Uses of Class
org.forester.phylogeny.Phylogeny

Packages that use Phylogeny

Package	Description
org.forester.analysis
org.forester.application
org.forester.archaeopteryx
org.forester.archaeopteryx.tools
org.forester.archaeopteryx.webservices
org.forester.development
org.forester.evoinference.distance
org.forester.evoinference.parsimony
org.forester.io.parsers
org.forester.io.parsers.nexus
org.forester.io.parsers.nhx
org.forester.io.parsers.phyloxml
org.forester.io.parsers.phyloxml.data
org.forester.io.parsers.tol
org.forester.io.parsers.util
org.forester.io.writers
org.forester.msa_compactor
org.forester.pccx
org.forester.phylogeny
org.forester.phylogeny.factories
org.forester.phylogeny.iterators
org.forester.rio
org.forester.sdi
org.forester.surfacing
org.forester.tools
org.forester.ws.seqdb

Uses of Phylogeny in org.forester.analysis

Methods in org.forester.analysis with parameters of type Phylogeny

Modifier and Type	Method and Description
static void	AncestralTaxonomyInference.inferTaxonomyFromDescendents(Phylogeny phy)

Constructors in org.forester.analysis with parameters of type Phylogeny

Constructor and Description
TaxonomyDataManager(MainFrameApplication mf, TreePanel treepanel, Phylogeny phy)
TaxonomyDataManager(MainFrameApplication mf, TreePanel treepanel, Phylogeny phy, boolean delete, boolean allow_simple_name)

Uses of Phylogeny in org.forester.application

Methods in org.forester.application with parameters of type Phylogeny

Modifier and Type	Method and Description
static void	support_transfer.moveBranchLengthsToBootstrap(Phylogeny p) Moves the values in the branch length field to the bootstrap field, for each PhylogenyNode of this Phylogeny.
static void	support_transfer.transferSupportValues(Phylogeny from, Phylogeny to) Modifies Phylogeny to with the support values from Phylogeny from.

Uses of Phylogeny in org.forester.archaeopteryx

Methods in org.forester.archaeopteryx that return Phylogeny

Modifier and Type	Method and Description
Phylogeny	TreePanel.getPhylogeny() Get a pointer to the phylogeny
static Phylogeny[]	AptxUtil.readPhylogeniesFromUrl(URL url, boolean phyloxml_validate_against_xsd, boolean replace_underscores, boolean internal_numbers_are_confidences, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean midpoint_reroot)

Methods in org.forester.archaeopteryx with parameters of type Phylogeny

Modifier and Type	Method and Description
void	MainPanel.addPhylogenyInNewTab(Phylogeny phy, Configuration config, String default_name, String full_path)
static MainFrame	Archaeopteryx.createApplication(Phylogeny phylogeny)
static MainFrame	Archaeopteryx.createApplication(Phylogeny[] phylogenies)
static MainFrame	Archaeopteryx.createApplication(Phylogeny[] phylogenies, String config_file_name, String title)
static MainFrame	Archaeopteryx.createApplication(Phylogeny phylogeny, Configuration config, String title)
static MainFrameApplication	MainFrameApplication.createInstance(Phylogeny[] phys, Configuration config)
static MainFrame	MainFrameApplication.createInstance(Phylogeny[] phys, Configuration config, String title, File current_dir)
static boolean	AptxUtil.isHasAtLeastNodeWithEvent(Phylogeny phy)
static boolean	AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero(Phylogeny phy) Returns true if at least one branch has a length larger than zero.
static boolean	AptxUtil.isHasAtLeastOneBranchWithSupportSD(Phylogeny phy)
static boolean	AptxUtil.isHasAtLeastOneBranchWithSupportValues(Phylogeny phy)
static boolean	AptxUtil.isHasAtLeastOneNodeWithScientificName(Phylogeny phy)
static boolean	AptxUtil.isHasAtLeastOneNodeWithSequenceAnnotation(Phylogeny phy)
void	TreePanel.setTree(Phylogeny t) Set a phylogeny tree.
static void	AptxUtil.writePhylogenyToGraphicsFile(Phylogeny phy, File outfile, int width, int height, AptxUtil.GraphicsExportType type, Configuration config)

Uses of Phylogeny in org.forester.archaeopteryx.tools

Constructors in org.forester.archaeopteryx.tools with parameters of type Phylogeny

Constructor and Description
AncestralTaxonomyInferrer(MainFrame mf, TreePanel treepanel, Phylogeny phy)
SequenceDataRetriver(MainFrameApplication mf, TreePanel treepanel, Phylogeny phy)

Uses of Phylogeny in org.forester.archaeopteryx.webservices

Methods in org.forester.archaeopteryx.webservices with parameters of type Phylogeny

Modifier and Type	Method and Description
static void	WebserviceUtil.processInstructions(PhylogeniesWebserviceClient client, Phylogeny phylogeny)

Uses of Phylogeny in org.forester.development

Methods in org.forester.development that return Phylogeny

Modifier and Type	Method and Description
static Phylogeny	DevelopmentTools.createBalancedPhylogeny(int levels, int children_per_node) Creates a completely balanced rooted phylogeny with a given number of levels and children per node.

Methods in org.forester.development with parameters of type Phylogeny

Modifier and Type	Method and Description
static void	DevelopmentTools.intervalNumberSpecies(Phylogeny t, int i) Sets the species name of the external Nodes of Phylogeny t to 1, 1+i, 2, 2+i, 3, 3+i, ....
static void	DevelopmentTools.numberSpeciesInDescOrder(Phylogeny t) Sets the species namea of the external Nodes of Phylogeny t to descending integers, ending with 1.
static void	DevelopmentTools.numberSpeciesInOrder(Phylogeny t) Sets the species namea of the external Nodes of Phylogeny t to ascending integers, starting with 1.
static void	DevelopmentTools.randomizeSpecies(int min, int max, Phylogeny t) Sets the species names of the external Nodes of Phylogeny t to a random positive integer number between (and including) min and max.

Uses of Phylogeny in org.forester.evoinference.distance

Methods in org.forester.evoinference.distance that return Phylogeny

Modifier and Type	Method and Description
Phylogeny	NeighborJoiningF.execute(BasicSymmetricalDistanceMatrix distance)
Phylogeny	NeighborJoining.execute(BasicSymmetricalDistanceMatrix distance)
Phylogeny	NeighborJoiningR.execute(BasicSymmetricalDistanceMatrix distance)

Methods in org.forester.evoinference.distance that return types with arguments of type Phylogeny

Modifier and Type	Method and Description
List<Phylogeny>	NeighborJoiningF.execute(List<BasicSymmetricalDistanceMatrix> distances_list)
List<Phylogeny>	NeighborJoining.execute(List<BasicSymmetricalDistanceMatrix> distances_list)
List<Phylogeny>	NeighborJoiningR.execute(List<BasicSymmetricalDistanceMatrix> distances_list)

Uses of Phylogeny in org.forester.evoinference.parsimony

Methods in org.forester.evoinference.parsimony with parameters of type Phylogeny

Modifier and Type	Method and Description
void	DolloParsimony.execute(Phylogeny p, CharacterStateMatrix<CharacterStateMatrix.BinaryStates> external_node_states_matrix)
void	SankoffParsimony.execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix)
void	FitchParsimony.execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix)
void	FitchParsimony.execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix, boolean verbose)

Uses of Phylogeny in org.forester.io.parsers

Methods in org.forester.io.parsers that return Phylogeny

Modifier and Type	Method and Description
Phylogeny	IteratingPhylogenyParser.next()
Phylogeny[]	PhylogenyParser.parse()

Uses of Phylogeny in org.forester.io.parsers.nexus

Methods in org.forester.io.parsers.nexus that return Phylogeny

Modifier and Type	Method and Description
Phylogeny	NexusPhylogeniesParser.next()
Phylogeny[]	NexusPhylogeniesParser.parse()

Uses of Phylogeny in org.forester.io.parsers.nhx

Methods in org.forester.io.parsers.nhx that return Phylogeny

Modifier and Type	Method and Description
Phylogeny	NHXParser.next()
Phylogeny[]	NHXParser.parse()
static Phylogeny[]	NHXParser.parse(Object nhx_source)

Uses of Phylogeny in org.forester.io.parsers.phyloxml

Methods in org.forester.io.parsers.phyloxml that return Phylogeny

Modifier and Type	Method and Description
Phylogeny[]	PhyloXmlParser.parse()

Methods in org.forester.io.parsers.phyloxml with parameters of type Phylogeny

Modifier and Type	Method and Description
static Map<String,Sequence>	PhyloXmlHandler.getSequenceMapByIdForPhylogeny(Phylogeny ph)

Uses of Phylogeny in org.forester.io.parsers.phyloxml.data

Methods in org.forester.io.parsers.phyloxml.data with parameters of type Phylogeny

Modifier and Type	Method and Description
static PhylogenyDataPhyloXmlParser	SequenceRelationParser.getInstance(Phylogeny phylogeny)

Uses of Phylogeny in org.forester.io.parsers.tol

Methods in org.forester.io.parsers.tol that return Phylogeny

Modifier and Type	Method and Description
Phylogeny[]	TolParser.parse()

Uses of Phylogeny in org.forester.io.parsers.util

Methods in org.forester.io.parsers.util that return Phylogeny

Modifier and Type	Method and Description
static Phylogeny[]	ParserUtils.readPhylogenies(File file)
static Phylogeny[]	ParserUtils.readPhylogenies(String file_name)

Uses of Phylogeny in org.forester.io.writers

Methods in org.forester.io.writers with parameters of type Phylogeny

Modifier and Type	Method and Description
void	PhylogenyWriter.toNewHampshire(Phylogeny[] trees, boolean write_distance_to_parent, File out_file, String separator)
StringBuffer	PhylogenyWriter.toNewHampshire(Phylogeny tree, boolean nh_write_distance_to_parent)
void	PhylogenyWriter.toNewHampshire(Phylogeny tree, boolean write_distance_to_parent, File out_file)
StringBuffer	PhylogenyWriter.toNewHampshire(Phylogeny tree, boolean nh_write_distance_to_parent, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
void	PhylogenyWriter.toNewHampshire(Phylogeny tree, boolean write_distance_to_parent, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs, File out_file)
StringBuffer	PhylogenyWriter.toNewHampshireX(Phylogeny tree)
void	PhylogenyWriter.toNewHampshireX(Phylogeny[] trees, File out_file, String separator)
void	PhylogenyWriter.toNewHampshireX(Phylogeny tree, File out_file)
void	PhylogenyWriter.toNexus(File out_file, Phylogeny tree, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
StringBuffer	PhylogenyWriter.toNexus(Phylogeny tree, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
void	PhylogenyWriter.toPhyloXML(File out_file, Phylogeny tree, int phyloxml_level)
void	PhylogenyWriter.toPhyloXML(Phylogeny[] trees, int phyloxml_level, File out_file, String separator)
StringBuffer	PhylogenyWriter.toPhyloXML(Phylogeny tree, int phyloxml_level)
void	PhylogenyWriter.toPhyloXML(Phylogeny phy, int phyloxml_level, File out_file)
void	PhylogenyWriter.toPhyloXML(Writer writer, Phylogeny[] trees, int phyloxml_level, String separator)
void	PhylogenyWriter.toPhyloXML(Writer writer, Phylogeny tree, int phyloxml_level)
static void	PhylogenyWriter.writeNexusTaxaBlock(Writer writer, Phylogeny tree)

Method parameters in org.forester.io.writers with type arguments of type Phylogeny

Modifier and Type	Method and Description
void	PhylogenyWriter.toNewHampshire(List<Phylogeny> trees, boolean write_distance_to_parent, File out_file, String separator)
void	PhylogenyWriter.toNewHampshireX(List<Phylogeny> trees, File out_file, String separator)
void	PhylogenyWriter.toPhyloXML(File out_file, List<Phylogeny> trees, int phyloxml_level, String separator)
void	PhylogenyWriter.toPhyloXML(Writer writer, List<Phylogeny> trees, int phyloxml_level, String separator)
static void	PhylogenyWriter.writeNexusTreesBlock(Writer writer, List<Phylogeny> trees, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)

Uses of Phylogeny in org.forester.msa_compactor

Methods in org.forester.msa_compactor that return Phylogeny

Modifier and Type	Method and Description
Phylogeny	MsaCompactor.calcTree()

Methods in org.forester.msa_compactor with parameters of type Phylogeny

Modifier and Type	Method and Description
void	MsaCompactor.displayTree(Phylogeny phy)

Uses of Phylogeny in org.forester.pccx

Methods in org.forester.pccx with parameters of type Phylogeny

Modifier and Type	Method and Description
void	ScoringMethodForExternalNode.calculateScoreForExternalNode(SortedMap<PhylogenyNode,Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options) This calculates the coverage score for one external node.
void	BranchCountingBasedScoringMethod.calculateScoreForExternalNode(SortedMap<PhylogenyNode,Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options)
double	BranchLengthBasedScoringMethod.getNormalizationFactor(Phylogeny phylogeny)
double	LogBranchLengthBasedScoringMethod.getNormalizationFactor(Phylogeny phylogeny)
double	ScoringMethodForExternalNode.getNormalizationFactor(Phylogeny phylogeny) This calculates a normalization factor, so that a normalized score of 1.0 means complete coverage.
double	BranchCountingBasedScoringMethod.getNormalizationFactor(Phylogeny phylogeny)

Method parameters in org.forester.pccx with type arguments of type Phylogeny

Modifier and Type	Method and Description
Coverage	CoverageCalculator.calculateCoverage(List<Phylogeny> phylogenies, List<String> names, boolean annotate_phylogenies)
Coverage	ExternalNodeBasedCoverageMethod.calculateCoverage(List<Phylogeny> phylogenies, List<String> names, CoverageCalculationOptions options, boolean annotate_phylogenies)
Coverage	CoverageCalculationMethod.calculateCoverage(List<Phylogeny> phylogenies, List<String> names, CoverageCalculationOptions options, boolean annotate_phylogenies)
List<String>	CoverageExtender.find(List<Phylogeny> phylogenies, List<String> already_covered, int number_names_to_find, CoverageCalculationOptions options, PrintStream out)
List<String>	BasicExternalNodeBasedCoverageExtender.find(List<Phylogeny> phylogenies, List<String> already_covered, int number_names_to_find, CoverageCalculationOptions options, PrintStream out)

Uses of Phylogeny in org.forester.phylogeny

Methods in org.forester.phylogeny that return Phylogeny

Modifier and Type	Method and Description
Phylogeny	Phylogeny.copy() Returns a deep copy of this Phylogeny.
Phylogeny	Phylogeny.copy(PhylogenyNode source) Returns a deep copy of this Phylogeny.
Phylogeny	Phylogeny.copyShallow() Returns a shallow copy of this Phylogeny.
Phylogeny	Phylogeny.copyShallow(PhylogenyNode source)
static Phylogeny	Phylogeny.createInstanceFromNhxString(String nhx)
static Phylogeny[]	PhylogenyMethods.readPhylogenies(PhylogenyParser parser, File file)
static Phylogeny[]	PhylogenyMethods.readPhylogenies(PhylogenyParser parser, List<File> files)

Methods in org.forester.phylogeny with parameters of type Phylogeny

Modifier and Type	Method and Description
static void	PhylogenyMethods.addMolecularSeqsToTree(Phylogeny phy, Msa msa)
static DescriptiveStatistics	PhylogenyMethods.calculateBranchLengthStatistics(Phylogeny phy)
static List<DescriptiveStatistics>	PhylogenyMethods.calculateConfidenceStatistics(Phylogeny phy)
static int	PhylogenyMethods.calculateMaxDepth(Phylogeny phy)
static double	PhylogenyMethods.calculateMaxDistanceToRoot(Phylogeny phy)
static PhylogenyNode	PhylogenyMethods.calculateNodeWithMaxDistanceToRoot(Phylogeny phy)
static DescriptiveStatistics	PhylogenyMethods.calculateNumberOfDescendantsPerNodeStatistics(Phylogeny phy)
static int	PhylogenyMethods.countNumberOfOneDescendantNodes(Phylogeny phy)
static int	PhylogenyMethods.countNumberOfPolytomies(Phylogeny phy)
static HashMap<String,PhylogenyNode>	PhylogenyMethods.createNameToExtNodeMap(Phylogeny phy)
static void	PhylogenyMethods.deleteExternalNodesNegativeSelection(Set<Long> to_delete, Phylogeny phy)
static void	PhylogenyMethods.deleteExternalNodesNegativeSelection(String[] node_names_to_delete, Phylogeny p)
static List<String>	PhylogenyMethods.deleteExternalNodesPositiveSelection(String[] node_names_to_keep, Phylogeny p)
static void	PhylogenyMethods.deleteExternalNodesPositiveSelectionT(List<Taxonomy> species_to_keep, Phylogeny phy)
static void	PhylogenyMethods.deleteInternalNodesWithOnlyOneDescendent(Phylogeny phy)
static void	PhylogenyMethods.deleteNonOrthologousExternalNodes(Phylogeny phy, PhylogenyNode n)
static List<List<PhylogenyNode>>	PhylogenyMethods.divideIntoSubTrees(Phylogeny phy, double min_distance_to_root)
static boolean	PhylogenyMethods.extractFastaInformation(Phylogeny phy)
static double	PhylogenyMethods.getMaximumConfidenceValue(Phylogeny phy) Returns the largest confidence value found on phy.
static int	PhylogenyMethods.getMinimumDescendentsPerInternalNodes(Phylogeny phy)
static boolean	PhylogenyMethods.isInternalNamesLookLikeConfidences(Phylogeny phy)
static void	PhylogenyMethods.midpointRoot(Phylogeny phylogeny)
static void	PhylogenyMethods.normalizeBootstrapValues(Phylogeny phylogeny, double max_bootstrap_value, double max_normalized_value)
static List<PhylogenyNode>	PhylogenyMethods.obtainAllNodesAsList(Phylogeny phy)
static void	PhylogenyMethods.postorderBranchColorAveragingExternalNodeBased(Phylogeny p)
static void	PhylogenyMethods.preOrderReId(Phylogeny phy)
static void	PhylogenyMethods.removeNode(PhylogenyNode remove_me, Phylogeny phylogeny)
static List<PhylogenyNode>	PhylogenyMethods.searchData(String query, Phylogeny phy, boolean case_sensitive, boolean partial, boolean regex, boolean search_domains, double domains_confidence_threshold)
static List<PhylogenyNode>	PhylogenyMethods.searchDataLogicalAnd(String[] queries, Phylogeny phy, boolean case_sensitive, boolean partial, boolean search_domains, double domains_confidence_threshold)
static void	PhylogenyMethods.setAllIndicatorsToZero(Phylogeny phy)
static List<PhylogenyNode>	PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes(Phylogeny reference, Phylogeny to_be_stripped) Removes from Phylogeny to_be_stripped all external Nodes which are associated with a species NOT found in Phylogeny reference.
static void	PhylogenyMethods.transferInternalNamesToBootstrapSupport(Phylogeny phy)
static void	PhylogenyMethods.transferInternalNodeNamesToConfidence(Phylogeny phy, String confidence_type)
static void	PhylogenyMethods.transferNodeNameToField(Phylogeny phy, PhylogenyMethods.PhylogenyNodeField field, boolean external_only)

Uses of Phylogeny in org.forester.phylogeny.factories

Methods in org.forester.phylogeny.factories that return Phylogeny

Modifier and Type	Method and Description
Phylogeny[]	PhylogenyFactory.create(Object source, Object creator) This must create a Phylogeny from source (e.g.
Phylogeny[]	ParserBasedPhylogenyFactory.create(Object source, Object parser)
Phylogeny[]	ParserBasedPhylogenyFactory.create(Object source, Object parser, String schema_location)

Uses of Phylogeny in org.forester.phylogeny.iterators

Constructors in org.forester.phylogeny.iterators with parameters of type Phylogeny

Constructor and Description
ExternalForwardIterator(Phylogeny phylogeny) Constructor for ExternalForwardIterator.
LevelOrderTreeIterator(Phylogeny phylogeny) Creates a new LevelOrderTreeIterator for iterating over all the nodes of Phylogeny phylogeny
PostorderTreeIterator(Phylogeny tree)
PreorderTreeIterator(Phylogeny tree)

Uses of Phylogeny in org.forester.rio

Methods in org.forester.rio that return Phylogeny

Modifier and Type	Method and Description
Phylogeny[]	RIO.getAnalyzedGeneTrees()
Phylogeny	RIO.getMinDuplicationsGeneTree()
Phylogeny	RIO.getSpeciesTree()

Methods in org.forester.rio with parameters of type Phylogeny

Modifier and Type	Method and Description
static IntMatrix	RIO.calculateOrthologTable(Phylogeny[] analyzed_gene_trees, boolean sort)
static RIO	RIO.executeAnalysis(File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(IteratingPhylogenyParser p, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree)
static RIO	RIO.executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree)
static RIO	RIO.executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO	RIO.executeAnalysis(Phylogeny[] gene_trees, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)

Uses of Phylogeny in org.forester.sdi

Methods in org.forester.sdi that return Phylogeny

Modifier and Type	Method and Description
Phylogeny	SDI.getGeneTree() Returns the gene tree.
Phylogeny	GSDIR.getMinDuplicationsSumGeneTree()
Phylogeny	SDI.getSpeciesTree() Returns the species tree.
Phylogeny[]	SDIR.infer(Phylogeny gene_tree, Phylogeny species_tree, boolean minimize_mapping_cost, boolean minimize_sum_of_dup, boolean minimize_height, boolean return_trees, int max_trees_to_return) Infers gene duplications on a possibly unrooted gene Phylogeny gene_tree.
static Phylogeny	SDIutil.parseSpeciesTree(Phylogeny gene_tree, File species_tree_file, boolean replace_undescores_in_nhx_trees, boolean ignore_quotes_in_nhx_trees, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees)

Methods in org.forester.sdi with parameters of type Phylogeny

Modifier and Type	Method and Description
static SDIutil.TaxonomyComparisonBase	SDIutil.determineTaxonomyComparisonBase(Phylogeny gene_tree)
static List<PhylogenyBranch>	SDIR.getBranchesInPreorder(Phylogeny t)
Phylogeny[]	SDIR.infer(Phylogeny gene_tree, Phylogeny species_tree, boolean minimize_mapping_cost, boolean minimize_sum_of_dup, boolean minimize_height, boolean return_trees, int max_trees_to_return) Infers gene duplications on a possibly unrooted gene Phylogeny gene_tree.
static Phylogeny	SDIutil.parseSpeciesTree(Phylogeny gene_tree, File species_tree_file, boolean replace_undescores_in_nhx_trees, boolean ignore_quotes_in_nhx_trees, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees)

Method parameters in org.forester.sdi with type arguments of type Phylogeny

Modifier and Type	Method and Description
static List<Integer>	GSDIR.getIndexesOfShortestTree(List<Phylogeny> assigned_trees)

Constructors in org.forester.sdi with parameters of type Phylogeny

Constructor and Description
GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model, boolean strip_gene_tree, boolean strip_species_tree)
GSDI(Phylogeny gene_tree, Phylogeny species_tree, boolean most_parsimonious_duplication_model, boolean strip_gene_tree, boolean strip_species_tree, boolean transfer_taxonomy)
GSDIR(Phylogeny gene_tree, Phylogeny species_tree, boolean strip_gene_tree, boolean strip_species_tree, boolean transfer_taxonomy)
SDI(Phylogeny gene_tree, Phylogeny species_tree) Constructor which sets the gene tree and the species tree to be compared.

Uses of Phylogeny in org.forester.surfacing

Methods in org.forester.surfacing that return Phylogeny

Modifier and Type	Method and Description
static Phylogeny	SurfacingUtil.createNjTreeBasedOnMatrixToFile(File nj_tree_outfile, DistanceMatrix distance)
static Phylogeny[]	SurfacingUtil.obtainAndPreProcessIntrees(File[] intree_files, int number_of_genomes, String[][] input_file_properties)
static Phylogeny	SurfacingUtil.obtainFirstIntree(File intree_file)

Methods in org.forester.surfacing with parameters of type Phylogeny

Modifier and Type	Method and Description
static DomainParsimonyCalculator	DomainParsimonyCalculator.createInstance(Phylogeny phylogeny)
static DomainParsimonyCalculator	DomainParsimonyCalculator.createInstance(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list)
static DomainParsimonyCalculator	DomainParsimonyCalculator.createInstance(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list, Map<String,Set<String>> domain_id_to_secondary_features_map)
static Map<String,Integer>	SurfacingUtil.createTaxCodeToIdMap(Phylogeny phy)
static void	SurfacingUtil.executeParsimonyAnalysis(long random_number_seed_for_fitch_parsimony, boolean radomize_fitch_parsimony, String outfile_name, DomainParsimonyCalculator domain_parsimony, Phylogeny phylogeny, Map<String,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, String parameters_str, Map<String,Set<String>>[] domain_id_to_secondary_features_maps, SortedSet<String> positive_filter, boolean output_binary_domain_combinations_for_graphs, List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch, List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch, BinaryDomainCombination.DomainCombinationType dc_type, Map<String,DescriptiveStatistics> protein_length_stats_by_dc, Map<String,DescriptiveStatistics> domain_number_stats_by_dc, Map<String,DescriptiveStatistics> domain_length_stats_by_domain, Map<String,Integer> tax_code_to_id_map, boolean write_to_nexus, boolean use_last_in_fitch_parsimony, boolean perform_dc_fich)
static void	SurfacingUtil.executeParsimonyAnalysisForSecondaryFeatures(String outfile_name, DomainParsimonyCalculator secondary_features_parsimony, Phylogeny phylogeny, String parameters_str, Map<Species,MappingResults> mapping_results_map, boolean use_last_in_fitch_parsimony)
static int	SurfacingUtil.getNumberOfNodesLackingName(Phylogeny p, StringBuilder names)
static String	SurfacingUtil.obtainHexColorStringDependingOnTaxonomyGroup(String tax_code, Phylogeny phy)
static String	SurfacingUtil.obtainTaxonomyGroup(String tax_code, Phylogeny species_tree)
void	PairwiseGenomeComparator.performPairwiseComparisons(StringBuilder html_desc, boolean sort_by_species_count_first, DomainSimilarityCalculator.Detailedness detailedness, boolean ignore_domains_without_combs_in_all_spec, boolean ignore_domains_specific_to_one_species, DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field, DomainSimilarity.PRINT_OPTION domain_similarity_print_option, DomainSimilarity.DomainSimilarityScoring scoring, Map<String,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, Species[] species, int number_of_genomes, List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains, PairwiseDomainSimilarityCalculator pw_calc, String automated_pairwise_comparison_suffix, boolean verbose, String automated_pairwise_comparison_prefix, String command_line_prg_name, File out_dir, boolean write_pairwise_comparisons, Map<String,Integer> tax_code_to_id_map, boolean calc_similarity_scores, Phylogeny phy)
static void	SurfacingUtil.preparePhylogeny(Phylogeny p, DomainParsimonyCalculator domain_parsimony, String date_time, String method, String name, String parameters_str)
static void	SurfacingUtil.preparePhylogenyForParsimonyAnalyses(Phylogeny intree, String[][] input_file_properties)
StringBuffer	DomainSimilarity.toStringBuffer(DomainSimilarity.PRINT_OPTION print_option, Map<String,Integer> tax_code_to_id_map, Phylogeny phy)
static void	SurfacingUtil.writeAllDomainsChangedOnAllSubtrees(Phylogeny p, boolean get_gains, String outdir, String suffix_for_filename)
static void	SurfacingUtil.writeDomainSimilaritiesToFile(StringBuilder html_desc, StringBuilder html_title, Writer simple_tab_writer, Writer single_writer, Map<Character,Writer> split_writers, SortedSet<DomainSimilarity> similarities, boolean treat_as_binary, List<Species> species_order, DomainSimilarity.PRINT_OPTION print_option, DomainSimilarity.DomainSimilarityScoring scoring, boolean verbose, Map<String,Integer> tax_code_to_id_map, Phylogeny phy, Set<String> pos_filter_doms)
static void	SurfacingUtil.writePhylogenyToFile(Phylogeny phylogeny, String filename)

Uses of Phylogeny in org.forester.tools

Methods in org.forester.tools that return types with arguments of type Phylogeny

Modifier and Type	Method and Description
static List<Phylogeny>	SupportCount.count(Phylogeny phylogeny, Phylogeny[] evaluator_phylogenies, boolean strip_evaluator_phylogenies, double similarity_threshold, boolean verbose) This counts the support of topology phylogeny by the topologies in phylogenies.

Methods in org.forester.tools with parameters of type Phylogeny

Modifier and Type	Method and Description
static double	SupportCount.compare(Phylogeny phylogeny, Phylogeny evaluator_phylogeny, boolean strip_evaluator_phylogeny, boolean update_support_in_phylogeny, boolean re_root)
static void	SupportCount.count(Phylogeny phylogeny, Phylogeny[] evaluator_phylogenies, boolean strip_evaluator_phylogenies, boolean verbose)
static void	SupportCount.count(Phylogeny phylogeny, Phylogeny[] evaluator_phylogenies, boolean strip_evaluator_phylogenies, boolean verbose)
static List<Phylogeny>	SupportCount.count(Phylogeny phylogeny, Phylogeny[] evaluator_phylogenies, boolean strip_evaluator_phylogenies, double similarity_threshold, boolean verbose) This counts the support of topology phylogeny by the topologies in phylogenies.
static List<Phylogeny>	SupportCount.count(Phylogeny phylogeny, Phylogeny[] evaluator_phylogenies, boolean strip_evaluator_phylogenies, double similarity_threshold, boolean verbose) This counts the support of topology phylogeny by the topologies in phylogenies.
static void	PhylogenyDecorator.decorate(Phylogeny phylogeny, Map<String,Map<String,String>> map, boolean picky)
static String	PhylogenyDecorator.decorate(Phylogeny phylogeny, Map<String,String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose)
static String	PhylogenyDecorator.decorate(Phylogeny phylogeny, Map<String,String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, Map<String,String> intermediate_map, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose)
static void	ConfidenceAssessor.evaluate(String confidence_type, Phylogeny[] evaluators, Phylogeny target, boolean strict, double value)
static void	ConfidenceAssessor.evaluate(String confidence_type, Phylogeny[] evaluators, Phylogeny target, boolean strict, double value)
static void	ConfidenceAssessor.evaluate(String confidence_type, Phylogeny[] evaluators, Phylogeny target, boolean strict, double value, int first, int last)
static void	ConfidenceAssessor.evaluate(String confidence_type, Phylogeny[] evaluators, Phylogeny target, boolean strict, double value, int first, int last)

Constructors in org.forester.tools with parameters of type Phylogeny

Constructor and Description
TreeSplitMatrix(Phylogeny evaluator, boolean strict, Phylogeny target)
TreeSplitMatrix(Phylogeny evaluator, boolean strict, Set<PhylogenyNode> target_external_nodes) 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.

Uses of Phylogeny in org.forester.ws.seqdb

Methods in org.forester.ws.seqdb with parameters of type Phylogeny

Modifier and Type	Method and Description
static SortedSet<String>	SequenceDbWsTools.obtainSeqInformation(Phylogeny phy, boolean ext_nodes_only, boolean allow_to_set_taxonomic_data, int lines_to_return)