIdentifier() - Method in class org.forester.ws.seqdb.UniProtEntry

getTaxonomyScientificName() - Method in class org.forester.ws.seqdb.EbiDbEntry

getTaxonomyScientificName() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

getTaxonomyScientificName() - Method in class org.forester.ws.seqdb.UniProtEntry

getTempDir() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

getTime() - Method in class org.forester.io.parsers.HmmPfamOutputParser

getTime() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

getTimeSumSDI() - Method in class org.forester.sdi.SDIR

Returns the sum of times (in ms) needed to run method infer of class SDI.

getTo() - Method in class org.forester.phylogeny.data.ProteinDomain

getTo() - Method in class org.forester.protein.BasicDomain

getTo() - Method in interface org.forester.protein.Domain

getTo() - Method in class org.forester.surfacing.SimpleDomain

getTotalCount() - Method in class org.forester.protein.BasicDomain

getTotalCount() - Method in interface org.forester.protein.Domain

getTotalCount() - Method in class org.forester.surfacing.SimpleDomain

getTotalGains() - Method in class org.forester.evoinference.parsimony.DolloParsimony

getTotalGains() - Method in class org.forester.evoinference.parsimony.FitchParsimony

getTotalGains() - Method in class org.forester.evoinference.parsimony.SankoffParsimony

getTotalGains() - Method in class org.forester.surfacing.DomainParsimonyCalculator

getTotalLength() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

getTotalLength() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

getTotalLength() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

getTotalLength() - Method in class org.forester.phylogeny.data.DomainArchitecture

getTotalLosses() - Method in class org.forester.evoinference.parsimony.DolloParsimony

getTotalLosses() - Method in class org.forester.evoinference.parsimony.FitchParsimony

getTotalLosses() - Method in class org.forester.evoinference.parsimony.SankoffParsimony

getTotalLosses() - Method in class org.forester.surfacing.DomainParsimonyCalculator

getTotalUnchanged() - Method in class org.forester.evoinference.parsimony.DolloParsimony

getTotalUnchanged() - Method in class org.forester.evoinference.parsimony.FitchParsimony

getTotalUnchanged() - Method in class org.forester.evoinference.parsimony.SankoffParsimony

getTotalUnchanged() - Method in class org.forester.surfacing.DomainParsimonyCalculator

getTransparency() - Method in class org.forester.phylogeny.data.NodeVisualData

getTreeColorSet() - Method in class org.forester.archaeopteryx.TreePanel

getTreeFontSet() - Method in class org.forester.archaeopteryx.MainPanel

getTreeUrlStr() - Method in class org.forester.archaeopteryx.ArchaeopteryxA

getTxId(String) - Static method in class org.forester.ws.wabi.TxSearch

getTxName(String) - Static method in class org.forester.ws.wabi.TxSearch

getType() - Method in class org.forester.go.BasicGoRelationship

getType() - Method in class org.forester.go.BasicGoSubset

getType() - Method in class org.forester.go.BasicGoXRef

getType() - Method in class org.forester.go.etc.OntologizerResult

getType() - Method in class org.forester.go.GoNameSpace

getType() - Method in interface org.forester.go.GoRelationship

getType() - Method in interface org.forester.go.GoSubset

getType() - Method in interface org.forester.go.GoXRef

getType() - Method in class org.forester.msa.BasicMsa

getType() - Method in interface org.forester.msa.Msa

getType() - Method in class org.forester.phylogeny.data.Annotation

getType() - Method in class org.forester.phylogeny.data.BinaryCharacters

getType() - Method in class org.forester.phylogeny.data.Confidence

getType() - Method in class org.forester.phylogeny.data.Sequence

getType() - Method in class org.forester.phylogeny.data.SequenceRelation

getType() - Method in class org.forester.phylogeny.data.Uri

getType() - Method in class org.forester.phylogeny.Phylogeny

getType() - Method in class org.forester.sequence.BasicSequence

getType() - Method in interface org.forester.sequence.MolecularSequence

getUltimateGoTerm(GoTerm, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils

getUnit() - Method in class org.forester.phylogeny.data.Date

getUnit() - Method in class org.forester.phylogeny.data.Property

getUnitsGainedOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator

getUnitsLostOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator

getUnitsOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator

getUri(int) - Method in class org.forester.phylogeny.data.Annotation

getUri(int) - Method in interface org.forester.phylogeny.data.MultipleUris

getUri(int) - Method in class org.forester.phylogeny.data.Sequence

getUri(int) - Method in class org.forester.phylogeny.data.Taxonomy

getUris() - Method in class org.forester.phylogeny.data.Annotation

getUris() - Method in interface org.forester.phylogeny.data.MultipleUris

getUris() - Method in class org.forester.phylogeny.data.Sequence

getUris() - Method in class org.forester.phylogeny.data.Taxonomy

getUrl() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient

getUrl() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient

Use QUERY_PLACEHOLDER to indicate position of query variable.

getValue() - Method in class org.forester.archaeopteryx.tools.PhyloInferenceDialog

getValue(int, int) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

getValue(int, int) - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix

getValue() - Method in interface org.forester.go.Mapping

getValue() - Method in class org.forester.go.PfamToGoMapping

getValue() - Method in class org.forester.phylogeny.data.Accession

getValue() - Method in class org.forester.phylogeny.data.BranchColor

getValue() - Method in class org.forester.phylogeny.data.BranchWidth

getValue() - Method in class org.forester.phylogeny.data.Confidence

getValue() - Method in class org.forester.phylogeny.data.Date

getValue() - Method in class org.forester.phylogeny.data.Identifier

getValue() - Method in class org.forester.phylogeny.data.Property

getValue() - Method in class org.forester.phylogeny.data.Uri

getValue(int) - Method in class org.forester.util.BasicDescriptiveStatistics

getValue(int, int) - Method in class org.forester.util.BasicTable

getValue(int) - Method in interface org.forester.util.DescriptiveStatistics

getValue(IDENTIFIER_TYPE, IDENTIFIER_TYPE) - Method in class org.forester.util.GeneralTable

getValueAsBoolean() - Method in class org.forester.io.parsers.phyloxml.XmlElement

getValueAsDouble() - Method in class org.forester.io.parsers.phyloxml.XmlElement

getValueAsInt() - Method in class org.forester.io.parsers.phyloxml.XmlElement

getValueAsString() - Method in class org.forester.io.parsers.phyloxml.XmlElement

getValueAsString(int, int) - Method in class org.forester.util.BasicTable

getValueAsString(IDENTIFIER_TYPE, IDENTIFIER_TYPE) - Method in class org.forester.util.GeneralTable

getValuePlusProvider() - Method in class org.forester.phylogeny.data.Identifier

getValues(int, int) - Method in class org.forester.evoinference.distance.Sarray

getValues(int, int) - Method in class org.forester.evoinference.distance.Sset

getValues() - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

getVector() - Method in class org.forester.phylogeny.data.NodeData

getVectorDataHeight() - Method in class org.forester.archaeopteryx.Configuration

getVectorDataMaxColor() - Method in class org.forester.archaeopteryx.Configuration

getVectorDataMeanColor() - Method in class org.forester.archaeopteryx.Configuration

getVectorDataMinColor() - Method in class org.forester.archaeopteryx.Configuration

getVectorDataWidth() - Method in class org.forester.archaeopteryx.Configuration

getWarningCount() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

getWarningCount() - Method in class org.forester.io.parsers.tol.TolParser

getWarningMessages() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

getWarningMessages() - Method in class org.forester.io.parsers.tol.TolParser

getWellColor() - Method in class org.forester.development.ResidueRenderer

getX() - Method in class org.forester.development.AbstractRenderer

getXcoord() - Method in class org.forester.phylogeny.PhylogenyNode

Used for drawing of Trees.

getXRef() - Method in class org.forester.go.BasicGoXRef

getXRef() - Method in interface org.forester.go.GoXRef

getXSecondary() - Method in class org.forester.phylogeny.PhylogenyNode

getY() - Method in class org.forester.development.AbstractRenderer

getYcoord() - Method in class org.forester.phylogeny.PhylogenyNode

Used for drawing of Trees.

getYSecondary() - Method in class org.forester.phylogeny.PhylogenyNode

GI_PATTERN - Static variable in class org.forester.util.SequenceAccessionTools

GLAUCOPHYTA_COLOR - Static variable in class org.forester.util.TaxonomyColors

GN_PATTERN - Static variable in class org.forester.applications.aaa

GO_LINK - Static variable in class org.forester.surfacing.SurfacingConstants

GO_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

goac - Class in org.forester.application

goac() - Constructor for class org.forester.application.goac

GOC_STR - Static variable in interface org.forester.go.GoXRef

GoId - Class in org.forester.go

GoId(String) - Constructor for class org.forester.go.GoId

GoNameSpace - Class in org.forester.go

GoNameSpace(GoNameSpace.GoNamespaceType) - Constructor for class org.forester.go.GoNameSpace

GoNameSpace(String) - Constructor for class org.forester.go.GoNameSpace

GoNameSpace.GoNamespaceType - Enum in org.forester.go

GOOGLE_SCHOLAR_SEARCH - Static variable in class org.forester.surfacing.SurfacingConstants

GOOGLE_WEB_SEARCH_LINK - Static variable in class org.forester.surfacing.SurfacingConstants

GoRelationship - Interface in org.forester.go

GoRelationship.Type - Enum in org.forester.go

GOSLIM_ASPERGILLUS_STR - Static variable in interface org.forester.go.GoSubset

GOSLIM_CANDIDA_STR - Static variable in interface org.forester.go.GoSubset

GOSLIM_GENERIC_STR - Static variable in interface org.forester.go.GoSubset

GOSLIM_GOA_STR - Static variable in interface org.forester.go.GoSubset

GOSLIM_PIR_STR - Static variable in interface org.forester.go.GoSubset

GOSLIM_PLANT_STR - Static variable in interface org.forester.go.GoSubset

GOSLIM_POMBE_STR - Static variable in interface org.forester.go.GoSubset

GOSLIM_YEAST_STR - Static variable in interface org.forester.go.GoSubset

GoSubset - Interface in org.forester.go

GoSubset.Type - Enum in org.forester.go

GOSUBSET_PROK_STR - Static variable in interface org.forester.go.GoSubset

GoTerm - Interface in org.forester.go

GoUtils - Class in org.forester.go

GoXRef - Interface in org.forester.go

GoXRef.Type - Enum in org.forester.go

gsdi - Class in org.forester.application

gsdi() - Constructor for class org.forester.application.gsdi

GSDI - Class in org.forester.sdi

GSDI(Phylogeny, Phylogeny, boolean, boolean, boolean) - Constructor for class org.forester.sdi.GSDI

GSDI(Phylogeny, Phylogeny, boolean, boolean, boolean, boolean) - Constructor for class org.forester.sdi.GSDI

GSDII - Interface in org.forester.sdi

GSDIR - Class in org.forester.sdi

GSDIR(Phylogeny, Phylogeny, boolean, boolean, boolean) - Constructor for class org.forester.sdi.GSDIR

guessMolecularSequenceType(String) - Static method in class org.forester.util.ForesterUtil

guessPathToMafft() - Static method in class org.forester.msa_compactor.MsaCompactor

H

HACROBIA_COLOR - Static variable in class org.forester.util.TaxonomyColors

HAS_PART_STR - Static variable in interface org.forester.go.GoRelationship

hashCode() - Method in class org.forester.go.BasicGoTerm

Hashcode is based on hashcode of GO id.

hashCode() - Method in class org.forester.go.GoId

hashCode() - Method in class org.forester.phylogeny.data.Accession

hashCode() - Method in class org.forester.phylogeny.data.Identifier

hashCode() - Method in class org.forester.phylogeny.data.Sequence

hashCode() - Method in class org.forester.phylogeny.data.Taxonomy

hashCode() - Method in class org.forester.phylogeny.PhylogenyBranch

hashCode() - Method in class org.forester.phylogeny.PhylogenyNode

hashCode() - Method in class org.forester.protein.BasicDomain

hashCode() - Method in class org.forester.protein.ProteinId

hashCode() - Method in class org.forester.sequence.BasicSequence

hashCode() - Method in class org.forester.species.BasicSpecies

hashCode() - Method in class org.forester.surfacing.BasicBinaryDomainCombination

hasNext() - Method in interface org.forester.io.parsers.IteratingPhylogenyParser

hasNext() - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser

hasNext() - Method in class org.forester.io.parsers.nhx.NHXParser

hasNext() - Method in class org.forester.phylogeny.iterators.ExternalForwardIterator

hasNext() - Method in class org.forester.phylogeny.iterators.LevelOrderTreeIterator

Returns true is this iterator has at least one more element, false otherwise.

hasNext() - Method in interface org.forester.phylogeny.iterators.PhylogenyNodeIterator

hasNext() - Method in class org.forester.phylogeny.iterators.PostorderTreeIterator

hasNext() - Method in class org.forester.phylogeny.iterators.PreorderTreeIterator

hasSequenceRelations() - Method in class org.forester.phylogeny.data.Sequence

Hello3d - Class in org.forester.development

Hello3d() - Constructor for class org.forester.development.Hello3d

HGNC_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

HmmerRest - Class in org.forester.development

HmmerRest() - Constructor for class org.forester.development.HmmerRest

HmmPfamOutputParser - Class in org.forester.io.parsers

HmmPfamOutputParser(File, String, String) - Constructor for class org.forester.io.parsers.HmmPfamOutputParser

HmmPfamOutputParser(File, String, Set<String>, HmmPfamOutputParser.FilterType) - Constructor for class org.forester.io.parsers.HmmPfamOutputParser

HmmPfamOutputParser.FilterType - Enum in org.forester.io.parsers

HmmPfamOutputParser.ReturnType - Enum in org.forester.io.parsers

HmmscanPerDomainTableParser - Class in org.forester.io.parsers

HmmscanPerDomainTableParser(File, String, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF) - Constructor for class org.forester.io.parsers.HmmscanPerDomainTableParser

HmmscanPerDomainTableParser(File, String, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF, boolean) - Constructor for class org.forester.io.parsers.HmmscanPerDomainTableParser

HmmscanPerDomainTableParser(File, String, Set<String>, HmmscanPerDomainTableParser.FilterType, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF) - Constructor for class org.forester.io.parsers.HmmscanPerDomainTableParser

HmmscanPerDomainTableParser(File, String, Set<String>, HmmscanPerDomainTableParser.FilterType, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF, boolean) - Constructor for class org.forester.io.parsers.HmmscanPerDomainTableParser

HmmscanPerDomainTableParser.FilterType - Enum in org.forester.io.parsers

HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF - Enum in org.forester.io.parsers

HmmscanPerDomainTableParser.ReturnType - Enum in org.forester.io.parsers

I

ICHTHYOSPOREA_AND_FILASTEREA - Static variable in class org.forester.util.TaxonomyColors

ID_REF - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

IDENTIFIER - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Identifier - Class in org.forester.phylogeny.data

Identifier() - Constructor for class org.forester.phylogeny.data.Identifier

Identifier(String) - Constructor for class org.forester.phylogeny.data.Identifier

Identifier(String, String) - Constructor for class org.forester.phylogeny.data.Identifier

IDENTIFIER_DEFAULT - Static variable in class org.forester.phylogeny.data.ProteinDomain

IDENTIFIER_PROVIDER_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

IdentifierParser - Class in org.forester.io.parsers.phyloxml.data

IllegalFormatUseException - Exception in org.forester.util

IllegalFormatUseException() - Constructor for exception org.forester.util.IllegalFormatUseException

IllegalFormatUseException(String) - Constructor for exception org.forester.util.IllegalFormatUseException

ImageLoader - Class in org.forester.archaeopteryx.tools

ImageLoader(TreePanel) - Constructor for class org.forester.archaeopteryx.tools.ImageLoader

IMG_STR - Static variable in interface org.forester.go.GoXRef

increaseCountingMap(Map<String, Integer>, String) - Static method in class org.forester.util.ForesterUtil

INDENT_PHYLOXML_DEAFULT - Static variable in class org.forester.io.writers.PhylogenyWriter

INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX - Static variable in class org.forester.application.surfacing

INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX - Static variable in class org.forester.application.surfacing

INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX - Static variable in class org.forester.application.surfacing

INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX - Static variable in class org.forester.application.surfacing

INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX - Static variable in class org.forester.application.surfacing

INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX - Static variable in class org.forester.application.surfacing

INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX - Static variable in class org.forester.application.surfacing

INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX - Static variable in class org.forester.application.surfacing

infer(List<MolecularSequence>, List<String>) - Method in class org.forester.msa.ClustalOmega

infer(File, List<String>) - Method in class org.forester.msa.ClustalOmega

infer(List<MolecularSequence>, List<String>) - Method in class org.forester.msa.Mafft

infer(File, List<String>) - Method in class org.forester.msa.Mafft

infer(File, List<String>) - Method in class org.forester.msa.MsaInferrer

infer(List<MolecularSequence>, List<String>) - Method in class org.forester.msa.MsaInferrer

infer(Phylogeny, Phylogeny, boolean, boolean, boolean, boolean, int) - Method in class org.forester.sdi.SDIR

Infers gene duplications on a possibly unrooted gene Phylogeny gene_tree.

InferenceManager - Class in org.forester.archaeopteryx.tools

inferTaxonomyFromDescendents(Phylogeny) - Static method in class org.forester.analysis.AncestralTaxonomyInference

init() - Method in class org.forester.archaeopteryx.ArchaeopteryxA

init() - Method in class org.forester.archaeopteryx.ArchaeopteryxE

init() - Method in class org.forester.phylogeny.data.Confidence

init() - Method in class org.forester.phylogeny.data.Sequence

init() - Method in class org.forester.phylogeny.data.Taxonomy

init() - Method in class org.forester.phylogeny.Phylogeny

Deletes this Phylogeny.

initialize(BasicSymmetricalDistanceMatrix) - Method in class org.forester.evoinference.distance.Sarray

initialize(int) - Method in class org.forester.evoinference.distance.Sarray

initialize(BasicSymmetricalDistanceMatrix) - Method in class org.forester.evoinference.distance.Sset

initialize(int) - Method in class org.forester.evoinference.distance.Sset

inreaseByOne(int, int) - Method in class org.forester.datastructures.IntMatrix

intervalNumberSpecies(Phylogeny, int) - Static method in class org.forester.development.DevelopmentTools

Sets the species name of the external Nodes of Phylogeny t to 1, 1+i, 2, 2+i, 3, 3+i, ....

IntMatrix - Class in org.forester.datastructures

IntMatrix(int) - Constructor for class org.forester.datastructures.IntMatrix

IntMatrix(List<String>) - Constructor for class org.forester.datastructures.IntMatrix

inverseMarkedOfWell(int, int) - Method in class org.forester.development.MsaRenderer

inverted_dcs - Class in org.forester.applications

inverted_dcs() - Constructor for class org.forester.applications.inverted_dcs

IS_DUPLICATION - Static variable in class org.forester.io.parsers.nhx.NHXtags

isAbbreviateScientificTaxonNames() - Method in class org.forester.archaeopteryx.Configuration

isAllDecendentsAreDuplications(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

isAllGap(int) - Method in class org.forester.msa.DeleteableMsa

isAllowErrorsInDistanceToParent() - Method in class org.forester.archaeopteryx.Options

isAllowProteinsWithSameName() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

isAllowThickStrokes() - Method in class org.forester.archaeopteryx.Configuration

isBackgroundColorGradient() - Method in class org.forester.archaeopteryx.Configuration

isBiologicalProcess() - Method in class org.forester.go.GoNameSpace

isCalcSimilarityScore() - Method in class org.forester.surfacing.BasicDomainSimilarityCalculator

isCellularComponent() - Method in class org.forester.go.GoNameSpace

isCollapse() - Method in class org.forester.phylogeny.PhylogenyNode

Returns whether this PhylogenyNode should be drawn as collapsed.

isColorByTaxonomicGroup() - Method in class org.forester.archaeopteryx.Configuration

isColorLabelsSameAsParentBranch() - Method in class org.forester.archaeopteryx.Configuration

isCombinable(String) - Method in class org.forester.surfacing.BasicCombinableDomains

isCombinable(String) - Method in interface org.forester.surfacing.CombinableDomains

isCompletelyBinary() - Method in class org.forester.phylogeny.Phylogeny

Returns whether this is a completely binary tree (i.e.

isContainsQueryForBlast(PhylogenyNode) - Static method in class org.forester.archaeopteryx.tools.Blast

isDirected() - Method in class org.forester.phylogeny.PhylogenyBranch

isDirectionTowards(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyBranch

isDuplication() - Method in class org.forester.phylogeny.data.Event

Returns true if this event contains one or more duplications events only

isDuplication() - Method in class org.forester.phylogeny.PhylogenyNode

Returns true if this PhylogenyNode represents a _duplication event, false otherwise.

isEmpty() - Method in class org.forester.datastructures.Queue

Returns whether or not this queue is empty.

isEmpty() - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

isEmpty() - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

isEmpty() - Method in class org.forester.phylogeny.data.Distribution

isEmpty() - Method in class org.forester.phylogeny.data.NodeData

isEmpty() - Method in class org.forester.phylogeny.data.NodeVisualData

isEmpty() - Method in class org.forester.phylogeny.data.Point

isEmpty() - Method in class org.forester.phylogeny.data.Polygon

isEmpty() - Method in class org.forester.phylogeny.data.Sequence

isEmpty() - Method in class org.forester.phylogeny.data.Taxonomy

isEmpty() - Method in class org.forester.phylogeny.Phylogeny

Checks whether a Phylogeny object is deleted (or empty).

isEmpty() - Method in class org.forester.phylogeny.PhylogenyNode

isEmpty() - Method in class org.forester.util.BasicTable

isEmpty(List<?>) - Static method in class org.forester.util.ForesterUtil

isEmpty(Set<?>) - Static method in class org.forester.util.ForesterUtil

isEmpty(String) - Static method in class org.forester.util.ForesterUtil

isEmpty() - Method in class org.forester.ws.seqdb.EbiDbEntry

isEmpty() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry

isEmpty() - Method in class org.forester.ws.seqdb.UniProtEntry

isEngulfed(Domain, List<Boolean>) - Static method in class org.forester.util.ForesterUtil

Returns true is Domain domain falls in an uninterrupted stretch of covered positions.

isEqual(PhylogenyData) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

isEqual(PhylogenyData) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

isEqual(PhylogenyData) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

isEqual(double, double) - Static method in class org.forester.evoinference.TestPhylogenyReconstruction

isEqual(PhylogenyData) - Method in class org.forester.go.BasicGoTerm

isEqual(double, double) - Static method in class org.forester.go.TestGo

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Accession

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Annotation

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.BinaryCharacters

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.BranchColor

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.BranchData

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.BranchWidth

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Confidence

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Date

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Distribution

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.DomainArchitecture

Returns true if the names and the order of the domains match (domain and linker lengths are ignored).

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Event

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Identifier

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.NodeData

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.NodeVisualData

isEqual(PhylogenyData) - Method in interface org.forester.phylogeny.data.PhylogenyData

Compares this PhylogenyData to PhylogenyData data.

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Point

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Polygon

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.PropertiesMap

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Property

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.ProteinDomain

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Reference

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Sequence

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.SequenceRelation

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Taxonomy

If this and taxonomy 'data' has an identifier, comparison will be based on that.

isEqual(PhylogenyData) - Method in class org.forester.phylogeny.data.Uri

isEqual(double, double) - Static method in class org.forester.surfacing.TestSurfacing

isEqual(double, double) - Static method in class org.forester.test.Test

isEqual(double, double) - Static method in class org.forester.util.ForesterUtil

isEven(int) - Static method in class org.forester.util.ForesterUtil

isExecuteableFile(File) - Static method in class org.forester.util.ExternalProgram

isExecuteableFile(File) - Static method in class org.forester.util.SystemCommandExecutor

isExternal() - Method in class org.forester.phylogeny.PhylogenyNode

Checks whether this PhylogenyNode is external (tip).

isFirstChildNode() - Method in class org.forester.phylogeny.PhylogenyNode

isFirstExternalNode() - Method in class org.forester.phylogeny.PhylogenyNode

isFusion() - Method in class org.forester.phylogeny.data.Event

isGapAt(int, int) - Method in class org.forester.msa.BasicMsa

isGapAt(int, int) - Method in interface org.forester.msa.Msa

isGapAt(int) - Method in class org.forester.sequence.BasicSequence

isGapAt(int) - Method in interface org.forester.sequence.MolecularSequence

isGeneLoss() - Method in class org.forester.phylogeny.data.Event

Returns true if this event contains one or more gene loss events only

isHasAssignedEvent() - Method in class org.forester.phylogeny.PhylogenyNode

Returns whether a _duplication or speciation event has been assigned for this PhylogenyNode.

isHasAtLeastNodeWithEvent(Phylogeny) - Static method in class org.forester.archaeopteryx.AptxUtil

isHasAtLeastOneBranchLengthLargerThanZero(Phylogeny) - Static method in class org.forester.archaeopteryx.AptxUtil

Returns true if at least one branch has a length larger than zero.

isHasAtLeastOneBranchWithSupportSD(Phylogeny) - Static method in class org.forester.archaeopteryx.AptxUtil

isHasAtLeastOneBranchWithSupportValues(Phylogeny) - Static method in class org.forester.archaeopteryx.AptxUtil

isHasAtLeastOneNodeWithScientificName(Phylogeny) - Static method in class org.forester.archaeopteryx.AptxUtil

isHasAtLeastOneNodeWithSequenceAnnotation(Phylogeny) - Static method in class org.forester.archaeopteryx.AptxUtil

isHasAttribute(String) - Method in class org.forester.io.parsers.phyloxml.XmlElement

isHasBinaryCharacters() - Method in class org.forester.phylogeny.data.NodeData

isHasBranchColor() - Method in class org.forester.phylogeny.data.BranchData

isHasBranchWidth() - Method in class org.forester.phylogeny.data.BranchData

isHasConfidences() - Method in class org.forester.phylogeny.data.BranchData

isHasDate() - Method in class org.forester.phylogeny.data.NodeData

isHasDistribution() - Method in class org.forester.phylogeny.data.NodeData

isHasEvent() - Method in class org.forester.phylogeny.data.NodeData

isHasExternalDescendant(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

isHasLengthStatistic(Species) - Method in class org.forester.surfacing.DomainLengths

isHasProperties() - Method in class org.forester.phylogeny.data.NodeData

isHasReference() - Method in class org.forester.phylogeny.data.NodeData

isHasSequence() - Method in class org.forester.phylogeny.data.NodeData

isHasTaxIdFromFakeTaxCode(String) - Static method in class org.forester.util.TaxonomyUtil

isHasTaxonomy() - Method in class org.forester.phylogeny.data.NodeData

isHasValue() - Method in class org.forester.io.parsers.phyloxml.XmlElement

isInstalled(String) - Static method in class org.forester.msa.MsaInferrer

isInternal() - Method in class org.forester.phylogeny.PhylogenyNode

Checks whether this PhylogenyNode is internal (tip).

isInternalNamesLookLikeConfidences(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

isIntersecting(String[], String[]) - Static method in class org.forester.util.ForesterUtil

This determines whether String[] a and String[] b have at least one String in common (intersect).

isLargerOrEqualToZero(double) - Static method in class org.forester.util.ForesterUtil

isLastChildNode() - Method in class org.forester.phylogeny.PhylogenyNode

Returns true if this node is the last child node of its _parent.

isLastExternalNode() - Method in class org.forester.phylogeny.PhylogenyNode

isLikelyFasta(File) - Static method in class org.forester.io.parsers.FastaParser

isLikelyFasta(InputStream) - Static method in class org.forester.io.parsers.FastaParser

isLineUpRendarableNodeData() - Method in class org.forester.archaeopteryx.Configuration

isLineUpRendarableNodeData() - Method in class org.forester.archaeopteryx.Options

isMac() - Static method in class org.forester.util.ForesterUtil

isMarked() - Method in class org.forester.development.ResidueRenderer

isMidpointReroot() - Method in class org.forester.archaeopteryx.Configuration

isMolecularFunction() - Method in class org.forester.go.GoNameSpace

isMolecularSequenceAligned() - Method in class org.forester.phylogeny.data.Sequence

isMouseEventAltered(MouseEvent) - Static method in class org.forester.development.MsaRenderer

isNull(BigDecimal) - Static method in class org.forester.util.ForesterUtil

isObsolete() - Method in class org.forester.go.BasicGoTerm

isObsolete() - Method in interface org.forester.go.GoTerm

isOptionHasAValue(String) - Method in class org.forester.util.CommandLineArguments

isOptionSet(String) - Method in class org.forester.util.CommandLineArguments

isOptionValueSet(String) - Method in class org.forester.util.CommandLineArguments

isOther() - Method in class org.forester.phylogeny.data.Event

isPerformBootstrapResampling() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

isProteinDbQuery(String) - Static method in class org.forester.util.SequenceAccessionTools

isQueryInteger() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient

isQueryInteger() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient

Is the query a number?

isReadableFile(File) - Static method in class org.forester.util.ForesterUtil

isReadableFile(String) - Static method in class org.forester.util.ForesterUtil

isRerootable() - Method in class org.forester.phylogeny.Phylogeny

isRightLineUpDomains() - Method in class org.forester.archaeopteryx.Configuration

isRightLineUpDomains() - Method in class org.forester.archaeopteryx.Options

isRoot() - Method in class org.forester.phylogeny.data.Event

isRoot() - Method in class org.forester.phylogeny.PhylogenyNode

Checks whether this PhylogenyNode is a root.

isRooted() - Method in class org.forester.phylogeny.Phylogeny

Returns true is this Phylogeny is rooted.

isSeemsEmpty(Point) - Static method in class org.forester.phylogeny.data.Point

isSelected() - Method in class org.forester.development.ResidueRenderer

isShowAnnotationRefSource() - Method in class org.forester.archaeopteryx.Configuration

isShowAnnotationRefSource() - Method in class org.forester.archaeopteryx.Options

isShowDefaultNodeShapesExternal() - Method in class org.forester.archaeopteryx.Configuration

isShowDefaultNodeShapesForMarkedNodes() - Method in class org.forester.archaeopteryx.Configuration

isShowDefaultNodeShapesInternal() - Method in class org.forester.archaeopteryx.Configuration

isShowDomainLabels() - Method in class org.forester.archaeopteryx.Configuration

isShowDomainLabels() - Method in class org.forester.archaeopteryx.Options

isSpeciation() - Method in class org.forester.phylogeny.data.Event

Returns true if this event contains one or more speciation events only

isSpeciation() - Method in class org.forester.phylogeny.PhylogenyNode

isSpeciationOrDuplication() - Method in class org.forester.phylogeny.data.Event

isTaxonomyHasIdentifierOfGivenProvider(Taxonomy, String[]) - Static method in class org.forester.phylogeny.PhylogenyMethods

isTransfer() - Method in class org.forester.phylogeny.data.Event

isTree() - Method in class org.forester.phylogeny.Phylogeny

isTrivial() - Method in class org.forester.go.etc.OntologizerResult

isUnassigned() - Method in class org.forester.go.GoNameSpace

isUnassigned() - Method in class org.forester.phylogeny.data.Event

isUnequal(double, double) - Static method in class org.forester.evoinference.TestPhylogenyReconstruction

isUseAccessors() - Method in class org.forester.go.PfamToGoParser

isValid() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

isValid() - Method in class org.forester.io.parsers.tol.TolParser

isVerbose() - Method in class org.forester.evoinference.parsimony.FitchParsimony

isWindows() - Static method in class org.forester.util.ForesterUtil

isWritableFile(File) - Static method in class org.forester.util.ForesterUtil

IteratingPhylogenyParser - Interface in org.forester.io.parsers

iteratorExternalForward() - Method in class org.forester.phylogeny.Phylogeny

iteratorLevelOrder() - Method in class org.forester.phylogeny.Phylogeny

iteratorPostorder() - Method in class org.forester.phylogeny.Phylogeny

iteratorPreorder() - Method in class org.forester.phylogeny.Phylogeny

J

JAVA_VENDOR - Static variable in class org.forester.util.ForesterUtil

JAVA_VERSION - Static variable in class org.forester.util.ForesterUtil

JAXP_SCHEMA_LANGUAGE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser

JAXP_SCHEMA_LANGUAGE - Static variable in class org.forester.io.parsers.tol.TolParser

JAXP_SCHEMA_SOURCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser

JAXP_SCHEMA_SOURCE - Static variable in class org.forester.io.parsers.tol.TolParser

K

KEGG_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

KEGG_STR - Static variable in interface org.forester.go.GoXRef

L

launch(String[]) - Method in class org.forester.util.ExternalProgram

launchWebBrowser(URI, boolean, JApplet, String) - Static method in class org.forester.archaeopteryx.AptxUtil

levelOrderReID() - Method in class org.forester.phylogeny.Phylogeny

Resets the ID numbers of the nodes of this Phylogeny in level order, starting with start_label (for the root).

LevelOrderTreeIterator - Class in org.forester.phylogeny.iterators

LevelOrderTreeIterator(Phylogeny) - Constructor for class org.forester.phylogeny.iterators.LevelOrderTreeIterator

Creates a new LevelOrderTreeIterator for iterating over all the nodes of Phylogeny phylogeny

LevelOrderTreeIterator(PhylogenyNode) - Constructor for class org.forester.phylogeny.iterators.LevelOrderTreeIterator

Creates a new LevelOrderTreeIterator for iterating over all the child nodes of PhylogenyNode node (including node itself).

LIMIT_SPEC_FOR_PROT_EX - Static variable in class org.forester.application.surfacing

limitRangeForColor(int) - Static method in class org.forester.util.ForesterUtil

Helper for method "stringToColor".

LINE_SEPARATOR - Static variable in class org.forester.util.ForesterUtil

listToSortedCountsMap(List<?>) - Static method in class org.forester.util.ForesterUtil

LIT_REF_DOI_PATTERN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

LOCAL_PHYLOXML_XSD_RESOURCE - Static variable in class org.forester.util.ForesterConstants

log(String, Writer) - Static method in class org.forester.surfacing.SurfacingUtil

LogBranchLengthBasedScoringMethod - Class in org.forester.pccx

LogBranchLengthBasedScoringMethod() - Constructor for class org.forester.pccx.LogBranchLengthBasedScoringMethod

M

Mafft - Class in org.forester.msa

main(String[]) - Static method in class org.forester.application.annotator

main(String[]) - Static method in class org.forester.application.check_fasta

main(String[]) - Static method in class org.forester.application.confadd

main(String[]) - Static method in class org.forester.application.count_support

main(String[]) - Static method in class org.forester.application.decorator

main(String[]) - Static method in class org.forester.application.decoratorX

main(String[]) - Static method in class org.forester.application.dom_dup

main(String[]) - Static method in class org.forester.application.fasta_split

main(String[]) - Static method in class org.forester.application.gene_tree_preprocess

main(String[]) - Static method in class org.forester.application.goac

main(String[]) - Static method in class org.forester.application.gsdi

main(String[]) - Static method in class org.forester.application.mcc

main(String[]) - Static method in class org.forester.application.meta_ontologizer

main(String[]) - Static method in class org.forester.application.msa_compactor

main(String[]) - Static method in class org.forester.application.nj

main(String[]) - Static method in class org.forester.application.obo_tool

main(String[]) - Static method in class org.forester.application.pccx

main(String[]) - Static method in class org.forester.application.pfam2go_extractor

main(String[]) - Static method in class org.forester.application.pfam_go

main(String[]) - Static method in class org.forester.application.pfamacc2go

main(String[]) - Static method in class org.forester.application.pfamacc2pfamid

main(String[]) - Static method in class org.forester.application.phylostrip

main(String[]) - Static method in class org.forester.application.phyloxml_converter

main(String[]) - Static method in class org.forester.application.rio

main(String[]) - Static method in class org.forester.application.support_statistics

main(String[]) - Static method in class org.forester.application.support_transfer

Transfers branch length values from one Phylogeny to another.

main(String[]) - Static method in class org.forester.application.surfacing

main(String[]) - Static method in class org.forester.application.table2fasta

main(String[]) - Static method in class org.forester.applications.aa

main(String[]) - Static method in class org.forester.applications.aaa

main(String[]) - Static method in class org.forester.applications.core_chars

main(String[]) - Static method in class org.forester.applications.domainloss_replacement

main(String[]) - Static method in class org.forester.applications.genome_counts_for_once_appearing_dcs

main(String[]) - Static method in class org.forester.applications.get_distances

main(String[]) - Static method in class org.forester.applications.get_genome_counts_per_char

main(String[]) - Static method in class org.forester.applications.get_loss_nodes

main(String[]) - Static method in class org.forester.applications.get_shared_chars

main(String[]) - Static method in class org.forester.applications.get_subtree_specific_chars

main(String[]) - Static method in class org.forester.applications.inverted_dcs

main(String[]) - Static method in class org.forester.applications.map_lengths

main(String[]) - Static method in class org.forester.applications.phylo2coloredgraphics

main(String[]) - Static method in class org.forester.applications.phylo2graphics

main(String[]) - Static method in class org.forester.applications.reinv_count

main(String[]) - Static method in class org.forester.applications.set_comparator

main(String[]) - Static method in class org.forester.applications.shared_chars_in_ext_nodes

main(String[]) - Static method in class org.forester.applications.simple_node_processor

main(String[]) - Static method in class org.forester.applications.subtree_feature_count

main(String[]) - Static method in class org.forester.applications.tax_code_cleaner

main(String[]) - Static method in class org.forester.applications.wiki_examples

main(String[]) - Static method in class org.forester.archaeopteryx.Archaeopteryx

main(String[]) - Static method in class org.forester.development.Hello3d

main(String[]) - Static method in class org.forester.development.HmmerRest

main(String[]) - Static method in class org.forester.development.RandomThing

main(String[]) - Static method in class org.forester.development.Test

main(String[]) - Static method in class org.forester.development.Time

main(String[]) - Static method in class org.forester.evoinference.TestPhylogenyReconstruction

main(String[]) - Static method in class org.forester.io.parsers.FastaParser

main(String[]) - Static method in class org.forester.msa_compactor.Chart

main(String[]) - Static method in class org.forester.rio.TestRIO

main(String[]) - Static method in class org.forester.sdi.TestGSDI

main(String[]) - Static method in class org.forester.test.examples.Example1

main(String[]) - Static method in class org.forester.test.examples.Example2

main(String[]) - Static method in class org.forester.test.examples.Example3

main(String[]) - Static method in class org.forester.test.examples.Example4

main(String[]) - Static method in class org.forester.test.examples.Example5

main(String[]) - Static method in class org.forester.test.Test

main(String[]) - Static method in class org.forester.util.CommandProcessBuilder

main(String[]) - Static method in class org.forester.ws.hmmer.Test

main(String[]) - Static method in class org.forester.ws.wabi.TxSearch

MainFrame - Class in org.forester.archaeopteryx

MainFrameApplet - Class in org.forester.archaeopteryx

MainFrameApplication - Class in org.forester.archaeopteryx

MainPanel - Class in org.forester.archaeopteryx

MainPanel(Configuration, MainFrame) - Constructor for class org.forester.archaeopteryx.MainPanel

map2file(File, Map<?, ?>, String, String) - Static method in class org.forester.util.ForesterUtil

map2writer(Writer, Map<?, ?>, String, String) - Static method in class org.forester.util.ForesterUtil

map_lengths - Class in org.forester.applications

map_lengths() - Constructor for class org.forester.applications.map_lengths

Mapping - Interface in org.forester.go

MappingResults - Class in org.forester.surfacing

MappingResults() - Constructor for class org.forester.surfacing.MappingResults

mapToStringBuffer(Map<Object, Object>, String) - Static method in class org.forester.util.ForesterUtil

match(Set<PhylogenyNode>) - Method in class org.forester.tools.TreeSplitMatrix

MATCHING_NODES_A - Static variable in class org.forester.archaeopteryx.TreeColorSet

MATCHING_NODES_A_AND_B - Static variable in class org.forester.archaeopteryx.TreeColorSet

MATCHING_NODES_B - Static variable in class org.forester.archaeopteryx.TreeColorSet

MATRIX - Static variable in class org.forester.io.parsers.nexus.NexusConstants

MAX_ALLOWED_BL_VALUE - Static variable in class org.forester.pccx.LogBranchLengthBasedScoringMethod

MAX_ALLOWED_OVERLAP_DEFAULT - Static variable in class org.forester.application.surfacing

MAX_SIMILARITY_SCORE - Static variable in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

MB_BL_PATTERN - Static variable in class org.forester.io.parsers.nhx.NHXParser

MB_PROB_PATTERN - Static variable in class org.forester.io.parsers.nhx.NHXParser

MB_PROB_SD_PATTERN - Static variable in class org.forester.io.parsers.nhx.NHXParser

mcc - Class in org.forester.application

mcc() - Constructor for class org.forester.application.mcc

median() - Method in class org.forester.util.BasicDescriptiveStatistics

median() - Method in interface org.forester.util.DescriptiveStatistics

META_CYC_STR - Static variable in interface org.forester.go.GoXRef

meta_ontologizer - Class in org.forester.application

meta_ontologizer() - Constructor for class org.forester.application.meta_ontologizer

MetaOntologizer - Class in org.forester.go.etc

MetaOntologizer() - Constructor for class org.forester.go.etc.MetaOntologizer

midpointRoot(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

midrange() - Method in class org.forester.util.BasicDescriptiveStatistics

midrange() - Method in interface org.forester.util.DescriptiveStatistics

MIM_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

MIN_ALLOWED_BL_VALUE - Static variable in class org.forester.pccx.BranchLengthBasedScoringMethod

MIN_ALLOWED_BL_VALUE - Static variable in class org.forester.pccx.LogBranchLengthBasedScoringMethod

MIN_LENGTH - Static variable in class org.forester.applications.aaa

MIN_SIMILARITY_SCORE - Static variable in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

ModelingUtils - Class in org.forester.pccx

ModelingUtils() - Constructor for class org.forester.pccx.ModelingUtils

MOLECULAR_FUNCTION_STR - Static variable in class org.forester.go.GoNameSpace

MolecularSequence - Interface in org.forester.sequence

MolecularSequence.TYPE - Enum in org.forester.sequence

mouseWheelMoved(MouseWheelEvent) - Method in class org.forester.archaeopteryx.TreePanel

moveBranchLengthsToBootstrap(Phylogeny) - Static method in class org.forester.application.support_transfer

Moves the values in the branch length field to the bootstrap field, for each PhylogenyNode of this Phylogeny.

Msa - Interface in org.forester.msa

Msa.MSA_FORMAT - Enum in org.forester.msa

msa_compactor - Class in org.forester.application

msa_compactor() - Constructor for class org.forester.application.msa_compactor

MSA_FILE_SUFFIX - Static variable in class org.forester.archaeopteryx.tools.PhylogeneticInferrer

MsaCompactor - Class in org.forester.msa_compactor

MsaCompactor(DeleteableMsa) - Constructor for class org.forester.msa_compactor.MsaCompactor

MsaFormatException - Exception in org.forester.msa

MsaFormatException(String) - Constructor for exception org.forester.msa.MsaFormatException

MsaInferrer - Class in org.forester.msa

MsaInferrer() - Constructor for class org.forester.msa.MsaInferrer

MsaMethods - Class in org.forester.msa

MsaProperties - Class in org.forester.msa_compactor

MsaProperties(int, int, double, double, double, double, String) - Constructor for class org.forester.msa_compactor.MsaProperties

MsaProperties(Msa, String, boolean) - Constructor for class org.forester.msa_compactor.MsaProperties

MsaRenderer - Class in org.forester.development

MsaRenderer(Msa, int, JComponent) - Constructor for class org.forester.development.MsaRenderer

MultipleUris - Interface in org.forester.phylogeny.data

N

NAME - Static variable in class org.forester.archaeopteryx.ArchaeopteryxA

NCBI_GI - Static variable in class org.forester.util.ForesterUtil

NCBI_NUCCORE - Static variable in class org.forester.util.ForesterUtil

NCBI_PROTEIN - Static variable in class org.forester.util.ForesterUtil

NCBI_TAXID_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

NCHAR - Static variable in class org.forester.io.parsers.nexus.NexusConstants

NEGATIVELY_REGULATES_STR - Static variable in interface org.forester.go.GoRelationship

NeighborJoining - Class in org.forester.evoinference.distance

NeighborJoiningF - Class in org.forester.evoinference.distance

NeighborJoiningR - Class in org.forester.evoinference.distance

neTest - Class in org.forester.development

neTest() - Constructor for class org.forester.development.neTest

neTest.DoublePointer - Class in org.forester.development

next() - Method in interface org.forester.io.parsers.IteratingPhylogenyParser

next() - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser

next() - Method in class org.forester.io.parsers.nhx.NHXParser

next() - Method in class org.forester.phylogeny.iterators.ExternalForwardIterator

next() - Method in class org.forester.phylogeny.iterators.LevelOrderTreeIterator

Returns the next PhylogenyNode.

next() - Method in interface org.forester.phylogeny.iterators.PhylogenyNodeIterator

next() - Method in class org.forester.phylogeny.iterators.PostorderTreeIterator

Advances the Iterator by one.

next() - Method in class org.forester.phylogeny.iterators.PreorderTreeIterator

Advances the Iterator by one.

NextBio_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

NEXUS - Static variable in class org.forester.io.parsers.nexus.NexusConstants

NEXUS_EXTERNAL_DOMAIN_COMBINATIONS - Static variable in class org.forester.application.surfacing

NEXUS_EXTERNAL_DOMAINS - Static variable in class org.forester.application.surfacing

NEXUS_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing

NexusBinaryStatesMatrixParser - Class in org.forester.io.parsers.nexus

NexusBinaryStatesMatrixParser() - Constructor for class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser

NexusCharactersParser - Class in org.forester.io.parsers.nexus

NexusCharactersParser() - Constructor for class org.forester.io.parsers.nexus.NexusCharactersParser

NexusConstants - Class in org.forester.io.parsers.nexus

NexusConstants() - Constructor for class org.forester.io.parsers.nexus.NexusConstants

NexusFormatException - Exception in org.forester.io.parsers.nexus

NexusFormatException() - Constructor for exception org.forester.io.parsers.nexus.NexusFormatException

NexusFormatException(String) - Constructor for exception org.forester.io.parsers.nexus.NexusFormatException

NexusPhylogeniesParser - Class in org.forester.io.parsers.nexus

NexusPhylogeniesParser() - Constructor for class org.forester.io.parsers.nexus.NexusPhylogeniesParser

NH_PARSING_IGNORE_QUOTES_DEFAULT - Static variable in class org.forester.archaeopteryx.Constants

NHX_SEPARATOR - Static variable in class org.forester.phylogeny.data.DomainArchitecture

NHXFormatException - Exception in org.forester.io.parsers.nhx

NHXFormatException() - Constructor for exception org.forester.io.parsers.nhx.NHXFormatException

NHXFormatException(String) - Constructor for exception org.forester.io.parsers.nhx.NHXFormatException

NHXParser - Class in org.forester.io.parsers.nhx

NHXParser() - Constructor for class org.forester.io.parsers.nhx.NHXParser

NHXParser.TAXONOMY_EXTRACTION - Enum in org.forester.io.parsers.nhx

NHXtags - Class in org.forester.io.parsers.nhx

NHXtags() - Constructor for class org.forester.io.parsers.nhx.NHXtags

NIF_SUBCELLULAR_STR - Static variable in interface org.forester.go.GoXRef

nj - Class in org.forester.application

nj() - Constructor for class org.forester.application.nj

NL - Static variable in class org.forester.surfacing.SurfacingConstants

NODE_BOX - Static variable in class org.forester.archaeopteryx.TreeColorSet

NODE_COLLAPSE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

NODE_COLOR_REF - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_COLOR_TYPE - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_FILL_GRADIENT - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_FILL_NONE - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_FILL_SOLID - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_FILL_TYPE_REF - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_FILL_TYPE_TYPE - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_ID_ATTR - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

NODE_ITALICIZENAME_ATTR - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

NODE_NAME - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

NODE_SHAPE_CIRCLE - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_SHAPE_RECTANGLE - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_SHAPE_REF - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_SHAPE_TYPE - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_SIZE_REF - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_SIZE_TYPE - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_TRANSPARENCY_REF - Static variable in class org.forester.phylogeny.data.NodeVisualData

NODE_TRANSPARENCY_TYPE - Static variable in class org.forester.phylogeny.data.NodeVisualData

NodeData - Class in org.forester.phylogeny.data

NodeData() - Constructor for class org.forester.phylogeny.data.NodeData

NodeDataField - Enum in org.forester.phylogeny.data

NodeVisualData - Class in org.forester.phylogeny.data

NodeVisualData() - Constructor for class org.forester.phylogeny.data.NodeVisualData

NodeVisualData(String, NodeVisualData.FontType, byte, Color, NodeVisualData.NodeShape, NodeVisualData.NodeFill, Color, float, float) - Constructor for class org.forester.phylogeny.data.NodeVisualData

NodeVisualData.FontType - Enum in org.forester.phylogeny.data

NodeVisualData.NodeFill - Enum in org.forester.phylogeny.data

NodeVisualData.NodeShape - Enum in org.forester.phylogeny.data

NONE - Static variable in class org.forester.surfacing.SurfacingConstants

normalizeBootstrapValues(Phylogeny, double, double) - Static method in class org.forester.phylogeny.PhylogenyMethods

normalizeString(String, int, boolean, char) - Static method in class org.forester.util.ForesterUtil

NTAX - Static variable in class org.forester.io.parsers.nexus.NexusConstants

NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR - Static variable in class org.forester.util.TaxonomyColors

NULL_BD - Static variable in class org.forester.util.ForesterUtil

NUMBERS_ONLY_PATTERN - Static variable in class org.forester.io.parsers.nhx.NHXParser

numberSpeciesInDescOrder(Phylogeny) - Static method in class org.forester.development.DevelopmentTools

Sets the species namea of the external Nodes of Phylogeny t to descending integers, ending with 1.

numberSpeciesInOrder(Phylogeny) - Static method in class org.forester.development.DevelopmentTools

Sets the species namea of the external Nodes of Phylogeny t to ascending integers, starting with 1.

O

obo_tool - Class in org.forester.application

obo_tool() - Constructor for class org.forester.application.obo_tool

OBOparser - Class in org.forester.go

OBOparser(File, OBOparser.ReturnType) - Constructor for class org.forester.go.OBOparser

OBOparser.ReturnType - Enum in org.forester.go

obtainAccessorFromDataFields(PhylogenyNode) - Static method in class org.forester.util.SequenceAccessionTools

obtainAllDistinctTaxonomies(PhylogenyNode) - Static method in class org.forester.archaeopteryx.AptxUtil

obtainAllNodesAsList(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

obtainAndPreProcessIntrees(File[], int, String[][]) - Static method in class org.forester.surfacing.SurfacingUtil

obtainColorDependingOnTaxonomyGroup(String) - Static method in class org.forester.util.ForesterUtil

obtainDistinctTaxonomies(PhylogenyNode) - Static method in class org.forester.archaeopteryx.TreePanelUtil

Returns the set of distinct taxonomies of all external nodes of node.

obtainDistinctTaxonomyCounts(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods

Returns a map of distinct taxonomies of all external nodes of node.

obtainEmblEntry(Accession) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

obtainEmblEntry(Accession, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

obtainEntry(String) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

obtainFirstIntree(File) - Static method in class org.forester.surfacing.SurfacingUtil

obtainFromSeqAccession(PhylogenyNode) - Static method in class org.forester.util.SequenceAccessionTools

obtainGenbankAccessorFromDataFields(PhylogenyNode) - Static method in class org.forester.util.SequenceAccessionTools

obtainGiNumberFromDataFields(PhylogenyNode) - Static method in class org.forester.util.SequenceAccessionTools

obtainHexColorStringDependingOnTaxonomyGroup(String, Phylogeny) - Static method in class org.forester.surfacing.SurfacingUtil

obtainIdAsShort(String) - Static method in class org.forester.protein.BasicDomain

obtainIdFromShort(short) - Static method in class org.forester.protein.BasicDomain

obtainInstance(String) - Static method in class org.forester.surfacing.AdjactantDirectedBinaryDomainCombination

obtainInstance(String, String) - Static method in class org.forester.surfacing.AdjactantDirectedBinaryDomainCombination

obtainInstance(String) - Static method in class org.forester.surfacing.BasicBinaryDomainCombination

obtainInstance(String, String) - Static method in class org.forester.surfacing.BasicBinaryDomainCombination

obtainInstance(String) - Static method in class org.forester.surfacing.DirectedBinaryDomainCombination

obtainInstance(String, String) - Static method in class org.forester.surfacing.DirectedBinaryDomainCombination

obtainLineage(Taxonomy) - Static method in class org.forester.ws.wabi.WabiTools

obtainNormalizedTaxonomyGroup(String) - Static method in class org.forester.util.ForesterUtil

obtainQueryForBlast(PhylogenyNode) - Static method in class org.forester.archaeopteryx.tools.Blast

obtainRank(Taxonomy) - Static method in class org.forester.ws.wabi.WabiTools

obtainReader(Object) - Static method in class org.forester.util.ForesterUtil

obtainRefSeqAccessorFromDataFields(PhylogenyNode) - Static method in class org.forester.util.SequenceAccessionTools

obtainRefSeqEntryFromEmbl(Accession) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

obtainRefSeqEntryFromEmbl(Accession, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

obtainSeqAccession(PhylogenyNode) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

obtainSeqInformation(boolean, int, SortedSet<String>, PhylogenyNode) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

obtainSeqInformation(boolean, SortedSet<String>, PhylogenyNode) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

obtainSeqInformation(Phylogeny, boolean, boolean, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

obtainSeqInformation(PhylogenyNode) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

obtainTaxonomyGroup(String, Phylogeny) - Static method in class org.forester.surfacing.SurfacingUtil

obtainUniProtAccessorFromDataFields(PhylogenyNode) - Static method in class org.forester.util.SequenceAccessionTools

obtainUniProtEntry(String) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

obtainUniProtEntry(String, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

obtainUniProtTaxonomy(Taxonomy, Object, TaxonomyDataManager.QUERY_TYPE) - Static method in class org.forester.analysis.TaxonomyDataManager

obtainUniProtTaxonomy(String, TaxonomyDataManager.QUERY_TYPE) - Static method in class org.forester.analysis.TaxonomyDataManager

OCCURS_IN_STR - Static variable in interface org.forester.go.GoRelationship

OntologizerResult - Class in org.forester.go.etc

OntologizerResult.TYPE - Enum in org.forester.go.etc

openNcbiBlastWeb(String, boolean, JApplet, TreePanel) - Static method in class org.forester.archaeopteryx.tools.Blast

Options - Class in org.forester.archaeopteryx

Options.CLADOGRAM_TYPE - Enum in org.forester.archaeopteryx

Options.NODE_LABEL_DIRECTION - Enum in org.forester.archaeopteryx

Options.PHYLOGENY_GRAPHICS_TYPE - Enum in org.forester.archaeopteryx

orderAppearance(PhylogenyNode, boolean, boolean, PhylogenyMethods.DESCENDANT_SORT_PRIORITY) - Static method in class org.forester.phylogeny.PhylogenyMethods

Arranges the order of childern for each node of this Phylogeny in such a way that either the branch with more children is on top (right) or on bottom (left), dependent on the value of boolean order.

org.forester.analysis - package org.forester.analysis

org.forester.application - package org.forester.application

org.forester.applications - package org.forester.applications

org.forester.archaeopteryx - package org.forester.archaeopteryx

org.forester.archaeopteryx.phylogeny.data - package org.forester.archaeopteryx.phylogeny.data

org.forester.archaeopteryx.tools - package org.forester.archaeopteryx.tools

org.forester.archaeopteryx.webservices - package org.forester.archaeopteryx.webservices

org.forester.datastructures - package org.forester.datastructures

org.forester.development - package org.forester.development

org.forester.evoinference - package org.forester.evoinference

org.forester.evoinference.distance - package org.forester.evoinference.distance

org.forester.evoinference.matrix.character - package org.forester.evoinference.matrix.character

org.forester.evoinference.matrix.distance - package org.forester.evoinference.matrix.distance

org.forester.evoinference.parsimony - package org.forester.evoinference.parsimony

org.forester.evoinference.tools - package org.forester.evoinference.tools

org.forester.go - package org.forester.go

org.forester.go.etc - package org.forester.go.etc

org.forester.io.parsers - package org.forester.io.parsers

org.forester.io.parsers.nexus - package org.forester.io.parsers.nexus

org.forester.io.parsers.nhx - package org.forester.io.parsers.nhx

org.forester.io.parsers.phyloxml - package org.forester.io.parsers.phyloxml

org.forester.io.parsers.phyloxml.data - package org.forester.io.parsers.phyloxml.data

org.forester.io.parsers.tol - package org.forester.io.parsers.tol

org.forester.io.parsers.util - package org.forester.io.parsers.util

org.forester.io.writers - package org.forester.io.writers

org.forester.msa - package org.forester.msa

org.forester.msa_compactor - package org.forester.msa_compactor

org.forester.pccx - package org.forester.pccx

org.forester.phylogeny - package org.forester.phylogeny

org.forester.phylogeny.data - package org.forester.phylogeny.data

org.forester.phylogeny.factories - package org.forester.phylogeny.factories

org.forester.phylogeny.iterators - package org.forester.phylogeny.iterators

org.forester.protein - package org.forester.protein

org.forester.rio - package org.forester.rio

org.forester.sdi - package org.forester.sdi

org.forester.sequence - package org.forester.sequence

org.forester.species - package org.forester.species

org.forester.surfacing - package org.forester.surfacing

org.forester.test - package org.forester.test

org.forester.test.examples - package org.forester.test.examples

org.forester.tools - package org.forester.tools

org.forester.util - package org.forester.util

org.forester.ws.hmmer - package org.forester.ws.hmmer

org.forester.ws.seqdb - package org.forester.ws.seqdb

org.forester.ws.wabi - package org.forester.ws.wabi

Orphanet_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

OS_ARCH - Static variable in class org.forester.util.ForesterUtil

OS_NAME - Static variable in class org.forester.util.ForesterUtil

OS_VERSION - Static variable in class org.forester.util.ForesterUtil

OTHER - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

OTHER_FUNGI_COLOR - Static variable in class org.forester.util.TaxonomyColors

OTHERNAME - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

OTHERNAME_NAME - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

OTHERNAMES - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

outOfMemoryError(OutOfMemoryError) - Static method in class org.forester.util.ForesterUtil

OVERVIEW - Static variable in class org.forester.archaeopteryx.TreeColorSet

P

pad(double, int, char, boolean) - Static method in class org.forester.util.ForesterUtil

pad(String, int, char, boolean) - Static method in class org.forester.util.ForesterUtil

pad(StringBuffer, int, char, boolean) - Static method in class org.forester.util.ForesterUtil

paint(Graphics) - Method in class org.forester.archaeopteryx.ArchaeopteryxA

Prints message when initialization is finished.

paint(Graphics) - Method in class org.forester.development.AbstractRenderer

paint(Graphics) - Method in class org.forester.development.MsaRenderer

paint(Graphics) - Method in class org.forester.development.ResidueRenderer

paintComponent(Graphics) - Method in class org.forester.archaeopteryx.TreePanel

PAIRWISE_DOMAIN_COMPARISONS_PREFIX - Static variable in class org.forester.application.surfacing

PairwiseDistanceCalculator - Class in org.forester.evoinference.distance

PairwiseDistanceCalculator.PWD_DISTANCE_METHOD - Enum in org.forester.evoinference.distance

PairwiseDomainSimilarity - Interface in org.forester.surfacing

PairwiseDomainSimilarityCalculator - Interface in org.forester.surfacing

PairwiseGenomeComparator - Class in org.forester.surfacing

PairwiseGenomeComparator() - Constructor for class org.forester.surfacing.PairwiseGenomeComparator

parse(File) - Static method in class org.forester.go.etc.OntologizerResult

parse() - Method in class org.forester.go.OBOparser

parse() - Method in class org.forester.go.PfamToGoParser

parse(File) - Static method in class org.forester.io.parsers.FastaParser

parse(InputStream) - Static method in class org.forester.io.parsers.FastaParser

parse(InputStream) - Static method in class org.forester.io.parsers.GeneralMsaParser

parse() - Method in class org.forester.io.parsers.HmmPfamOutputParser

parse() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

parse() - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser

parse() - Method in class org.forester.io.parsers.nexus.NexusCharactersParser

parse() - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser

parse() - Method in class org.forester.io.parsers.nexus.PaupLogParser

parse() - Method in class org.forester.io.parsers.nhx.NHXParser

parse(Object) - Static method in class org.forester.io.parsers.nhx.NHXParser

parse() - Method in interface org.forester.io.parsers.PhylogenyParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.AccessionParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.AnnotationParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.BinaryCharactersParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.BranchWidthParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.ColorParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.ConfidenceParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.DateParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.DistributionParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.DomainArchitectureParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.EventParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.IdentifierParser

parse(XmlElement) - Method in interface org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.PointParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.PolygonParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.PropertyParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.ProteinDomainParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.ReferenceParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.SequenceParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.SequenceRelationParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.TaxonomyParser

parse(XmlElement) - Method in class org.forester.io.parsers.phyloxml.data.UriParser

parse() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

parse(Object) - Method in class org.forester.io.parsers.SymmetricalDistanceMatrixParser

parse() - Method in class org.forester.io.parsers.tol.TolParser

parse(Object, char) - Static method in class org.forester.util.BasicTableParser

parse(Object, char, boolean, boolean) - Static method in class org.forester.util.BasicTableParser

parse(Object, char, boolean, boolean, String, boolean) - Static method in class org.forester.util.BasicTableParser

parseAccessorFromString(String) - Static method in class org.forester.util.SequenceAccessionTools

parseDouble(String) - Static method in class org.forester.util.ForesterUtil

parseEnsemlAccessorFromString(String) - Static method in class org.forester.util.SequenceAccessionTools

parseGenbankAccessorFromString(String) - Static method in class org.forester.util.SequenceAccessionTools

parseGenbankProteinAccessorFromString(String) - Static method in class org.forester.util.SequenceAccessionTools

parseGInumberFromString(String) - Static method in class org.forester.util.SequenceAccessionTools

parseGoIds(Object, String, String) - Static method in class org.forester.go.GoUtils

parseInt(String) - Static method in class org.forester.util.ForesterUtil

parseMappingTable(File) - Static method in class org.forester.tools.PhylogenyDecorator

parseMsa(File) - Static method in class org.forester.io.parsers.FastaParser

parseMsa(InputStream) - Static method in class org.forester.io.parsers.FastaParser

parseMsa(String) - Static method in class org.forester.io.parsers.FastaParser

parseMsa(byte[]) - Static method in class org.forester.io.parsers.FastaParser

parseNHX(String, PhylogenyNode, NHXParser.TAXONOMY_EXTRACTION, boolean, boolean, boolean) - Static method in class org.forester.io.parsers.nhx.NHXParser

parseProperty(Property) - Method in class org.forester.phylogeny.data.NodeVisualData

ParserBasedPhylogenyFactory - Class in org.forester.phylogeny.factories

parseRefSeqAccessorFromString(String) - Static method in class org.forester.util.SequenceAccessionTools

ParserUtils - Class in org.forester.io.parsers.util

ParserUtils() - Constructor for class org.forester.io.parsers.util.ParserUtils

parseSpeciesTree(Phylogeny, File, boolean, boolean, NHXParser.TAXONOMY_EXTRACTION) - Static method in class org.forester.sdi.SDIutil

parseUniProtAccessorFromString(String) - Static method in class org.forester.util.SequenceAccessionTools

PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_DOLLO_GAINS_D - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_DOLLO_LOSSES_D - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_DOLLO_PRESENT_D - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_FITCH_GAINS_BC - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_FITCH_LOSSES_BC - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_FITCH_PRESENT_BC - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS - Static variable in class org.forester.application.surfacing

PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS - Static variable in class org.forester.application.surfacing

PART_OF_STR - Static variable in interface org.forester.go.GoRelationship

PATTERN_SP_STYLE_TAXONOMY - Static variable in class org.forester.surfacing.SurfacingUtil

PaupLogParser - Class in org.forester.io.parsers.nexus

PaupLogParser() - Constructor for class org.forester.io.parsers.nexus.PaupLogParser

pccx - Class in org.forester.application

pccx() - Constructor for class org.forester.application.pccx

PDB - Static variable in class org.forester.util.ForesterUtil

PDB_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

pearsonianSkewness() - Method in class org.forester.util.BasicDescriptiveStatistics

pearsonianSkewness() - Method in interface org.forester.util.DescriptiveStatistics

Determines relationship between the mean and the median.

performBinning(double[], double, double, int) - Static method in class org.forester.util.BasicDescriptiveStatistics

performDomainArchitectureAnalysis(SortedMap<String, Set<String>>, SortedMap<String, Integer>, int, File, File) - Static method in class org.forester.surfacing.SurfacingUtil

performPairwiseComparisons(StringBuilder, boolean, DomainSimilarityCalculator.Detailedness, boolean, boolean, DomainSimilarity.DomainSimilaritySortField, DomainSimilarity.PRINT_OPTION, DomainSimilarity.DomainSimilarityScoring, Map<String, List<GoId>>, Map<GoId, GoTerm>, GoNameSpace, Species[], int, List<GenomeWideCombinableDomains>, PairwiseDomainSimilarityCalculator, String, boolean, String, String, File, boolean, Map<String, Integer>, boolean, Phylogeny) - Method in class org.forester.surfacing.PairwiseGenomeComparator

performPairwiseComparisonsJacknifed(Species[], int, List<GenomeWideCombinableDomains>, boolean, int, double, long) - Method in class org.forester.surfacing.PairwiseGenomeComparator

pfam2go_extractor - Class in org.forester.application

pfam2go_extractor() - Constructor for class org.forester.application.pfam2go_extractor

PFAM_FAMILY_ID_LINK - Static variable in class org.forester.surfacing.SurfacingConstants

pfam_go - Class in org.forester.application

pfam_go() - Constructor for class org.forester.application.pfam_go

PFAM_INST - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

PFAM_NAME - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

PFAM_SERVER - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

pfamacc2go - Class in org.forester.application

pfamacc2go() - Constructor for class org.forester.application.pfamacc2go

pfamacc2pfamid - Class in org.forester.application

pfamacc2pfamid() - Constructor for class org.forester.application.pfamacc2pfamid

PfamToGoMapping - Class in org.forester.go

PfamToGoMapping(String, GoId) - Constructor for class org.forester.go.PfamToGoMapping

PfamToGoParser - Class in org.forester.go

PfamToGoParser(File) - Constructor for class org.forester.go.PfamToGoParser

PharmGKB_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

phylo2coloredgraphics - Class in org.forester.applications

phylo2coloredgraphics() - Constructor for class org.forester.applications.phylo2coloredgraphics

phylo2graphics - Class in org.forester.applications

phylo2graphics() - Constructor for class org.forester.applications.phylo2graphics

PHYLO_XML_END - Static variable in class org.forester.io.writers.PhylogenyWriter

PHYLO_XML_INTENDATION_BASE - Static variable in class org.forester.io.writers.PhylogenyWriter

PHYLO_XML_LOCATION - Static variable in class org.forester.util.ForesterConstants

PHYLO_XML_NAMESPACE_LINE - Static variable in class org.forester.io.writers.PhylogenyWriter

PHYLO_XML_REFERENCE - Static variable in class org.forester.util.ForesterConstants

PHYLO_XML_SUFFIX - Static variable in class org.forester.util.ForesterConstants

PHYLO_XML_VERSION - Static variable in class org.forester.util.ForesterConstants

PHYLO_XML_VERSION_ENCODING_LINE - Static variable in class org.forester.io.writers.PhylogenyWriter

PHYLO_XML_XSD - Static variable in class org.forester.util.ForesterConstants

PhylogeneticInferenceOptions - Class in org.forester.archaeopteryx.tools

PhylogeneticInferenceOptions() - Constructor for class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

PhylogeneticInferrer - Class in org.forester.archaeopteryx.tools

PhylogeneticInferrer(List<MolecularSequence>, PhylogeneticInferenceOptions, MainFrameApplication) - Constructor for class org.forester.archaeopteryx.tools.PhylogeneticInferrer

PhylogeneticInferrer(Msa, PhylogeneticInferenceOptions, MainFrameApplication) - Constructor for class org.forester.archaeopteryx.tools.PhylogeneticInferrer

PhylogeneticInferrer.MSA_PRG - Enum in org.forester.archaeopteryx.tools

PhylogeniesWebserviceClient - Interface in org.forester.archaeopteryx.webservices

PHYLOGENY - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

PHYLOGENY - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

Phylogeny - Class in org.forester.phylogeny

Phylogeny() - Constructor for class org.forester.phylogeny.Phylogeny

Default Phylogeny constructor.

PHYLOGENY_BRANCHLENGTH_UNIT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

PHYLOGENY_DESCRIPTION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

PHYLOGENY_IS_REROOTABLE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

PHYLOGENY_IS_ROOTED_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

PHYLOGENY_NAME - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

PHYLOGENY_TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

PhylogenyBranch - Class in org.forester.phylogeny

PhylogenyBranch(PhylogenyNode, PhylogenyNode) - Constructor for class org.forester.phylogeny.PhylogenyBranch

PhylogenyBranch(PhylogenyNode, PhylogenyNode, boolean) - Constructor for class org.forester.phylogeny.PhylogenyBranch

PhylogenyData - Interface in org.forester.phylogeny.data

PhylogenyDataPhyloXmlParser - Interface in org.forester.io.parsers.phyloxml.data

PhylogenyDataUtil - Class in org.forester.phylogeny.data

PhylogenyDataUtil() - Constructor for class org.forester.phylogeny.data.PhylogenyDataUtil

PhylogenyDecorator - Class in org.forester.tools

PhylogenyDecorator.FIELD - Enum in org.forester.tools

PhylogenyFactory - Interface in org.forester.phylogeny.factories

PhylogenyMethods - Class in org.forester.phylogeny

PhylogenyMethods.DESCENDANT_SORT_PRIORITY - Enum in org.forester.phylogeny

PhylogenyMethods.PhylogenyNodeField - Enum in org.forester.phylogeny

PhylogenyNode - Class in org.forester.phylogeny

Warning.

PhylogenyNode() - Constructor for class org.forester.phylogeny.PhylogenyNode

Default constructor for PhylogenyNode.

PhylogenyNode(String) - Constructor for class org.forester.phylogeny.PhylogenyNode

PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE - Enum in org.forester.phylogeny

PhylogenyNodeIterator - Interface in org.forester.phylogeny.iterators

PhylogenyParser - Interface in org.forester.io.parsers

PhylogenyParserException - Exception in org.forester.io.parsers.util

PhylogenyParserException() - Constructor for exception org.forester.io.parsers.util.PhylogenyParserException

PhylogenyParserException(String) - Constructor for exception org.forester.io.parsers.util.PhylogenyParserException

PhylogenyWriter - Class in org.forester.io.writers

PhylogenyWriter() - Constructor for class org.forester.io.writers.PhylogenyWriter

PhylogenyWriter.FORMAT - Enum in org.forester.io.writers

PhyloInferenceDialog - Class in org.forester.archaeopteryx.tools

PhyloInferenceDialog(MainFrameApplication, PhylogeneticInferenceOptions, boolean) - Constructor for class org.forester.archaeopteryx.tools.PhyloInferenceDialog

phylostrip - Class in org.forester.application

phylostrip() - Constructor for class org.forester.application.phylostrip

phyloxml_converter - Class in org.forester.application

phyloxml_converter() - Constructor for class org.forester.application.phyloxml_converter

PhyloXmlDataFormatException - Exception in org.forester.io.parsers.phyloxml

PhyloXmlDataFormatException() - Constructor for exception org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException

PhyloXmlDataFormatException(String) - Constructor for exception org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException

PhyloXmlException - Exception in org.forester.io.parsers.phyloxml

PhyloXmlException() - Constructor for exception org.forester.io.parsers.phyloxml.PhyloXmlException

PhyloXmlException(String) - Constructor for exception org.forester.io.parsers.phyloxml.PhyloXmlException

PhyloXmlHandler - Class in org.forester.io.parsers.phyloxml

PhyloXmlMapping - Class in org.forester.io.parsers.phyloxml

PhyloXmlNodeWriter - Class in org.forester.io.writers

PhyloXmlNodeWriter() - Constructor for class org.forester.io.writers.PhyloXmlNodeWriter

PhyloXmlParser - Class in org.forester.io.parsers.phyloxml

PhyloXmlUtil - Class in org.forester.io.parsers.phyloxml

PhyloXmlUtil() - Constructor for class org.forester.io.parsers.phyloxml.PhyloXmlUtil

pivot() - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

pivot() - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

PLACOZOA_COLOR - Static variable in class org.forester.util.TaxonomyColors

PLUS_MINUS - Static variable in interface org.forester.util.DescriptiveStatistics

PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX - Static variable in class org.forester.application.surfacing

PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT - Static variable in class org.forester.application.surfacing

PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT - Static variable in class org.forester.application.surfacing

PLUS_MINUS_ANALYSIS_OPTION - Static variable in class org.forester.application.surfacing

PLUS_MINUS_DC_SUFFIX_HTML - Static variable in class org.forester.application.surfacing

PLUS_MINUS_DOM_SUFFIX - Static variable in class org.forester.application.surfacing

PLUS_MINUS_DOM_SUFFIX_HTML - Static variable in class org.forester.application.surfacing

PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX - Static variable in class org.forester.application.surfacing

PMID_STR - Static variable in interface org.forester.go.GoXRef

PO_STR - Static variable in interface org.forester.go.GoXRef

POINT - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Point - Class in org.forester.phylogeny.data

Point() - Constructor for class org.forester.phylogeny.data.Point

Point(String, BigDecimal, BigDecimal) - Constructor for class org.forester.phylogeny.data.Point

Point(String, BigDecimal, BigDecimal, BigDecimal, String) - Constructor for class org.forester.phylogeny.data.Point

POINT_ALTITUDE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

POINT_ALTITUDE_UNIT_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

POINT_GEODETIC_DATUM - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

POINT_LATITUDE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

POINT_LONGITUDE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

PointParser - Class in org.forester.io.parsers.phyloxml.data

POLYGON - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Polygon - Class in org.forester.phylogeny.data

Polygon(List<Point>) - Constructor for class org.forester.phylogeny.data.Polygon

PolygonParser - Class in org.forester.io.parsers.phyloxml.data

PORIFERA_COLOR - Static variable in class org.forester.util.TaxonomyColors

POSITIVELY_REGULATES_STR - Static variable in interface org.forester.go.GoRelationship

postorderBranchColorAveragingExternalNodeBased(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

PostOrderStackObject - Class in org.forester.phylogeny.iterators

PostOrderStackObject(PhylogenyNode, int) - Constructor for class org.forester.phylogeny.iterators.PostOrderStackObject

PostorderTreeIterator - Class in org.forester.phylogeny.iterators

PostorderTreeIterator(Phylogeny) - Constructor for class org.forester.phylogeny.iterators.PostorderTreeIterator

preorderPrint() - Method in class org.forester.phylogeny.PhylogenyNode

Prints to the console the subtree originating from this PhylogenyNode in preorder.

preOrderReId(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

PreorderTreeIterator - Class in org.forester.phylogeny.iterators

PreorderTreeIterator(Phylogeny) - Constructor for class org.forester.phylogeny.iterators.PreorderTreeIterator

PreorderTreeIterator(PhylogenyNode) - Constructor for class org.forester.phylogeny.iterators.PreorderTreeIterator

preparePhylogeny(Phylogeny, DomainParsimonyCalculator, String, String, String, String) - Static method in class org.forester.surfacing.SurfacingUtil

preparePhylogenyForParsimonyAnalyses(Phylogeny, String[][]) - Static method in class org.forester.surfacing.SurfacingUtil

PRG_NAME - Static variable in class org.forester.application.surfacing

PRG_NAME - Static variable in class org.forester.archaeopteryx.Constants

print(Graphics, PageFormat, int) - Method in class org.forester.archaeopteryx.TreePanel

print(String) - Method in class org.forester.util.EasyWriter

printArray(Object[]) - Static method in class org.forester.util.ForesterUtil

printCountingMap(Map<String, Integer>) - Static method in class org.forester.util.ForesterUtil

printErrorMessage(String, String) - Static method in class org.forester.util.ForesterUtil

printExtNodes() - Method in class org.forester.phylogeny.Phylogeny

Prints descriptions of all external Nodes of this Phylogeny to System.out.

println(String) - Method in class org.forester.util.EasyWriter

println() - Method in class org.forester.util.EasyWriter

printOutPercentageOfMultidomainProteins(SortedMap<Integer, Integer>, Writer) - Static method in class org.forester.surfacing.SurfacingUtil

printProgramInformation(String, String, String) - Static method in class org.forester.util.ForesterUtil

printProgramInformation(String, String, String, String, String) - Static method in class org.forester.util.ForesterUtil

printProgramInformation(String, String, String, String, String, String, String) - Static method in class org.forester.util.ForesterUtil

printWarningMessage(String, String) - Static method in class org.forester.archaeopteryx.AptxUtil

printWarningMessage(String, String) - Static method in class org.forester.util.ForesterUtil

processFilter(File, SortedSet<String>) - Static method in class org.forester.surfacing.SurfacingUtil

processInputGenomesFile(File) - Static method in class org.forester.surfacing.SurfacingUtil

processInstructions(PhylogeniesWebserviceClient, Phylogeny) - Static method in class org.forester.archaeopteryx.webservices.WebserviceUtil

processPlusMinusAnalysisOption(CommandLineArguments, List<String>, List<String>, List<String>, List<Object>) - Static method in class org.forester.surfacing.SurfacingUtil

processPlusMinusFile(File, List<String>, List<String>, List<String>, List<Object>) - Static method in class org.forester.surfacing.SurfacingUtil

ProcessPool - Class in org.forester.archaeopteryx.tools

ProcessRunning - Class in org.forester.archaeopteryx.tools

programMessage(String, String) - Static method in class org.forester.util.ForesterUtil

PropertiesMap - Class in org.forester.phylogeny.data

PropertiesMap() - Constructor for class org.forester.phylogeny.data.PropertiesMap

PROPERTY - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Property - Class in org.forester.phylogeny.data

Property(String, String, String, String, Property.AppliesTo) - Constructor for class org.forester.phylogeny.data.Property

Property(String, String, String, String, Property.AppliesTo, String) - Constructor for class org.forester.phylogeny.data.Property

Property.AppliesTo - Enum in org.forester.phylogeny.data

PROPERTY_APPLIES_TO - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

PROPERTY_DATATYPE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

PROPERTY_REF - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

PROPERTY_UNIT - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

PropertyParser - Class in org.forester.io.parsers.phyloxml.data

Protein - Interface in org.forester.protein

ProteinCountsBasedPairwiseDomainSimilarityCalculator - Class in org.forester.surfacing

ProteinCountsBasedPairwiseDomainSimilarityCalculator() - Constructor for class org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator

ProteinDomain - Class in org.forester.phylogeny.data

ProteinDomain(String, int, int) - Constructor for class org.forester.phylogeny.data.ProteinDomain

ProteinDomain(String, int, int, double) - Constructor for class org.forester.phylogeny.data.ProteinDomain

ProteinDomain(String, int, int, String) - Constructor for class org.forester.phylogeny.data.ProteinDomain

ProteinDomain(String, int, int, String, double) - Constructor for class org.forester.phylogeny.data.ProteinDomain

ProteinDomainParser - Class in org.forester.io.parsers.phyloxml.data

ProteinId - Class in org.forester.protein

ProteinId(String) - Constructor for class org.forester.protein.ProteinId

proteinToDomainCombinations(Protein, String, String) - Static method in class org.forester.surfacing.SurfacingUtil

PROTOSTOMIA_COLOR - Static variable in class org.forester.util.TaxonomyColors

putDisplayColors(String, Color) - Method in class org.forester.archaeopteryx.Configuration

PWD_FILE_SUFFIX - Static variable in class org.forester.archaeopteryx.tools.PhylogeneticInferrer

Q

QUERY_PLACEHOLDER - Static variable in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient

queryDb(String, int, String) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

queryEmblDb(Accession, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

queryEmblDbForRefSeqEntry(Accession, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

queryUniprot(String, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools

Queue - Class in org.forester.datastructures

Queue() - Constructor for class org.forester.datastructures.Queue

This created a new, empty Queue object.

R

RANDOM_NUMBER_SEED_DEFAULT - Static variable in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

randomize(long) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

randomizeSpecies(int, int, Phylogeny) - Static method in class org.forester.development.DevelopmentTools

Sets the species names of the external Nodes of Phylogeny t to a random positive integer number between (and including) min and max.

RandomThing - Class in org.forester.development

RandomThing() - Constructor for class org.forester.development.RandomThing

RANGE_PATTERN - Static variable in class org.forester.applications.aaa

Reactome_PATTERN - Static variable in class org.forester.ws.seqdb.UniProtEntry

REACTOME_STR - Static variable in interface org.forester.go.GoXRef

readMsaFromFile() - Method in class org.forester.archaeopteryx.MainFrameApplication

readPhylogenies(File) - Static method in class org.forester.io.parsers.util.ParserUtils

readPhylogenies(String) - Static method in class org.forester.io.parsers.util.ParserUtils

readPhylogenies(PhylogenyParser, File) - Static method in class org.forester.phylogeny.PhylogenyMethods

readPhylogenies(PhylogenyParser, List<File>) - Static method in class org.forester.phylogeny.PhylogenyMethods

readPhylogeniesFromUrl(URL, boolean, boolean, boolean, NHXParser.TAXONOMY_EXTRACTION, boolean) - Static method in class org.forester.archaeopteryx.AptxUtil

readSeqsFromFileforPI() - Method in class org.forester.archaeopteryx.MainFrameApplication

readUrl(String) - Static method in class org.forester.util.ForesterUtil

recalculateNumberOfExternalDescendants(boolean) - Method in class org.forester.phylogeny.Phylogeny

(Re)counts the number of children for each PhylogenyNode of this Phylogeny.

REFERENCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Reference - Class in org.forester.phylogeny.data

Reference(String) - Constructor for class org.forester.phylogeny.data.Reference

Reference(String, String) - Constructor for class org.forester.phylogeny.data.Reference

REFERENCE_DESC - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

REFERENCE_DOI_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

ReferenceParser - Class in org.forester.io.parsers.phyloxml.data

refExists(String) - Method in class org.forester.phylogeny.data.PropertiesMap

reformat(File, String, File, String, File, double, String, List<PfamToGoMapping>) - Static method in class org.forester.go.etc.MetaOntologizer

REGULATES_STR - Static variable in interface org.forester.go.GoRelationship

reinv_count - Class in org.forester.applications

reinv_count() - Constructor for class org.forester.applications.reinv_count

RELEASE - Static variable in class org.forester.util.ForesterConstants

remove() - Method in class org.forester.phylogeny.iterators.ExternalForwardIterator

Not supported.

remove() - Method in class org.forester.phylogeny.iterators.LevelOrderTreeIterator

Not supported.

remove() - Method in class org.forester.phylogeny.iterators.PostorderTreeIterator

remove() - Method in class org.forester.phylogeny.iterators.PreorderTreeIterator

Not supported.

removeChildNode(int) - Method in class org.forester.phylogeny.PhylogenyNode

removeChildNode(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode

removeConnections() - Method in class org.forester.phylogeny.PhylogenyNode

removeNode(PhylogenyNode, Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

removeOverlappingDomains(int, boolean, Protein) - Static method in class org.forester.util.ForesterUtil

Example regarding engulfment: ------------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_ ignored

removePairing(double, int, int) - Method in class org.forester.evoinference.distance.Sarray

removePairing(int, int, int) - Method in class org.forester.evoinference.distance.Sarray

removePairing(double, int, int) - Method in class org.forester.evoinference.distance.Sset

removePairing(int, int, int) - Method in class org.forester.evoinference.distance.Sset

removeProcess(long) - Method in class org.forester.archaeopteryx.tools.ProcessPool

removePropertiesWithGivenReferencePrefix(String) - Method in class org.forester.phylogeny.data.PropertiesMap

removeProperty(String) - Method in class org.forester.phylogeny.data.PropertiesMap

removeSequence(Msa, String) - Static method in class org.forester.msa.MsaMethods

removeSequences(Msa, List<String>) - Static method in class org.forester.msa.MsaMethods

removeSequencesByMinimalLength(Msa, int) - Static method in class org.forester.msa.MsaMethods

removeSequencesByMinimalLength(int) - Method in class org.forester.msa_compactor.MsaCompactor

removeSequencesByRow(Msa, List<Integer>) - Static method in class org.forester.msa.MsaMethods

removeSuffix(String) - Static method in class org.forester.util.ForesterUtil

removeViaGapAverage(double) - Method in class org.forester.msa_compactor.MsaCompactor

removeViaLength(int) - Method in class org.forester.msa_compactor.MsaCompactor

removeWhiteSpace(String) - Static method in class org.forester.util.ForesterUtil

Removes all white space from String s.

removeWorstOffenders(int) - Method in class org.forester.msa_compactor.MsaCompactor

render(float, float, Graphics2D, TreePanel, boolean) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

render(float, float, Graphics2D, TreePanel, boolean) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

render(float, float, Graphics2D, TreePanel, boolean) - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData

This can be used to render phylogeny data as graphics (for example, display of the domain structure).

render(float, float, Graphics2D, TreePanel, boolean) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

RenderableDomainArchitecture - Class in org.forester.archaeopteryx.phylogeny.data

RenderableDomainArchitecture(DomainArchitecture) - Constructor for class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

RenderableDomainArchitecture(DomainArchitecture, String) - Constructor for class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

RenderableMsaSequence - Class in org.forester.archaeopteryx.phylogeny.data

RenderablePhylogenyData - Interface in org.forester.archaeopteryx.phylogeny.data

RenderableVector - Class in org.forester.archaeopteryx.phylogeny.data

REPLACE_UNDERSCORES_DEFAULT - Static variable in class org.forester.io.parsers.nhx.NHXParser

REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE - Static variable in class org.forester.application.gsdi

replaceIllegalNhxCharacters(String) - Static method in class org.forester.util.ForesterUtil

replaceIllegalXmlCharacters(String) - Static method in class org.forester.phylogeny.data.PhylogenyDataUtil

reRoot(long) - Method in class org.forester.phylogeny.Phylogeny

Places the root of this Phylogeny on the parent branch of the PhylogenyNode with a corresponding ID.

reRoot(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny

Places the root of this Phylogeny on the parent branch PhylogenyNode n.

reRoot(PhylogenyNode, double) - Method in class org.forester.phylogeny.Phylogeny

resample(Msa, int, long) - Static method in class org.forester.evoinference.tools.BootstrapResampler

resample(int[]) - Method in class org.forester.msa.ResampleableMsa

ResampleableMsa - Class in org.forester.msa

ResampleableMsa(BasicMsa) - Constructor for class org.forester.msa.ResampleableMsa

reset() - Method in interface org.forester.io.parsers.IteratingPhylogenyParser

reset() - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser

reset() - Method in class org.forester.io.parsers.nhx.NHXParser

reset() - Method in class org.forester.phylogeny.iterators.ExternalForwardIterator

DOCUMENT ME!

reset() - Method in class org.forester.phylogeny.iterators.LevelOrderTreeIterator

Resets the iterator.

reset() - Method in interface org.forester.phylogeny.iterators.PhylogenyNodeIterator

reset() - Method in class org.forester.phylogeny.iterators.PostorderTreeIterator

reset() - Method in class org.forester.phylogeny.iterators.PreorderTreeIterator

resetWellColor(double, double, Color, Color) - Method in class org.forester.development.ResidueRenderer

resetWellColor(double, double, double, Color, Color, Color) - Method in class org.forester.development.ResidueRenderer

resetWellColors() - Method in class org.forester.development.MsaRenderer

resetWellSize(int) - Method in class org.forester.development.MsaRenderer

RESID_STR - Static variable in interface org.forester.go.GoXRef

ResidueRenderer - Class in org.forester.development

ResidueRenderer(char, MsaRenderer) - Constructor for class org.forester.development.ResidueRenderer

RestUtil - Class in org.forester.ws.wabi

This is to access the Web API for Biology (WABI) at DDBJ.

RestUtil() - Constructor for class org.forester.ws.wabi.RestUtil

RHEA_STR - Static variable in interface org.forester.go.GoXRef

RHIZARIA_COLOR - Static variable in class org.forester.util.TaxonomyColors

RHODOPHYTA_COLOR - Static variable in class org.forester.util.TaxonomyColors

rio - Class in org.forester.application

rio() - Constructor for class org.forester.application.rio

RIO - Class in org.forester.rio

RIO.REROOTING - Enum in org.forester.rio

RIOException - Exception in org.forester.rio

RIOException() - Constructor for exception org.forester.rio.RIOException

RIOException(String) - Constructor for exception org.forester.rio.RIOException

RNA_REGEXP - Static variable in interface org.forester.sequence.MolecularSequence

round(double, int) - Static method in class org.forester.util.ForesterUtil

ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

roundToInt(double) - Static method in class org.forester.util.ForesterUtil

Rounds d to an int.

roundToInt(float) - Static method in class org.forester.util.ForesterUtil

roundToShort(double) - Static method in class org.forester.util.ForesterUtil

run() - Method in class org.forester.analysis.TaxonomyDataManager

run() - Method in class org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer

run() - Method in class org.forester.archaeopteryx.tools.ImageLoader

run() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferrer

run() - Method in class org.forester.archaeopteryx.tools.SequenceDataRetriver

run() - Method in class org.forester.archaeopteryx.UrlTreeReader

RunnableProcess - Class in org.forester.archaeopteryx.tools

RunnableProcess() - Constructor for class org.forester.archaeopteryx.tools.RunnableProcess

S

SABIO_RK_STR - Static variable in interface org.forester.go.GoXRef

sampleStandardDeviation() - Method in class org.forester.util.BasicDescriptiveStatistics

sampleStandardDeviation() - Method in interface org.forester.util.DescriptiveStatistics

sampleStandardUnit(double) - Method in class org.forester.util.BasicDescriptiveStatistics

sampleStandardUnit(double, double, double) - Static method in class org.forester.util.BasicDescriptiveStatistics

Computes the sample standard unit (z-score).

sampleStandardUnit(double) - Method in interface org.forester.util.DescriptiveStatistics

sampleVariance() - Method in class org.forester.util.BasicDescriptiveStatistics

sampleVariance() - Method in interface org.forester.util.DescriptiveStatistics

sanitizeString(String) - Static method in class org.forester.util.ForesterUtil

SankoffParsimony<STATE_TYPE> - Class in org.forester.evoinference.parsimony

IN PROGRESS! DO NOT USE!

SankoffParsimony() - Constructor for class org.forester.evoinference.parsimony.SankoffParsimony

santitizeStringForNH(String) - Static method in class org.forester.util.ForesterUtil

Sarray - Class in org.forester.evoinference.distance

Sarray() - Constructor for class org.forester.evoinference.distance.Sarray

SAX_FEATURES_VALIDATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser

SAX_FEATURES_VALIDATION - Static variable in class org.forester.io.parsers.tol.TolParser

ScoringMethodForExternalNode - Interface in org.forester.pccx

SDI - Class in org.forester.sdi

SDI(Phylogeny, Phylogeny) - Constructor for class org.forester.sdi.SDI

Constructor which sets the gene tree and the species tree to be compared.

SDIException - Exception in org.forester.sdi

SDIException() - Constructor for exception org.forester.sdi.SDIException

SDIException(String) - Constructor for exception org.forester.sdi.SDIException

SDIR - Class in org.forester.sdi

SDIR() - Constructor for class org.forester.sdi.SDIR

Default contructor which creates an "empty" object..

SDIutil - Class in org.forester.sdi

SDIutil() - Constructor for class org.forester.sdi.SDIutil

SDIutil.ALGORITHM - Enum in org.forester.sdi

SDIutil.TaxonomyComparisonBase - Enum in org.forester.sdi

searchData(String, Phylogeny, boolean, boolean, boolean, boolean, double) - Static method in class org.forester.phylogeny.PhylogenyMethods

searchDataLogicalAnd(String[], Phylogeny, boolean, boolean, boolean, double) - Static method in class org.forester.phylogeny.PhylogenyMethods

searchLineage(List<String>, List<TxSearch.RANKS>) - Static method in class org.forester.ws.wabi.TxSearch

searchLineage(List<String>, List<TxSearch.RANKS>, String) - Static method in class org.forester.ws.wabi.TxSearch

searchParam(String, TxSearch.TAX_NAME_CLASS, TxSearch.TAX_RANK, int, boolean) - Static method in class org.forester.ws.wabi.TxSearch

searchSimple(String) - Static method in class org.forester.ws.wabi.TxSearch

SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO - Static variable in class org.forester.application.surfacing

SEPARATOR - Static variable in interface org.forester.protein.BinaryDomainCombination

SEQ_EXTRACT_SUFFIX - Static variable in class org.forester.application.surfacing

SEQ_TYPE_DNA - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

SEQ_TYPE_PROTEIN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

SEQ_TYPE_RNA - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

seqIsLikelyToBeAa(String) - Static method in class org.forester.util.ForesterUtil

SEQUENCE - Static variable in class org.forester.archaeopteryx.TreeColorSet

SEQUENCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Sequence - Class in org.forester.phylogeny.data

Sequence() - Constructor for class org.forester.phylogeny.data.Sequence

Sequence(MolecularSequence) - Constructor for class org.forester.phylogeny.data.Sequence

SEQUENCE_ACCESSION - Static variable in class org.forester.io.parsers.nhx.NHXtags

SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_DOMAIN_ARCHITECURE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_GENE_NAME - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_LOCATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_MOL_SEQ - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_MOL_SEQ_ALIGNED_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_NAME - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_RELATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_RELATION_DISTANCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_RELATION_ID_REF0 - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_RELATION_ID_REF1 - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_RELATION_TYPE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY - Static variable in class org.forester.phylogeny.data.SequenceRelation

SEQUENCE_RELATION_TYPE_ORTHOLOGY - Static variable in class org.forester.phylogeny.data.SequenceRelation

SEQUENCE_RELATION_TYPE_OTHER - Static variable in class org.forester.phylogeny.data.SequenceRelation

SEQUENCE_RELATION_TYPE_PARALOGY - Static variable in class org.forester.phylogeny.data.SequenceRelation

SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY - Static variable in class org.forester.phylogeny.data.SequenceRelation

SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY - Static variable in class org.forester.phylogeny.data.SequenceRelation

SEQUENCE_RELATION_TYPE_UNKNOWN - Static variable in class org.forester.phylogeny.data.SequenceRelation

SEQUENCE_RELATION_TYPE_XENOLOGY - Static variable in class org.forester.phylogeny.data.SequenceRelation

SEQUENCE_SOURCE_ID - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_SYMBOL - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_SYMBOL_PATTERN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

SEQUENCE_TYPE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SEQUENCE_TYPES - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

SEQUENCE_X_REFS - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

SequenceAccessionTools - Class in org.forester.util

SequenceDatabaseEntry - Interface in org.forester.ws.seqdb

SequenceDataRetriver - Class in org.forester.archaeopteryx.tools

SequenceDataRetriver(MainFrameApplication, TreePanel, Phylogeny) - Constructor for class org.forester.archaeopteryx.tools.SequenceDataRetriver

SequenceDbWsTools - Class in org.forester.ws.seqdb

SequenceDbWsTools() - Constructor for class org.forester.ws.seqdb.SequenceDbWsTools

SequenceParser - Class in org.forester.io.parsers.phyloxml.data

SequenceRelation - Class in org.forester.phylogeny.data

SequenceRelation() - Constructor for class org.forester.phylogeny.data.SequenceRelation

SequenceRelation.SEQUENCE_RELATION_TYPE - Enum in org.forester.phylogeny.data

SequenceRelationParser - Class in org.forester.io.parsers.phyloxml.data

SequenceWriter - Class in org.forester.io.writers

SequenceWriter() - Constructor for class org.forester.io.writers.SequenceWriter

SequenceWriter.SEQ_FORMAT - Enum in org.forester.io.writers

serialVersionUID - Static variable in class org.forester.archaeopteryx.FontChooser

set(int, int, int) - Method in class org.forester.datastructures.IntMatrix

set_comparator - Class in org.forester.applications

set_comparator() - Constructor for class org.forester.applications.set_comparator

setAbbreviateScientificTaxonNames(boolean) - Method in class org.forester.archaeopteryx.Configuration

setAccession(Accession) - Method in class org.forester.phylogeny.data.Sequence

setAccession(String) - Method in class org.forester.protein.BasicProtein

setAddTaxonomyImagesCB(boolean) - Method in class org.forester.archaeopteryx.Configuration

setAllIndicatorsToZero(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

setAllNodesToNotCollapse() - Method in class org.forester.phylogeny.Phylogeny

Sets all Nodes of this Phylogeny to not-collapsed.

setAllowDomainsToBeIgnored(boolean) - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

setAllowErrorsInDistanceToParent(boolean) - Method in class org.forester.archaeopteryx.Options

setAllowErrorsInDistanceToParent(boolean) - Method in class org.forester.io.parsers.nhx.NHXParser

setAllowNonUniqueQuery(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser

setArrowCursor() - Method in class org.forester.archaeopteryx.MainPanel

setAuthority(String) - Method in class org.forester.phylogeny.data.Taxonomy

setBackgroundColorGradient(boolean) - Method in class org.forester.archaeopteryx.Configuration

setBackgroundColorGradient(boolean) - Method in class org.forester.archaeopteryx.Options

setBaseFontFamilyName(String) - Method in class org.forester.archaeopteryx.Configuration

setBaseFontSize(int) - Method in class org.forester.archaeopteryx.Configuration

setBinaryCharacters(BinaryCharacters) - Method in class org.forester.phylogeny.data.NodeData

setBootstrapConfidence(PhylogenyNode, double) - Static method in class org.forester.phylogeny.PhylogenyMethods

Convenience method.

setBootstrapSamples(int) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

setBranchColor(BranchColor) - Method in class org.forester.phylogeny.data.BranchData

setBranchColorValue(PhylogenyNode, Color) - Static method in class org.forester.phylogeny.PhylogenyMethods

setBranchData(BranchData) - Method in class org.forester.phylogeny.PhylogenyNode

setBranchWidth(BranchWidth) - Method in class org.forester.phylogeny.data.BranchData

setBranchWidthValue(PhylogenyNode, double) - Static method in class org.forester.phylogeny.PhylogenyMethods

Convenience method

setCalculateNormalizedShannonEntropy(boolean) - Method in class org.forester.msa_compactor.MsaCompactor

setCharacter(int, String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

setCharacter(int, String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

setChild1(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode

Sets the first child PhylogenyNode of this PhylogenyNode to n.

setChild2(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode

Sets the second child PhylogenyNode of this PhylogenyNode to n.

setChildNode(int, PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode

Inserts PhylogenyNode n at the specified position i into the list of child nodes.

setCollapse(boolean) - Method in class org.forester.phylogeny.PhylogenyNode

Sets whether this PhylogenyNode should be drawn as collapsed.

setColorizeBranches(boolean) - Method in class org.forester.archaeopteryx.Configuration

setColorLabelsSameAsParentBranch(boolean) - Method in class org.forester.archaeopteryx.Configuration

setColorLabelsSameAsParentBranch(boolean) - Method in class org.forester.archaeopteryx.Options

setColorMap(Map<String, Color>) - Static method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

setComment(String) - Method in class org.forester.go.BasicGoTerm

setCommonName(String) - Method in class org.forester.phylogeny.data.Taxonomy

setConfidence(Confidence) - Method in class org.forester.phylogeny.data.Annotation

setConfidence(Confidence) - Method in class org.forester.phylogeny.data.Event

setConfidence(Confidence) - Method in class org.forester.phylogeny.data.SequenceRelation

setConfidence(Confidence) - Method in class org.forester.phylogeny.Phylogeny

setConfidence(PhylogenyNode, double) - Static method in class org.forester.phylogeny.PhylogenyMethods

Convenience method.

setConfidence(PhylogenyNode, double, String) - Static method in class org.forester.phylogeny.PhylogenyMethods

Convenience method.

setCopiedAndPastedNodes(Set<Long>) - Method in class org.forester.archaeopteryx.MainPanel

setDate(Date) - Method in class org.forester.phylogeny.data.NodeData

setDefaultNodeFill(NodeVisualData.NodeFill) - Method in class org.forester.archaeopteryx.Configuration

setDefaultNodeShape(NodeVisualData.NodeShape) - Method in class org.forester.archaeopteryx.Configuration

setDefaultNodeShapeSize(short) - Method in class org.forester.archaeopteryx.Configuration

setDefinition(String) - Method in class org.forester.go.BasicGoTerm

setDesc(String) - Method in class org.forester.phylogeny.data.Annotation

setDesc(String) - Method in class org.forester.phylogeny.data.Date

setDescription(String) - Method in class org.forester.phylogeny.Phylogeny

setDescription(String) - Method in class org.forester.protein.BasicProtein

setDescription(String) - Method in class org.forester.surfacing.MappingResults

setDescription(String) - Method in class org.forester.util.BasicDescriptiveStatistics

setDescription(String) - Method in interface org.forester.util.DescriptiveStatistics

setDetailedness(DomainSimilarityCalculator.Detailedness) - Method in class org.forester.surfacing.DomainSimilarity

setDirectionTowards(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyBranch

setDisplayAsPhylogram(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplayColors(SortedMap<String, Color>) - Method in class org.forester.archaeopteryx.Configuration

setDisplayConfidenceValues(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplayGeneNames(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplayInternalData(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplayMultipleSequenceAlignment(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplayNodeNames(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplaySequenceAcc(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplaySequenceNames(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplaySequenceRelations(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplaySequenceSymbols(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplayTaxonomyCode(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplayTaxonomyCommonNames(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplayTaxonomyImages(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDisplayTaxonomyScientificNames(boolean) - Method in class org.forester.archaeopteryx.Configuration

setDistance(Double) - Method in class org.forester.phylogeny.data.SequenceRelation

setDistanceToParent(double) - Method in class org.forester.phylogeny.PhylogenyNode

Sets the length of the branch leading to the _parent of this PhylogenyNode to double d.

setDistanceUnit(String) - Method in class org.forester.phylogeny.Phylogeny

setDistribution(Distribution) - Method in class org.forester.phylogeny.data.NodeData

Convenience method -- always sets the first Distribution.

setDistribution(int, Distribution) - Method in class org.forester.phylogeny.data.NodeData

setDoi(String) - Method in class org.forester.phylogeny.data.Reference

setDomainArchitecture(DomainArchitecture) - Method in class org.forester.phylogeny.data.Sequence

setDomainsIgnoredDueToEval(int) - Method in class org.forester.io.parsers.HmmPfamOutputParser

setDomainsIgnoredDueToIndividualScoreCutoff(int) - Method in class org.forester.io.parsers.HmmPfamOutputParser

setDuplications(int) - Method in class org.forester.phylogeny.data.Event

setDynamicallyHideData(boolean) - Method in class org.forester.archaeopteryx.Configuration

setEdited(boolean) - Method in class org.forester.archaeopteryx.TreePanel

setEValueMaximum(double) - Method in class org.forester.io.parsers.HmmPfamOutputParser

setEvent(Event) - Method in class org.forester.phylogeny.data.NodeData

setEvidence(String) - Method in class org.forester.phylogeny.data.Annotation

setExtDescNodeDataToReturn(NodeDataField) - Method in class org.forester.archaeopteryx.Configuration

setExtDescNodeDataToReturn(NodeDataField) - Method in class org.forester.archaeopteryx.Options

setFillType(NodeVisualData.NodeFill) - Method in class org.forester.phylogeny.data.NodeVisualData

setFillType(String) - Method in class org.forester.phylogeny.data.NodeVisualData

setFlaggedStatusOfOutlierWells(boolean) - Method in class org.forester.development.MsaRenderer

setFlaggedStatusOfSelectedWells(boolean) - Method in class org.forester.development.MsaRenderer

setFont(Font) - Method in class org.forester.archaeopteryx.FontChooser

setFontColor(Color) - Method in class org.forester.phylogeny.data.NodeVisualData

setFontName(String) - Method in class org.forester.phylogeny.data.NodeVisualData

setFontSize(int) - Method in class org.forester.phylogeny.data.NodeVisualData

setFontStyle(NodeVisualData.FontType) - Method in class org.forester.phylogeny.data.NodeVisualData

setFontStyle(int) - Method in class org.forester.phylogeny.data.NodeVisualData

setFontStyle(String) - Method in class org.forester.phylogeny.data.NodeVisualData

setFrameXSize(int) - Method in class org.forester.archaeopteryx.Configuration

setFrameYSize(int) - Method in class org.forester.archaeopteryx.Configuration

setFsEValueMaximum(double) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

setGeneLosses(int) - Method in class org.forester.phylogeny.data.Event

setGeneName(String) - Method in class org.forester.phylogeny.data.Sequence

setGoSubsets(List<GoSubset>) - Method in class org.forester.go.BasicGoTerm

setGuessRootedness(boolean) - Method in class org.forester.io.parsers.nhx.NHXParser

setId(long) - Method in class org.forester.phylogeny.PhylogenyNode

Sets the Id of this PhylogenyNode to i.

setIdentifier(int, String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

setIdentifier(int, String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

setIdentifier(int, String) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

setIdentifier(int, String) - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix

setIdentifier(int, String) - Method in class org.forester.msa.BasicMsa

setIdentifier(int, String) - Method in class org.forester.msa.DeleteableMsa

setIdentifier(int, String) - Method in interface org.forester.msa.Msa

setIdentifier(Identifier) - Method in class org.forester.phylogeny.data.Taxonomy

setIdentifier(Identifier) - Method in class org.forester.phylogeny.Phylogeny

setIdentifier(String) - Method in class org.forester.sequence.BasicSequence

setIdToNodeMap(HashMap<Long, PhylogenyNode>) - Method in class org.forester.phylogeny.Phylogeny

setIEValueMaximum(double) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

setIgnoreDufs(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser

setIgnoreDufs(boolean) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

setIgnoreEngulfedDomains(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser

To ignore domains which are completely engulfed by domains (individual ones or stretches of overlapping ones) with better support values.

setIgnoreEngulfedDomains(boolean) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

To ignore domains which are completely engulfed by domains (individual ones or stretches of overlapping ones) with better support values.

setIgnoreQuotes(boolean) - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser

setIgnoreQuotes(boolean) - Method in class org.forester.io.parsers.nhx.NHXParser

setIgnoreVirusLikeIds(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser

setIgnoreVirusLikeIds(boolean) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

setImageMap(Hashtable<String, BufferedImage>) - Method in class org.forester.archaeopteryx.TreePanel

setIndentPhyloxml(boolean) - Method in class org.forester.io.writers.PhylogenyWriter

setIndicator(byte) - Method in class org.forester.phylogeny.PhylogenyNode

Sets the _indicator value of this PhylogenyNode to i.

setIndicatorsToZero() - Method in class org.forester.phylogeny.Phylogeny

Sets the indicators of all Nodes of this Phylogeny to 0.

setIndividualDomainScoreCutoffs(Map<String, String>) - Method in class org.forester.io.parsers.HmmPfamOutputParser

Sets the individual domain score cutoff values (for example, gathering thresholds from Pfam).

setIndividualScoreCutoffs(Map<String, Double>) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

Sets the individual score cutoff values (for example, gathering thresholds from Pfam).

setInfileName(String) - Method in class org.forester.msa_compactor.MsaCompactor

setInputMatrixType(SymmetricalDistanceMatrixParser.InputMatrixType) - Method in class org.forester.io.parsers.SymmetricalDistanceMatrixParser

setIntermediateFilesBase(String) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

setIsFlaggingStatusChangedToFalse() - Method in class org.forester.development.MsaRenderer

setIsMarked(boolean) - Method in class org.forester.development.ResidueRenderer

setIsSelected(boolean) - Method in class org.forester.development.ResidueRenderer

setKeyDomainCount(int) - Method in class org.forester.surfacing.BasicCombinableDomains

setKeyDomainCount(int) - Method in interface org.forester.surfacing.CombinableDomains

Sets how many times the key domain is present in a given species genome.

setLabel(int, String) - Method in class org.forester.datastructures.IntMatrix

setLineage(List<String>) - Method in class org.forester.phylogeny.data.Taxonomy

setLineUpRendarableNodeData(boolean) - Method in class org.forester.archaeopteryx.Configuration

setLineUpRendarableNodeData(boolean) - Method in class org.forester.archaeopteryx.Options

setLink(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode

Sets the linked PhylogenyNode of this PhylogenyNode to n.

setLocation(String) - Method in class org.forester.phylogeny.data.Sequence

setMafftOptions(String) - Method in class org.forester.msa_compactor.MsaCompactor

setMarkedOfAllWellsToFalse() - Method in class org.forester.development.MsaRenderer

setMax(double) - Method in class org.forester.development.MsaRenderer

setMax(BigDecimal) - Method in class org.forester.phylogeny.data.Date

setMaxAllowedOverlap(int) - Method in class org.forester.io.parsers.HmmPfamOutputParser

setMaxAllowedOverlap(int) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

setMeanColor(Color) - Method in class org.forester.development.MsaRenderer

setMidpointReroot(boolean) - Method in class org.forester.archaeopteryx.Configuration

setMin(double) - Method in class org.forester.development.MsaRenderer

setMin(BigDecimal) - Method in class org.forester.phylogeny.data.Date

setMinConfidenceValue(double) - Method in class org.forester.archaeopteryx.Configuration

setMolecularSequence(String) - Method in class org.forester.phylogeny.data.Sequence

setMolecularSequenceAligned(boolean) - Method in class org.forester.phylogeny.data.Sequence

setMsaPrgParameters(String) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

setMsaProcessingMaxAllowedGapRatio(double) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

setMsaProcessingMinAllowedLength(int) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

setName(String) - Method in class org.forester.phylogeny.data.Sequence

setName(String) - Method in class org.forester.phylogeny.Phylogeny

Sets the name of this Phylogeny to s.

setName(String) - Method in class org.forester.phylogeny.PhylogenyNode

Sets the name of this node.

setName(String) - Method in class org.forester.protein.BasicProtein

setNodeColor(Color) - Method in class org.forester.phylogeny.data.NodeVisualData

setNodeLabelDirection(Options.NODE_LABEL_DIRECTION) - Method in class org.forester.archaeopteryx.Configuration

setNodeName(String) - Method in class org.forester.phylogeny.data.NodeData

setNodeVisualData(NodeVisualData) - Method in class org.forester.phylogeny.data.NodeData

setNorm(boolean) - Method in class org.forester.msa_compactor.MsaCompactor

setNumberOfDigitsAfterCommaForBranchLengthValue(short) - Method in class org.forester.archaeopteryx.Configuration

setNumberOfDigitsAfterCommaForConfidenceValues(short) - Method in class org.forester.archaeopteryx.Configuration

setOutFileBase(File) - Method in class org.forester.msa_compactor.MsaCompactor

setOutputFormat(Msa.MSA_FORMAT) - Method in class org.forester.msa_compactor.MsaCompactor

setParameter(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

setParameter(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

setParameter(double) - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData

setParameter(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

setParent(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode

Sets the _parent PhylogenyNode of this PhylogenyNode to n.

setPathToMafft(String) - Method in class org.forester.msa_compactor.MsaCompactor

setPeformPhylogenticInference(boolean) - Method in class org.forester.msa_compactor.MsaCompactor

setPerformBootstrapResampling(boolean) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

setPhylogenyGraphicsType(Options.PHYLOGENY_GRAPHICS_TYPE) - Method in class org.forester.archaeopteryx.Configuration

setPrintLineWidth(float) - Method in class org.forester.archaeopteryx.Configuration

setProperties(PropertiesMap) - Method in class org.forester.phylogeny.data.Annotation

setProperties(PropertiesMap) - Method in class org.forester.phylogeny.data.NodeData

setProvider(String) - Method in class org.forester.ws.seqdb.EbiDbEntry

setPwdDistanceMethod(PairwiseDistanceCalculator.PWD_DISTANCE_METHOD) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

setRandomize(boolean) - Method in class org.forester.evoinference.parsimony.FitchParsimony

setRandomize(boolean) - Method in class org.forester.evoinference.parsimony.SankoffParsimony

setRandomNumberGeneratorSeed(long) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

setRandomNumberSeed(long) - Method in class org.forester.evoinference.parsimony.FitchParsimony

setRandomNumberSeed(long) - Method in class org.forester.evoinference.parsimony.SankoffParsimony

setRank(String) - Method in class org.forester.phylogeny.data.Taxonomy

setRealign(boolean) - Method in class org.forester.msa_compactor.MsaCompactor

setRef0(Sequence) - Method in class org.forester.phylogeny.data.SequenceRelation

setRef1(Sequence) - Method in class org.forester.phylogeny.data.SequenceRelation

setReference(int, Reference) - Method in class org.forester.phylogeny.data.NodeData

setReference(Reference) - Method in class org.forester.phylogeny.data.NodeData

Convenience method -- always sets the first Reference.

setRelevantSequenceRelationTypes(Collection<SequenceRelation.SEQUENCE_RELATION_TYPE>) - Method in class org.forester.phylogeny.Phylogeny

setRemovedSeqsOutBase(File) - Method in class org.forester.msa_compactor.MsaCompactor

setRenderingFactorWidth(float) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

setRenderingFactorWidth(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

setRenderingFactorWidth(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

setRenderingHeight(float) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

setRenderingHeight(float) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

setRenderingHeight(float) - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData

setRenderingHeight(float) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

setReplaceUnderscores(boolean) - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser

setReplaceUnderscores(boolean) - Method in class org.forester.io.parsers.nhx.NHXParser

setReplaceUnderscoresInNhParsing(boolean) - Method in class org.forester.archaeopteryx.Configuration

setRerootable(boolean) - Method in class org.forester.phylogeny.Phylogeny

setResidueAt(int, int, char) - Method in class org.forester.msa.BasicMsa

setResidueAt(int, int, char) - Method in class org.forester.msa.DeleteableMsa

setResidueAt(int, int, char) - Method in interface org.forester.msa.Msa

setResidueAt(int, int, char) - Method in class org.forester.msa.ResampleableMsa

setReturnGainLossMatrix(boolean) - Method in class org.forester.evoinference.parsimony.DolloParsimony

setReturnGainLossMatrix(boolean) - Method in class org.forester.evoinference.parsimony.FitchParsimony

setReturnGainLossMatrix(boolean) - Method in class org.forester.evoinference.parsimony.SankoffParsimony

setReturnInternalStates(boolean) - Method in class org.forester.evoinference.parsimony.DolloParsimony

setReturnInternalStates(boolean) - Method in class org.forester.evoinference.parsimony.FitchParsimony

setReturnInternalStates(boolean) - Method in class org.forester.evoinference.parsimony.SankoffParsimony

setReturnType(HmmPfamOutputParser.ReturnType) - Method in class org.forester.io.parsers.HmmPfamOutputParser

setReturnType(HmmscanPerDomainTableParser.ReturnType) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser

setRightLineUpDomains(boolean) - Method in class org.forester.archaeopteryx.Configuration

setRightLineUpDomains(boolean) - Method in class org.forester.archaeopteryx.Options

setRoot(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny

setRooted(boolean) - Method in class org.forester.phylogeny.Phylogeny

Sets whether this Phylogeny is rooted or not.

setRow(String, int) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

setScientificName(String) - Method in class org.forester.phylogeny.data.Taxonomy

setScientificName(PhylogenyNode, String) - Static method in class org.forester.phylogeny.PhylogenyMethods

setSequence(int, Sequence) - Method in class org.forester.phylogeny.data.NodeData

setSequence(Sequence) - Method in class org.forester.phylogeny.data.NodeData

Convenience method -- always sets the first Sequence.

setSequenceRelationQueries(Collection<Sequence>) - Method in class org.forester.phylogeny.Phylogeny

setShape(NodeVisualData.NodeShape) - Method in class org.forester.phylogeny.data.NodeVisualData

setShape(String) - Method in class org.forester.phylogeny.data.NodeVisualData

setShowAnnotationRefSource(boolean) - Method in class org.forester.archaeopteryx.Options

setShowDefaultNodeShapesExternal(boolean) - Method in class org.forester.archaeopteryx.Configuration

setShowDefaultNodeShapesForMarkedNodes(boolean) - Method in class org.forester.archaeopteryx.Configuration

setShowDefaultNodeShapesInternal(boolean) - Method in class org.forester.archaeopteryx.Configuration

setShowDomainLabels(boolean) - Method in class org.forester.archaeopteryx.Configuration

setShowDomainLabels(boolean) - Method in class org.forester.archaeopteryx.Options

setShowScale(boolean) - Method in class org.forester.archaeopteryx.Configuration

setSize(float) - Method in class org.forester.phylogeny.data.NodeVisualData

setSource(Object) - Method in interface org.forester.io.parsers.IteratingPhylogenyParser

setSource(Object) - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser

setSource(Object) - Method in class org.forester.io.parsers.nexus.NexusCharactersParser

setSource(Object) - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser

setSource(Object) - Method in class org.forester.io.parsers.nexus.PaupLogParser

setSource(Object) - Method in class org.forester.io.parsers.nhx.NHXParser

setSource(Object) - Method in interface org.forester.io.parsers.PhylogenyParser

setSource(Object) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

setSource(Object) - Method in class org.forester.io.parsers.tol.TolParser

setSource(String) - Method in class org.forester.phylogeny.data.Annotation

setSourceId(String) - Method in class org.forester.phylogeny.data.Sequence

setSpeciations(int) - Method in class org.forester.phylogeny.data.Event

setSpeciesOrder(List<Species>) - Method in class org.forester.surfacing.DomainSimilarity

setStandardDeviation(double) - Method in class org.forester.phylogeny.data.Confidence

setState(int, int, S) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

setState(String, int, S) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

setState(String, String, S) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

setState(int, int, S) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

setState(String, int, S) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

setState(String, String, S) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

setStep(int) - Method in class org.forester.msa_compactor.MsaCompactor

setStepForDiagnostics(int) - Method in class org.forester.msa_compactor.MsaCompactor

setSumExtNodes(int) - Method in class org.forester.phylogeny.PhylogenyNode

Sets the total number of external Nodes originating from this PhylogenyNode to i (int).

setSumOfFailures(int) - Method in class org.forester.surfacing.MappingResults

setSumOfSuccesses(int) - Method in class org.forester.surfacing.MappingResults

setSymbol(String) - Method in class org.forester.phylogeny.data.Sequence

setTaxonomy(int, Taxonomy) - Method in class org.forester.phylogeny.data.NodeData

setTaxonomy(Taxonomy) - Method in class org.forester.phylogeny.data.NodeData

Convenience method -- always sets the first Taxonomy.

setTaxonomyCode(String) - Method in class org.forester.phylogeny.data.Taxonomy

setTaxonomyCode(PhylogenyNode, String) - Static method in class org.forester.phylogeny.PhylogenyMethods

Convenience method to set the taxonomy code of a phylogeny node.

setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION) - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser

setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION) - Method in class org.forester.io.parsers.nhx.NHXParser

setTotalLength(int) - Method in class org.forester.phylogeny.data.DomainArchitecture

setTransparency(float) - Method in class org.forester.phylogeny.data.NodeVisualData

setTree(Phylogeny) - Method in class org.forester.archaeopteryx.TreePanel

Set a phylogeny tree.

setType(String) - Method in class org.forester.phylogeny.data.Annotation

setType(String) - Method in class org.forester.phylogeny.data.BinaryCharacters

setType(String) - Method in class org.forester.phylogeny.data.Confidence

setType(String) - Method in class org.forester.phylogeny.data.Sequence

setType(SequenceRelation.SEQUENCE_RELATION_TYPE) - Method in class org.forester.phylogeny.data.SequenceRelation

setType(String) - Method in class org.forester.phylogeny.Phylogeny

setUnit(String) - Method in class org.forester.phylogeny.data.Date

setUris(List<Uri>) - Method in class org.forester.phylogeny.data.Annotation

setUris(List<Uri>) - Method in interface org.forester.phylogeny.data.MultipleUris

setUris(List<Uri>) - Method in class org.forester.phylogeny.data.Sequence

setUris(List<Uri>) - Method in class org.forester.phylogeny.data.Taxonomy

setUseAccessors(boolean) - Method in class org.forester.go.PfamToGoParser

setUseLast(boolean) - Method in class org.forester.evoinference.parsimony.FitchParsimony

This sets whether to use the first or last state in the sorted states at the undecided internal nodes.

setUseLast(boolean) - Method in class org.forester.evoinference.parsimony.SankoffParsimony

This sets whether to use the first or last state in the sorted states at the undecided internal nodes.

setUseMean(boolean) - Method in class org.forester.development.MsaRenderer

setUseStyle(boolean) - Method in class org.forester.archaeopteryx.Configuration

setValidateAgainstSchema(String) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

setValidateAgainstSchema(String) - Method in class org.forester.io.parsers.tol.TolParser

setValue(int, int, double) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

setValue(int, int, double) - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix

setValue(String) - Method in class org.forester.io.parsers.phyloxml.XmlElement

[Careful, this does not call "new String(...)"]

setValue(Color) - Method in class org.forester.phylogeny.data.BranchColor

setValue(double) - Method in class org.forester.phylogeny.data.Confidence

setValue(BigDecimal) - Method in class org.forester.phylogeny.data.Date

setValue(String) - Method in class org.forester.phylogeny.data.Property

setValue(String) - Method in class org.forester.phylogeny.data.Reference

setValue(int, int, E) - Method in class org.forester.util.BasicTable

setValue(IDENTIFIER_TYPE, IDENTIFIER_TYPE, VALUE_TYPE) - Method in class org.forester.util.GeneralTable

setVector(List<Double>) - Method in class org.forester.phylogeny.data.NodeData

setVerbose(boolean) - Method in class org.forester.evoinference.parsimony.FitchParsimony

setVerbose(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser

setWaitCursor() - Method in class org.forester.archaeopteryx.MainPanel

setWaitCursor() - Method in class org.forester.archaeopteryx.TreePanel

setXcoord(float) - Method in class org.forester.phylogeny.PhylogenyNode

Used for drawing of Trees.

setXSecondary(float) - Method in class org.forester.phylogeny.PhylogenyNode

setYcoord(float) - Method in class org.forester.phylogeny.PhylogenyNode

Used for drawing of Trees.

setYSecondary(float) - Method in class org.forester.phylogeny.PhylogenyNode

setZippedInputstream(boolean) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser

setZippedInputstream(boolean) - Method in class org.forester.io.parsers.tol.TolParser

shared_chars_in_ext_nodes - Class in org.forester.applications

shared_chars_in_ext_nodes() - Constructor for class org.forester.applications.shared_chars_in_ext_nodes

showDialog(Component, String) - Method in class org.forester.archaeopteryx.FontChooser

showErrorMessage(Component, String) - Static method in class org.forester.archaeopteryx.AptxUtil

showExtDescNodeDataUserSelectedHelper(ControlPanel, PhylogenyNode, List<String>) - Static method in class org.forester.archaeopteryx.TreePanelUtil

showExtDescNodeDataUserSelectedHelperHelper(String, StringBuilder) - Static method in class org.forester.archaeopteryx.TreePanelUtil

showInformationMessage(Component, String, String) - Static method in class org.forester.archaeopteryx.TreePanelUtil

showTextFrame(String, String) - Method in class org.forester.archaeopteryx.ArchaeopteryxE

showTextFrame(String, String) - Method in class org.forester.archaeopteryx.MainFrame

showWhole() - Method in class org.forester.archaeopteryx.MainFrame

simple_node_processor - Class in org.forester.applications

simple_node_processor() - Constructor for class org.forester.applications.simple_node_processor

SimpleDomain - Class in org.forester.surfacing

SimpleDomain(String) - Constructor for class org.forester.surfacing.SimpleDomain

size() - Method in class org.forester.archaeopteryx.tools.ProcessPool

size() - Method in class org.forester.datastructures.IntMatrix

size() - Method in class org.forester.evoinference.distance.Sarray

size() - Method in class org.forester.evoinference.distance.Sset

size() - Method in class org.forester.phylogeny.data.PropertiesMap

sortDomainsWithAscendingConfidenceValues(Protein) - Static method in class org.forester.surfacing.SurfacingUtil

sortNodeDescendents(PhylogenyNode, PhylogenyMethods.DESCENDANT_SORT_PRIORITY) - Static method in class org.forester.phylogeny.PhylogenyMethods

SPECIAL_DOMAIN_COLORING - Static variable in class org.forester.archaeopteryx.TreePanel

SPECIATION - Static variable in class org.forester.archaeopteryx.TreeColorSet

Species - Interface in org.forester.species

SPECIES_NAME - Static variable in class org.forester.io.parsers.nhx.NHXtags

SPECIES_SEPARATOR - Static variable in class org.forester.surfacing.DomainSimilarity

Sset - Class in org.forester.evoinference.distance

Sset() - Constructor for class org.forester.evoinference.distance.Sset

STANDARD - Static variable in class org.forester.io.parsers.nexus.NexusConstants

standardErrorOfMean() - Method in class org.forester.util.BasicDescriptiveStatistics

standardErrorOfMean() - Method in interface org.forester.util.DescriptiveStatistics

start() - Method in class org.forester.archaeopteryx.ArchaeopteryxA

start() - Method in class org.forester.archaeopteryx.ArchaeopteryxE

start(MainFrame, String) - Method in class org.forester.archaeopteryx.tools.RunnableProcess

startDocument() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler

startDocument() - Method in class org.forester.io.parsers.tol.TolXmlHandler

startElement(String, String, String, Attributes) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler

startElement(String, String, String, Attributes) - Method in class org.forester.io.parsers.tol.TolXmlHandler

storeDomainArchitectures(String, SortedMap<String, Set<String>>, List<Protein>, Map<String, Integer>) - Static method in class org.forester.surfacing.SurfacingUtil

STRAMENOPILES_COLOR - Static variable in class org.forester.util.TaxonomyColors

stringArrayToString(String[]) - Static method in class org.forester.util.ForesterUtil

stringArrayToString(String[], String) - Static method in class org.forester.util.ForesterUtil

StringInt - Class in org.forester.util

StringInt(String, int) - Constructor for class org.forester.util.StringInt

StringInt.DescendingIntComparator - Class in org.forester.util

stringListToArray(List<String>) - Static method in class org.forester.util.ForesterUtil

stringListToString(List<String>, String) - Static method in class org.forester.util.ForesterUtil

stringSetToArray(Set<String>) - Static method in class org.forester.util.ForesterUtil

subtree_feature_count - Class in org.forester.applications

subtree_feature_count() - Constructor for class org.forester.applications.subtree_feature_count

sumDeviations() - Method in class org.forester.util.BasicDescriptiveStatistics

sumDeviations() - Method in interface org.forester.util.DescriptiveStatistics

SUPPORT - Static variable in class org.forester.io.parsers.nhx.NHXtags

support_statistics - Class in org.forester.application

support_statistics() - Constructor for class org.forester.application.support_statistics

support_transfer - Class in org.forester.application

support_transfer() - Constructor for class org.forester.application.support_transfer

SupportCount - Class in org.forester.tools

surfacing - Class in org.forester.application

surfacing() - Constructor for class org.forester.application.surfacing

SurfacingConstants - Class in org.forester.surfacing

SurfacingConstants() - Constructor for class org.forester.surfacing.SurfacingConstants

SurfacingUtil - Class in org.forester.surfacing

swapChildren() - Method in class org.forester.phylogeny.PhylogenyNode

Swaps the the two childern of a PhylogenyNode node of this Phylogeny.

SYMBOLS - Static variable in class org.forester.io.parsers.nexus.NexusConstants

SymmetricalDistanceMatrixParser - Class in org.forester.io.parsers

SymmetricalDistanceMatrixParser.InputMatrixType - Enum in org.forester.io.parsers

SystemCommandExecutor - Class in org.forester.util

SystemCommandExecutor(List<String>) - Constructor for class org.forester.util.SystemCommandExecutor

Pass in the system command you want to run as a List of Strings, as shown here: List commands = new ArrayList(); commands.add("/sbin/ping"); commands.add("-c"); commands.add("5"); commands.add("www.google.com"); SystemCommandExecutor commandExecutor = new SystemCommandExecutor(commands); commandExecutor.executeCommand(); Note: I've removed the other constructor that was here to support executing the sudo command.

T

table2fasta - Class in org.forester.application

table2fasta() - Constructor for class org.forester.application.table2fasta

TAX_CODE - Static variable in class org.forester.io.parsers.util.ParserUtils

tax_code_cleaner - Class in org.forester.applications

tax_code_cleaner() - Constructor for class org.forester.applications.tax_code_cleaner

TAX_CODE_LO - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXLABELS - Static variable in class org.forester.io.parsers.nexus.NexusConstants

TAXOMONY_CODE_PATTERN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

TAXOMONY_CODE_PATTERN_A - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXOMONY_CODE_PATTERN_A_LO - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXOMONY_CODE_PATTERN_BRACKETED - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXOMONY_CODE_PATTERN_PFR - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXOMONY_SN_PATTERN_GENUS - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXOMONY_SN_PATTERN_SN - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXOMONY_SN_PATTERN_SNS - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXOMONY_SN_PATTERN_SNS2 - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXOMONY_SN_PATTERN_SP - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXOMONY_SN_PATTERN_STRAIN_1 - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXOMONY_SN_PATTERN_STRAIN_2 - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN - Static variable in class org.forester.io.parsers.util.ParserUtils

TAXONOMY - Static variable in class org.forester.archaeopteryx.TreeColorSet

TAXONOMY - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Taxonomy - Class in org.forester.phylogeny.data

Taxonomy() - Constructor for class org.forester.phylogeny.data.Taxonomy

TAXONOMY_AUTHORITY - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

TAXONOMY_CODE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

TAXONOMY_COMMON_NAME - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

TAXONOMY_ID - Static variable in class org.forester.io.parsers.nhx.NHXtags

TAXONOMY_NAME - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

TAXONOMY_RANK - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

TAXONOMY_RANKS_LIST - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

TAXONOMY_RANKS_SET - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

TAXONOMY_SCIENTIFIC_NAME - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

TAXONOMY_SYNONYM - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

taxonomyBasedDeletionOfExternalNodes(Phylogeny, Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

Removes from Phylogeny to_be_stripped all external Nodes which are associated with a species NOT found in Phylogeny reference.

TaxonomyColors - Class in org.forester.util

TaxonomyColors() - Constructor for class org.forester.util.TaxonomyColors

TaxonomyDataManager - Class in org.forester.analysis

TaxonomyDataManager(MainFrameApplication, TreePanel, Phylogeny) - Constructor for class org.forester.analysis.TaxonomyDataManager

TaxonomyDataManager(MainFrameApplication, TreePanel, Phylogeny, boolean, boolean) - Constructor for class org.forester.analysis.TaxonomyDataManager

TaxonomyParser - Class in org.forester.io.parsers.phyloxml.data

TaxonomyUtil - Class in org.forester.util

TaxonomyUtil() - Constructor for class org.forester.util.TaxonomyUtil

TC_STR - Static variable in interface org.forester.go.GoXRef

TERMINATE - Static variable in interface org.forester.sequence.MolecularSequence

Test - Class in org.forester.development

Test() - Constructor for class org.forester.development.Test

test(File) - Static method in class org.forester.evoinference.TestPhylogenyReconstruction

test(File) - Static method in class org.forester.go.TestGo

test() - Static method in class org.forester.pccx.TestPccx

test() - Static method in class org.forester.rio.TestRIO

test() - Static method in class org.forester.sdi.TestGSDI

test(File) - Static method in class org.forester.surfacing.TestSurfacing

Test - Class in org.forester.test

Test() - Constructor for class org.forester.test.Test

Test - Class in org.forester.ws.hmmer

Test() - Constructor for class org.forester.ws.hmmer.Test

testEngulfingOverlapRemoval() - Static method in class org.forester.test.Test

TestGo - Class in org.forester.go

TestGo() - Constructor for class org.forester.go.TestGo

TestGSDI - Class in org.forester.sdi

TestGSDI() - Constructor for class org.forester.sdi.TestGSDI

testNHXparsingFromURL() - Static method in class org.forester.test.Test

testNHXparsingFromURL2() - Static method in class org.forester.test.Test

testOverlapRemoval() - Static method in class org.forester.test.Test

TestPccx - Class in org.forester.pccx

TestPccx() - Constructor for class org.forester.pccx.TestPccx

testPfamTreeReading() - Static method in class org.forester.test.Test

TestPhylogenyReconstruction - Class in org.forester.evoinference

TestPhylogenyReconstruction() - Constructor for class org.forester.evoinference.TestPhylogenyReconstruction

testPhyloXMLparsingFromURL() - Static method in class org.forester.test.Test

TestRIO - Class in org.forester.rio

TestRIO() - Constructor for class org.forester.rio.TestRIO

TestSurfacing - Class in org.forester.surfacing

TestSurfacing() - Constructor for class org.forester.surfacing.TestSurfacing

testToLReading() - Static method in class org.forester.test.Test

testTreeBaseReading() - Static method in class org.forester.test.Test

testTreeFamReading() - Static method in class org.forester.test.Test

Time - Class in org.forester.development

Time() - Constructor for class org.forester.development.Time

toArray(int) - Method in class org.forester.evoinference.distance.Sarray

toArray(int) - Method in class org.forester.evoinference.distance.Sset

toBinaryDomainCombinations() - Method in class org.forester.surfacing.AdjactantDirectedCombinableDomains

toBinaryDomainCombinations() - Method in class org.forester.surfacing.BasicCombinableDomains

toBinaryDomainCombinations() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

toBinaryDomainCombinations() - Method in interface org.forester.surfacing.CombinableDomains

toBinaryDomainCombinations() - Method in class org.forester.surfacing.DirectedCombinableDomains

toBinaryDomainCombinations() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains

This should return all binary domain combinations present in the genome.

toChar() - Method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates

toDomainArchitectureString(String) - Method in class org.forester.protein.BasicProtein

toDomainArchitectureString(String, int, String) - Method in class org.forester.protein.BasicProtein

toFasta(MolecularSequence, int) - Static method in class org.forester.io.writers.SequenceWriter

toFasta(String, String, int) - Static method in class org.forester.io.writers.SequenceWriter

toFasta(MolecularSequence, Writer, int) - Static method in class org.forester.io.writers.SequenceWriter

toGraphDescribingLanguage(BinaryDomainCombination.OutputFormat, String, String) - Method in interface org.forester.protein.BinaryDomainCombination

toGraphDescribingLanguage(BinaryDomainCombination.OutputFormat, String, String) - Method in class org.forester.surfacing.BasicBinaryDomainCombination

TOL_NAME - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

TOL_TAXONOMY_ID_TYPE - Static variable in class org.forester.io.parsers.tol.TolXmlMapping

TOL_URL_BASE - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

TOL_WEBSERVER - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

TolParser - Class in org.forester.io.parsers.tol

TolParser() - Constructor for class org.forester.io.parsers.tol.TolParser

TolXmlHandler - Class in org.forester.io.parsers.tol

TolXmlMapping - Class in org.forester.io.parsers.tol

toNewHampshire(List<Phylogeny>, boolean, File, String) - Method in class org.forester.io.writers.PhylogenyWriter

toNewHampshire(Phylogeny, boolean, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE) - Method in class org.forester.io.writers.PhylogenyWriter

toNewHampshire(Phylogeny, boolean) - Method in class org.forester.io.writers.PhylogenyWriter

toNewHampshire(Phylogeny, boolean, File) - Method in class org.forester.io.writers.PhylogenyWriter

toNewHampshire(Phylogeny, boolean, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE, File) - Method in class org.forester.io.writers.PhylogenyWriter

toNewHampshire(Phylogeny[], boolean, File, String) - Method in class org.forester.io.writers.PhylogenyWriter

toNewHampshire() - Method in class org.forester.phylogeny.Phylogeny

toNewHampshire(PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE) - Method in class org.forester.phylogeny.Phylogeny

toNewHampshire(boolean, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE) - Method in class org.forester.phylogeny.PhylogenyNode

toNewHampshireX(List<Phylogeny>, File, String) - Method in class org.forester.io.writers.PhylogenyWriter

toNewHampshireX(Phylogeny) - Method in class org.forester.io.writers.PhylogenyWriter

toNewHampshireX(Phylogeny, File) - Method in class org.forester.io.writers.PhylogenyWriter

toNewHampshireX(Phylogeny[], File, String) - Method in class org.forester.io.writers.PhylogenyWriter

toNewHampshireX() - Method in class org.forester.phylogeny.Phylogeny

toNewHampshireX() - Method in class org.forester.phylogeny.PhylogenyNode

Converts this PhylogenyNode to a New Hampshire X (NHX) String representation.

toNexus(File, Phylogeny, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE) - Method in class org.forester.io.writers.PhylogenyWriter

toNexus(Phylogeny, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE) - Method in class org.forester.io.writers.PhylogenyWriter

toNexus() - Method in class org.forester.phylogeny.Phylogeny

toNexus(PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE) - Method in class org.forester.phylogeny.Phylogeny

toNHX() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

toNHX() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

toNHX() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

toNHX() - Method in class org.forester.go.BasicGoTerm

toNHX() - Method in class org.forester.phylogeny.data.Accession

toNHX() - Method in class org.forester.phylogeny.data.Annotation

toNHX() - Method in class org.forester.phylogeny.data.BinaryCharacters

toNHX() - Method in class org.forester.phylogeny.data.BranchColor

toNHX() - Method in class org.forester.phylogeny.data.BranchData

toNHX() - Method in class org.forester.phylogeny.data.BranchWidth

toNHX() - Method in class org.forester.phylogeny.data.Confidence

toNHX() - Method in class org.forester.phylogeny.data.Date

toNHX() - Method in class org.forester.phylogeny.data.Distribution

toNHX() - Method in class org.forester.phylogeny.data.DomainArchitecture

toNHX() - Method in class org.forester.phylogeny.data.Event

toNHX() - Method in class org.forester.phylogeny.data.Identifier

toNHX() - Method in class org.forester.phylogeny.data.NodeData

toNHX() - Method in class org.forester.phylogeny.data.NodeVisualData

toNHX() - Method in interface org.forester.phylogeny.data.PhylogenyData

toNHX() - Method in class org.forester.phylogeny.data.Point

toNHX() - Method in class org.forester.phylogeny.data.Polygon

toNHX() - Method in class org.forester.phylogeny.data.PropertiesMap

toNHX() - Method in class org.forester.phylogeny.data.Property

toNHX() - Method in class org.forester.phylogeny.data.ProteinDomain

toNHX() - Method in class org.forester.phylogeny.data.Reference

toNHX() - Method in class org.forester.phylogeny.data.Sequence

toNHX() - Method in class org.forester.phylogeny.data.SequenceRelation

toNHX() - Method in class org.forester.phylogeny.data.Taxonomy

toNHX() - Method in class org.forester.phylogeny.data.Uri

toPhyloXML(Writer, int, String) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

toPhyloXML(Writer, int, String) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

toPhyloXML(Writer, int, String) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

toPhyloXML(Writer, int, String) - Method in class org.forester.go.BasicGoTerm

toPhyloXML(File, List<Phylogeny>, int, String) - Method in class org.forester.io.writers.PhylogenyWriter

toPhyloXML(File, Phylogeny, int) - Method in class org.forester.io.writers.PhylogenyWriter

toPhyloXML(Phylogeny, int) - Method in class org.forester.io.writers.PhylogenyWriter

toPhyloXML(Phylogeny[], int, File, String) - Method in class org.forester.io.writers.PhylogenyWriter

toPhyloXML(Phylogeny, int, File) - Method in class org.forester.io.writers.PhylogenyWriter

toPhyloXML(Writer, List<Phylogeny>, int, String) - Method in class org.forester.io.writers.PhylogenyWriter

toPhyloXML(Writer, Phylogeny, int) - Method in class org.forester.io.writers.PhylogenyWriter

toPhyloXML(Writer, Phylogeny[], int, String) - Method in class org.forester.io.writers.PhylogenyWriter

toPhyloXml(Writer, PhylogenyNode, int, String) - Static method in class org.forester.io.writers.PhyloXmlNodeWriter

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Accession

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Annotation

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.BinaryCharacters

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.BranchColor

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.BranchData

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.BranchWidth

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Confidence

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Date

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Distribution

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.DomainArchitecture

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Event

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Identifier

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.NodeData

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.NodeVisualData

toPhyloXML(Writer, int, String) - Method in interface org.forester.phylogeny.data.PhylogenyData

Writes a phyloXML representation of this phylogeny data.

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Point

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Polygon

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.PropertiesMap

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Property

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.ProteinDomain

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Reference

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Sequence

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.SequenceRelation

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Taxonomy

toPhyloXML(Writer, int, String) - Method in class org.forester.phylogeny.data.Uri

toPhyloXML(int) - Method in class org.forester.phylogeny.Phylogeny

toShortString() - Method in class org.forester.go.GoNameSpace

toString() - Method in enum org.forester.archaeopteryx.AptxUtil.GraphicsExportType

toString() - Method in class org.forester.archaeopteryx.tools.ProcessRunning

toString() - Method in class org.forester.datastructures.IntMatrix

toString() - Method in class org.forester.evoinference.distance.Sarray

toString() - Method in class org.forester.evoinference.distance.Sset

toString() - Method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates

toString() - Method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates

toString() - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

toString() - Method in class org.forester.go.BasicGoRelationship

toString() - Method in class org.forester.go.BasicGoSubset

toString() - Method in class org.forester.go.BasicGoTerm

toString() - Method in class org.forester.go.BasicGoXRef

toString() - Method in class org.forester.go.GoId

toString() - Method in class org.forester.go.GoNameSpace

toString() - Method in class org.forester.go.PfamToGoMapping

toString() - Method in class org.forester.io.parsers.phyloxml.XmlElement

toString() - Method in class org.forester.msa.BasicMsa

toString() - Method in enum org.forester.phylogeny.data.Accession.Source

toString() - Method in class org.forester.phylogeny.data.Accession

toString() - Method in class org.forester.phylogeny.data.Annotation

toString() - Method in class org.forester.phylogeny.data.BinaryCharacters

toString() - Method in class org.forester.phylogeny.data.BranchColor

toString() - Method in class org.forester.phylogeny.data.BranchWidth

toString() - Method in class org.forester.phylogeny.data.Confidence

toString() - Method in class org.forester.phylogeny.data.Date

toString() - Method in class org.forester.phylogeny.data.Distribution

toString() - Method in class org.forester.phylogeny.data.DomainArchitecture

toString() - Method in class org.forester.phylogeny.data.Event

toString() - Method in class org.forester.phylogeny.data.Identifier

toString() - Method in enum org.forester.phylogeny.data.NodeDataField

toString() - Method in class org.forester.phylogeny.data.NodeVisualData

toString() - Method in class org.forester.phylogeny.data.Point

toString() - Method in class org.forester.phylogeny.data.PropertiesMap

toString() - Method in class org.forester.phylogeny.data.Property

toString() - Method in class org.forester.phylogeny.data.ProteinDomain

toString() - Method in class org.forester.phylogeny.data.Reference

toString() - Method in class org.forester.phylogeny.data.Sequence

toString() - Method in class org.forester.phylogeny.data.Taxonomy

toString() - Method in class org.forester.phylogeny.data.Uri

toString() - Method in class org.forester.phylogeny.Phylogeny

Converts this Phylogeny to a New Hampshire X (String) representation.

toString() - Method in class org.forester.phylogeny.PhylogenyBranch

toString() - Method in class org.forester.phylogeny.PhylogenyNode

toString() - Method in class org.forester.protein.BasicDomain

toString() - Method in class org.forester.protein.BasicProtein

toString() - Method in class org.forester.protein.ProteinId

toString() - Method in class org.forester.sdi.GSDI

toString() - Method in class org.forester.sdi.SDI

toString() - Method in class org.forester.sequence.BasicSequence

toString() - Method in class org.forester.species.BasicSpecies

toString() - Method in class org.forester.surfacing.BasicBinaryDomainCombination

toString() - Method in class org.forester.surfacing.BasicCombinableDomains

toString() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

toString() - Method in class org.forester.tools.TreeSplitMatrix

toString() - Method in class org.forester.util.BasicDescriptiveStatistics

toString() - Method in class org.forester.util.BasicTable

toString() - Method in interface org.forester.util.DescriptiveStatistics

toString() - Method in class org.forester.util.GeneralTable

toString(NumberFormat) - Method in class org.forester.util.GeneralTable

toString() - Method in enum org.forester.ws.wabi.TxSearch.RANKS

toString() - Method in enum org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS

toString() - Method in enum org.forester.ws.wabi.TxSearch.TAX_RANK

toStringBuffer(DistanceMatrix.Format) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

toStringBuffer(DistanceMatrix.Format) - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix

toStringBuffer() - Method in class org.forester.protein.BasicDomain

toStringBuffer(DomainSimilarity.PRINT_OPTION, Map<String, Integer>, Phylogeny) - Method in class org.forester.surfacing.DomainSimilarity

toStringBuffer(double, double, int, char, int, int, String) - Method in class org.forester.util.AsciiHistogram

toStringBuffer(int, char, int, int, String) - Method in class org.forester.util.AsciiHistogram

toStringBuffer(int, char, int, int) - Method in class org.forester.util.AsciiHistogram

toStringBuilder(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder) - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains

toStringBuilder(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder) - Method in interface org.forester.surfacing.GenomeWideCombinableDomains

toWriter(Writer) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

toWriter(Writer, CharacterStateMatrix.Format) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

toWriter(Writer) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

toWriter(Writer, CharacterStateMatrix.Format) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix

transferInternalNamesToBootstrapSupport(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods

transferInternalNodeNamesToConfidence(Phylogeny, String) - Static method in class org.forester.phylogeny.PhylogenyMethods

transferNodeNameToField(Phylogeny, PhylogenyMethods.PhylogenyNodeField, boolean) - Static method in class org.forester.phylogeny.PhylogenyMethods

transferSupportValues(Phylogeny, Phylogeny) - Static method in class org.forester.application.support_transfer

Modifies Phylogeny to with the support values from Phylogeny from.

TRANSLATE - Static variable in class org.forester.io.parsers.nexus.NexusConstants

TREE - Static variable in class org.forester.io.parsers.nexus.NexusConstants

TREE_BASE_DESC - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

TREE_BASE_INST - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

TREE_BASE_NAME - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

TREE_FAM_INST - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

TREE_FAM_NAME - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

TREE_FAM_URL_BASE - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

TREEBASE_PHYLOWS_STUDY_URL_BASE - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

TREEBASE_PHYLOWS_TREE_URL_BASE - Static variable in class org.forester.archaeopteryx.webservices.WebserviceUtil

TreeColorSet - Class in org.forester.archaeopteryx

TreeFontSet - Class in org.forester.archaeopteryx

TreePanel - Class in org.forester.archaeopteryx

TreePanelUtil - Class in org.forester.archaeopteryx

TreePanelUtil() - Constructor for class org.forester.archaeopteryx.TreePanelUtil

TreeSplitMatrix - Class in org.forester.tools

TreeSplitMatrix(Phylogeny, boolean, Phylogeny) - Constructor for class org.forester.tools.TreeSplitMatrix

TreeSplitMatrix(Phylogeny, boolean, Set<PhylogenyNode>) - Constructor for class org.forester.tools.TreeSplitMatrix

If strict is true, target nodes (all external nodes of the phylogeny for which support values are to be calculated) is not used for anything during construction.

TxSearch - Class in org.forester.ws.wabi

This is to access the Web API for Biology (WABI) at DDBJ.

TxSearch() - Constructor for class org.forester.ws.wabi.TxSearch

TxSearch.RANKS - Enum in org.forester.ws.wabi

TxSearch.TAX_NAME_CLASS - Enum in org.forester.ws.wabi

TxSearch.TAX_RANK - Enum in org.forester.ws.wabi

TYPE_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

typesToNames - Static variable in class org.forester.phylogeny.data.SequenceRelation

U

UM_BBD_ENZYME_ID_STR - Static variable in interface org.forester.go.GoXRef

UM_BBD_PATHWAY_ID_STR - Static variable in interface org.forester.go.GoXRef

UM_BBD_REACTIONID_STR - Static variable in interface org.forester.go.GoXRef

UNASSIGNED_STR - Static variable in class org.forester.go.GoNameSpace

unexpectedFatalError(Error) - Static method in class org.forester.util.ForesterUtil

unexpectedFatalError(Exception) - Static method in class org.forester.util.ForesterUtil

unexpectedFatalError(String) - Static method in class org.forester.util.ForesterUtil

unexpectedFatalError(String, Exception) - Static method in class org.forester.util.ForesterUtil

unexpectedFatalError(String, String) - Static method in class org.forester.util.ForesterUtil

unexpectedFatalError(String, String, Exception) - Static method in class org.forester.util.ForesterUtil

UNIPATHWAY_STR - Static variable in interface org.forester.go.GoXRef

UNIPROT_KB - Static variable in class org.forester.util.ForesterUtil

UNIPROT_KB_BASE_PATTERN_STR - Static variable in class org.forester.util.SequenceAccessionTools

UNIPROT_KB_PATTERN_0 - Static variable in class org.forester.util.SequenceAccessionTools

UNIPROT_KB_PATTERN_1 - Static variable in class org.forester.util.SequenceAccessionTools

UNIPROT_KB_PATTERN_2 - Static variable in class org.forester.util.SequenceAccessionTools

UNIPROT_TAX_PROVIDER - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

UNIPROT_TAXONOMY_ID_LINK - Static variable in class org.forester.surfacing.SurfacingConstants

UniProtEntry - Class in org.forester.ws.seqdb

UniProtTaxonomy - Class in org.forester.ws.seqdb

UniProtTaxonomy(String) - Constructor for class org.forester.ws.seqdb.UniProtTaxonomy

UniProtTaxonomy(List<String>, String, String, String, String, String, String) - Constructor for class org.forester.ws.seqdb.UniProtTaxonomy

UNKNOWN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

UNKNOWN_GEODETIC_DATUM - Static variable in class org.forester.phylogeny.data.Point

unRoot() - Method in class org.forester.phylogeny.Phylogeny

Removes the root PhylogenyNode this Phylogeny.

unSelectUnMarkAll() - Method in class org.forester.development.MsaRenderer

UNSPECIFIED_AA - Static variable in interface org.forester.sequence.MolecularSequence

UNSPECIFIED_NUC - Static variable in interface org.forester.sequence.MolecularSequence

update(Graphics) - Method in class org.forester.archaeopteryx.TreePanel

updateProcessMenu() - Method in class org.forester.archaeopteryx.MainFrame

updateProgress(double) - Static method in class org.forester.util.ForesterUtil

updateProgress(int, DecimalFormat) - Static method in class org.forester.util.ForesterUtil

URI - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

Uri - Class in org.forester.phylogeny.data

Uri(String, String, String) - Constructor for class org.forester.phylogeny.data.Uri

Uri(URI) - Constructor for class org.forester.phylogeny.data.Uri

Uri(URI, String, String) - Constructor for class org.forester.phylogeny.data.Uri

URI_DESC_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

UriParser - Class in org.forester.io.parsers.phyloxml.data

UrlTreeReader - Class in org.forester.archaeopteryx

UTF8 - Static variable in class org.forester.util.ForesterConstants

UTREE - Static variable in class org.forester.io.parsers.nexus.NexusConstants

V

validateAllowedOptions(List<String>) - Method in class org.forester.util.CommandLineArguments

validateAllowedOptionsAsString(List<String>) - Method in class org.forester.util.CommandLineArguments

validateMandatoryOptions(List<String>) - Method in class org.forester.util.CommandLineArguments

validateMandatoryOptionsAsString(List<String>) - Method in class org.forester.util.CommandLineArguments

valueChanged(ListSelectionEvent) - Method in class org.forester.archaeopteryx.FontChooser

valueOf(String) - Static method in enum org.forester.archaeopteryx.AptxUtil.GraphicsExportType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.archaeopteryx.Configuration.UI

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.archaeopteryx.Options.CLADOGRAM_TYPE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.archaeopteryx.tools.PhylogeneticInferrer.MSA_PRG

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.Format

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.NucleotideStates

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.evoinference.matrix.distance.DistanceMatrix.Format

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.go.etc.OntologizerResult.TYPE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.go.GoNameSpace.GoNamespaceType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.go.GoRelationship.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.go.GoSubset.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.go.GoXRef.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.go.OBOparser.ReturnType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.io.parsers.HmmPfamOutputParser.FilterType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.io.parsers.HmmPfamOutputParser.ReturnType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.FilterType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.ReturnType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.io.parsers.SymmetricalDistanceMatrixParser.InputMatrixType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.io.writers.PhylogenyWriter.FORMAT

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.io.writers.SequenceWriter.SEQ_FORMAT

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.msa.Msa.MSA_FORMAT

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.phylogeny.data.Accession.Source

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.phylogeny.data.Event.EventType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.phylogeny.data.NodeDataField

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.phylogeny.data.NodeVisualData.FontType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.phylogeny.data.NodeVisualData.NodeFill

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.phylogeny.data.NodeVisualData.NodeShape

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.phylogeny.data.Property.AppliesTo

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.phylogeny.PhylogenyMethods.PhylogenyNodeField

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.protein.BinaryDomainCombination.DomainCombinationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.protein.BinaryDomainCombination.OutputFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.rio.RIO.REROOTING

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.sdi.SDIutil.ALGORITHM

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.sdi.SDIutil.TaxonomyComparisonBase

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.sequence.MolecularSequence.TYPE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.surfacing.DomainCountsDifferenceUtil.COPY_CALCULATION_MODE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarity.PRINT_OPTION

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarityCalculator.Detailedness

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.tools.PhylogenyDecorator.FIELD

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.util.ForesterConstants.PhylogeneticTreeFormats

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.ws.wabi.TxSearch.RANKS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.forester.ws.wabi.TxSearch.TAX_RANK

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.forester.archaeopteryx.AptxUtil.GraphicsExportType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.archaeopteryx.Configuration.UI

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.archaeopteryx.Options.CLADOGRAM_TYPE

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.archaeopteryx.tools.PhylogeneticInferrer.MSA_PRG

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.Format

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.NucleotideStates

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.evoinference.matrix.distance.DistanceMatrix.Format

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.go.etc.OntologizerResult.TYPE

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.go.GoNameSpace.GoNamespaceType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.go.GoRelationship.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.go.GoSubset.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.go.GoXRef.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.go.OBOparser.ReturnType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.io.parsers.HmmPfamOutputParser.FilterType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.io.parsers.HmmPfamOutputParser.ReturnType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.FilterType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.ReturnType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.io.parsers.SymmetricalDistanceMatrixParser.InputMatrixType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.io.writers.PhylogenyWriter.FORMAT

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.io.writers.SequenceWriter.SEQ_FORMAT

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.msa.Msa.MSA_FORMAT

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.phylogeny.data.Accession.Source

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.phylogeny.data.Event.EventType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.phylogeny.data.NodeDataField

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.phylogeny.data.NodeVisualData.FontType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.phylogeny.data.NodeVisualData.NodeFill

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.phylogeny.data.NodeVisualData.NodeShape

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.phylogeny.data.Property.AppliesTo

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.phylogeny.PhylogenyMethods.PhylogenyNodeField

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.protein.BinaryDomainCombination.DomainCombinationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.protein.BinaryDomainCombination.OutputFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.rio.RIO.REROOTING

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.sdi.SDIutil.ALGORITHM

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.sdi.SDIutil.TaxonomyComparisonBase

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.sequence.MolecularSequence.TYPE

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.surfacing.DomainCountsDifferenceUtil.COPY_CALCULATION_MODE

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.surfacing.DomainSimilarity.PRINT_OPTION

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.surfacing.DomainSimilarityCalculator.Detailedness

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.tools.PhylogenyDecorator.FIELD

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.util.ForesterConstants.PhylogeneticTreeFormats

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.ws.wabi.TxSearch.RANKS

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.forester.ws.wabi.TxSearch.TAX_RANK

Returns an array containing the constants of this enum type, in the order they are declared.

VECTOR_DEFAULT_WIDTH - Static variable in class org.forester.archaeopteryx.phylogeny.data.RenderableVector

VECTOR_PROPERTY_REF - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

VECTOR_PROPERTY_TYPE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil

VERBOSE - Static variable in class org.forester.application.surfacing

VIRUSES - Static variable in class org.forester.ws.seqdb.UniProtTaxonomy

W

W3C_XML_SCHEMA - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser

W3C_XML_SCHEMA - Static variable in class org.forester.io.parsers.tol.TolParser

WabiTools - Class in org.forester.ws.wabi

WabiTools() - Constructor for class org.forester.ws.wabi.WabiTools

waitFor() - Method in class org.forester.util.ExternalProgram

WebservicesManager - Class in org.forester.archaeopteryx.webservices

WebservicesManager.WsPhylogenyFormat - Enum in org.forester.archaeopteryx.webservices

WebserviceUtil - Class in org.forester.archaeopteryx.webservices

WebserviceUtil() - Constructor for class org.forester.archaeopteryx.webservices.WebserviceUtil

WIDTH - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping

wiki_examples - Class in org.forester.applications

wiki_examples() - Constructor for class org.forester.applications.wiki_examples

WIKIPEDIA_STR - Static variable in interface org.forester.go.GoXRef

WindowsUtils - Class in org.forester.util

wordWrap(String, int) - Static method in class org.forester.util.ForesterUtil

write(Writer) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

write(Writer, Msa.MSA_FORMAT) - Method in class org.forester.msa.BasicMsa

write(Writer, Msa.MSA_FORMAT) - Method in interface org.forester.msa.Msa

writeAllDomainsChangedOnAllSubtrees(Phylogeny, boolean, String, String) - Static method in class org.forester.surfacing.SurfacingUtil

writeAndAlignRemovedSeqs() - Method in class org.forester.msa_compactor.MsaCompactor

writeBinaryDomainCombinationsFileForGraphAnalysis(String[][], File, GenomeWideCombinableDomains, int, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder) - Static method in class org.forester.surfacing.SurfacingUtil

writeBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates>, CharacterStateMatrix.GainLossStates, String, String, String, Map<String, String>) - Static method in class org.forester.surfacing.SurfacingUtil

writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis(CharacterStateMatrix<CharacterStateMatrix.GainLossStates>, CharacterStateMatrix.GainLossStates, String, String, String, BinaryDomainCombination.OutputFormat) - Static method in class org.forester.surfacing.SurfacingUtil

writeBinaryStatesMatrixToList(Map<String, List<GoId>>, Map<GoId, GoTerm>, GoNameSpace, boolean, CharacterStateMatrix<CharacterStateMatrix.GainLossStates>, CharacterStateMatrix.GainLossStates, String, String, String, String, String, Map<String, Set<String>>[], SortedSet<String>, SortedSet<String>, String, Map<String, Integer>) - Static method in class org.forester.surfacing.SurfacingUtil

writeDomainCombinationsCountsFile(String[][], File, Writer, GenomeWideCombinableDomains, int, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder) - Static method in class org.forester.surfacing.SurfacingUtil

writeDomainSimilaritiesToFile(StringBuilder, StringBuilder, Writer, Writer, Map<Character, Writer>, SortedSet<DomainSimilarity>, boolean, List<Species>, DomainSimilarity.PRINT_OPTION, DomainSimilarity.DomainSimilarityScoring, boolean, Map<String, Integer>, Phylogeny, Set<String>) - Static method in class org.forester.surfacing.SurfacingUtil

writeHtmlHead(Writer, String) - Static method in class org.forester.surfacing.SurfacingUtil

writeMatrixToFile(CharacterStateMatrix<?>, String, CharacterStateMatrix.Format) - Static method in class org.forester.surfacing.SurfacingUtil

writeMatrixToFile(File, List<DistanceMatrix>) - Static method in class org.forester.surfacing.SurfacingUtil

writeMsa(File) - Method in class org.forester.msa_compactor.MsaCompactor

writeNexusBinaryChractersBlock(Writer) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

writeNexusCharstatelabels(Writer) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

writeNexusMatrix(Writer) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

writeNexusTaxaBlock(Writer) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix

writeNexusTaxaBlock(Writer, Phylogeny) - Static method in class org.forester.io.writers.PhylogenyWriter

writeNexusTreesBlock(Writer, List<Phylogeny>, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE) - Static method in class org.forester.io.writers.PhylogenyWriter

writePhylogenyToFile(Phylogeny, String) - Static method in class org.forester.surfacing.SurfacingUtil

writePhylogenyToGraphicsFile(File, File, int, int, AptxUtil.GraphicsExportType, Configuration) - Static method in class org.forester.archaeopteryx.AptxUtil

writePhylogenyToGraphicsFile(Phylogeny, File, int, int, AptxUtil.GraphicsExportType, Configuration) - Static method in class org.forester.archaeopteryx.AptxUtil

writePhylogenyToGraphicsFileNonInteractive(File, int, int, TreePanel, ControlPanel, AptxUtil.GraphicsExportType, Options) - Static method in class org.forester.archaeopteryx.AptxUtil

writePresentToNexus(File, File, SortedSet<String>, List<GenomeWideCombinableDomains>) - Static method in class org.forester.surfacing.SurfacingUtil

writeProteinListsForAllSpecies(File, SortedMap<Species, List<Protein>>, List<GenomeWideCombinableDomains>, double, Set<String>) - Static method in class org.forester.surfacing.SurfacingUtil

writeSeqs(List<MolecularSequence>, File, SequenceWriter.SEQ_FORMAT, int) - Static method in class org.forester.io.writers.SequenceWriter

writeSeqs(List<MolecularSequence>, Writer, SequenceWriter.SEQ_FORMAT, int) - Static method in class org.forester.io.writers.SequenceWriter

writeTaxonomyLinks(Writer, String, Map<String, Integer>) - Static method in class org.forester.surfacing.SurfacingUtil

X

X - Static variable in class org.forester.ws.seqdb.UniProtTaxonomy

XML_SCHEMA_INSTANCE - Static variable in class org.forester.util.ForesterConstants

XmlElement - Class in org.forester.io.parsers.phyloxml

XmlElement(String, String, String, Attributes) - Constructor for class org.forester.io.parsers.phyloxml.XmlElement

XX_STR - Static variable in interface org.forester.go.GoXRef

Z

ZERO_DIFF - Static variable in class org.forester.util.ForesterUtil

_

__RELEASE - Static variable in class org.forester.archaeopteryx.Constants

__SNAPSHOT_RELEASE - Static variable in class org.forester.archaeopteryx.Constants

__SYNTH_LF - Static variable in class org.forester.archaeopteryx.Constants

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