Constant Field Values

Contents

• org.forester.*

org.forester.*

org.forester.application.gsdi

Modifier and Type	Constant Field	Value
public static final boolean	REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE	true

org.forester.application.surfacing

Modifier and Type	Constant Field	Value
public static final String	ALL_PFAMS_ENCOUNTERED_SUFFIX	"_all_encountered_pfams"
public static final String	ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX	"_all_encountered_pfams_with_go_annotation"
public static final String	ALL_PFAMS_GAINED_AS_DC_SUFFIX	"_all_pfams_gained_as_dc"
public static final String	ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX	"_all_pfams_gained_as_domains"
public static final String	ALL_PFAMS_LOST_AS_DC_SUFFIX	"_all_pfams_lost_as_dc"
public static final String	ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX	"_all_pfams_lost_as_domains"
public static final String	BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES	"PER_NODE_EVENTS"
public static final String	BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES	"PER_SUBTREE_EVENTS"
public static final String	BDC_PRESENT_NEXUS	"_dc.nex"
public static final String	BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO	"_dc_dollo.xml"
public static final String	BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH	"_dc_fitch.xml"
public static final String	BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED	"_dc_MAPPED_secondary_features_fitch.xml"
public static final String	D_PROMISCUITY_FILE_SUFFIX	"_domain_promiscuities"
public static final String	DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX	".dcc"
public static final String	DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION	"dcc"
public static final String	DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS	"graph_analysis_out"
public static final String	DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS	"_dc.dot"
public static final String	DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO	"_d_dollo.xml"
public static final String	DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH	"_d_fitch.xml"
public static final String	DOMAINS_PRESENT_NEXUS	"_dom.nex"
public static final String	ENCOUNTERED_PFAMS_SUMMARY_SUFFIX	"_encountered_pfams_summary"
public static final String	INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX	"_indep_dc_gains_fitch_counts_MAPPED.txt"
public static final String	INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX	"_indep_dc_gains_fitch_counts.txt"
public static final String	INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX	"_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt"
public static final String	INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX	"_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt"
public static final String	INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX	"_indep_dc_gains_fitch_lists_for_go_mapping.txt"
public static final String	INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX	"_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt"
public static final String	INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX	"_indep_dc_gains_fitch_lists_MAPPED.txt"
public static final String	INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX	"_indep_dc_gains_fitch_lists.txt"
public static final int	MAX_ALLOWED_OVERLAP_DEFAULT	-1
public static final String	NEXUS_EXTERNAL_DOMAIN_COMBINATIONS	"_dc.nex"
public static final String	NEXUS_EXTERNAL_DOMAINS	"_dom.nex"
public static final String	NEXUS_SECONDARY_FEATURES	"_secondary_features.nex"
public static final String	PAIRWISE_DOMAIN_COMPARISONS_PREFIX	"pwc_"
public static final String	PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES	"_dollo_goid_d"
public static final String	PARSIMONY_OUTPUT_DOLLO_GAINS_D	"_dollo_gains_d"
public static final String	PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D	"_dollo_gains_d.html"
public static final String	PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES	"_dollo_gains_secondary_features"
public static final String	PARSIMONY_OUTPUT_DOLLO_LOSSES_D	"_dollo_losses_d"
public static final String	PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D	"_dollo_losses_d.html"
public static final String	PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES	"_dollo_losses_secondary_features"
public static final String	PARSIMONY_OUTPUT_DOLLO_PRESENT_D	"_dollo_present_d"
public static final String	PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D	"_dollo_present_d.html"
public static final String	PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES	"_dollo_present_secondary_features"
public static final String	PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES	"_fitch_goid_dc"
public static final String	PARSIMONY_OUTPUT_FITCH_GAINS_BC	"_fitch_gains_dc"
public static final String	PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC	"_fitch_gains_dc.html"
public static final String	PARSIMONY_OUTPUT_FITCH_LOSSES_BC	"_fitch_losses_dc"
public static final String	PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC	"_fitch_losses_dc.html"
public static final String	PARSIMONY_OUTPUT_FITCH_PRESENT_BC	"_fitch_present_dc"
public static final String	PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS	"_fitch_present_dc.dot"
public static final String	PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC	"_fitch_present_dc.html"
public static final String	PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS	"_dollo_glc_dc"
public static final String	PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS	"_dollo_glc_d"
public static final String	PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES	"_dollo_glc_secondary_features"
public static final String	PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS	"_fitch_glc_dc"
public static final String	PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS	"_fitch_glc_d"
public static final String	PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS	"_dollo_gl_dc"
public static final String	PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS	"_dollo_gl_d"
public static final String	PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES	"_dollo_gl_secondary_features"
public static final String	PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS	"_fitch_gl_dc"
public static final String	PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS	"_fitch_gl_d"
public static final String	PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX	"_plus_minus_go_ids_all.txt"
public static final double	PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT	1.0
public static final int	PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT	0
public static final String	PLUS_MINUS_ANALYSIS_OPTION	"plus_minus"
public static final String	PLUS_MINUS_DC_SUFFIX_HTML	"_plus_minus_dc.html"
public static final String	PLUS_MINUS_DOM_SUFFIX	"_plus_minus_dom.txt"
public static final String	PLUS_MINUS_DOM_SUFFIX_HTML	"_plus_minus_dom.html"
public static final String	PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX	"_plus_minus_go_ids_passing.txt"
public static final String	PRG_NAME	"surfacing"
public static final String	SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO	"_secondary_features_dollo.xml"
public static final String	SEQ_EXTRACT_SUFFIX	".prot"
public static final boolean	VERBOSE	false

org.forester.applications.aaa

Modifier and Type	Constant Field	Value
public static final int	MIN_LENGTH	85

org.forester.applications.get_shared_chars

Modifier and Type	Constant Field	Value
public static final boolean	DEBUG	true

org.forester.archaeopteryx.ArchaeopteryxA

Modifier and Type	Constant Field	Value
public static final String	NAME	"ArchaeopteryxA"

org.forester.archaeopteryx.Constants

Modifier and Type	Constant Field	Value
public static final boolean	__RELEASE	false
public static final boolean	__SNAPSHOT_RELEASE	false
public static final boolean	__SYNTH_LF	false
public static final boolean	ALLOW_DDBJ_BLAST	false
public static final boolean	NH_PARSING_IGNORE_QUOTES_DEFAULT	false
public static final String	PRG_NAME	"Archaeopteryx"

org.forester.archaeopteryx.FontChooser

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	62256323L

org.forester.archaeopteryx.TreeColorSet

Modifier and Type	Constant Field	Value
public static final String	ANNOTATION	"Annotation"
public static final String	BACKGROUND	"Background"
public static final String	BACKGROUND_GRADIENT_BOTTOM	"Background Gradient Bottom"
public static final String	BINARY_DOMAIN_COMBINATIONS	"Binary Domain Combinations"
public static final String	BRANCH	"Branch"
public static final String	BRANCH_LENGTH	"Branch Length"
public static final String	COLLAPSED	"Collapsed"
public static final String	CONFIDENCE	"Confidence"
public static final String	DOMAIN_BASE	"Domain Base"
public static final String	DOMAIN_LABEL	"Domain Label"
public static final String	DUPLICATION	"Duplication"
public static final String	DUPLICATION_OR_SPECATION	"Duplication or Specation"
public static final String	MATCHING_NODES_A	"Matching A"
public static final String	MATCHING_NODES_A_AND_B	"Matching A and B"
public static final String	MATCHING_NODES_B	"Matching B"
public static final String	NODE_BOX	"Node Box"
public static final String	OVERVIEW	"Overview"
public static final String	SEQUENCE	"Sequence"
public static final String	SPECIATION	"Speciation"
public static final String	TAXONOMY	"Taxonomy"

org.forester.archaeopteryx.TreePanel

Modifier and Type	Constant Field	Value
public static final boolean	SPECIAL_DOMAIN_COLORING	true

org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_WIDTH	400

org.forester.archaeopteryx.phylogeny.data.RenderableVector

Modifier and Type	Constant Field	Value
public static final int	VECTOR_DEFAULT_WIDTH	120

org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions

Modifier and Type	Constant Field	Value
public static final long	RANDOM_NUMBER_SEED_DEFAULT	42L

org.forester.archaeopteryx.tools.PhylogeneticInferrer

Modifier and Type	Constant Field	Value
public static final String	MSA_FILE_SUFFIX	".aln"
public static final String	PWD_FILE_SUFFIX	".pwd"

org.forester.archaeopteryx.tools.SequenceDataRetriver

Modifier and Type	Constant Field	Value
public static final boolean	DEBUG	false

org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient

Modifier and Type	Constant Field	Value
public static final String	QUERY_PLACEHOLDER	"__query__"

org.forester.archaeopteryx.webservices.WebserviceUtil

Modifier and Type	Constant Field	Value
public static final String	PFAM_INST	"pfam"
public static final String	PFAM_NAME	"Pfam"
public static final String	PFAM_SERVER	"http://pfam.xfam.org"
public static final String	TOL_NAME	"Tree of Life (ToL)"
public static final String	TOL_URL_BASE	"http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id="
public static final String	TOL_WEBSERVER	"http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id=__query__"
public static final String	TREE_BASE_DESC	"This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment."
public static final String	TREE_BASE_INST	"treebase"
public static final String	TREE_BASE_NAME	"TreeBASE"
public static final String	TREE_FAM_INST	"tree_fam"
public static final String	TREE_FAM_NAME	"TreeFam"
public static final String	TREE_FAM_URL_BASE	"http://www.treefam.org/family/TF"
public static final String	TREEBASE_PHYLOWS_STUDY_URL_BASE	"http://purl.org/phylo/treebase/phylows/study/TB2:S"
public static final String	TREEBASE_PHYLOWS_TREE_URL_BASE	"http://purl.org/phylo/treebase/phylows/tree/TB2:Tr"

org.forester.evoinference.distance.PairwiseDistanceCalculator

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA	10.0

org.forester.evoinference.distance.Sarray

Modifier and Type	Constant Field	Value
public static final int	FACTOR	1000000

org.forester.evoinference.distance.Sset

Modifier and Type	Constant Field	Value
public static final int	FACTOR	1000000

org.forester.go.GoNameSpace

Modifier and Type	Constant Field	Value
public static final String	BIOLOGICAL_PROCESS_STR	"biological_process"
public static final String	CELLULAR_COMPONENT_STR	"cellular_component"
public static final String	MOLECULAR_FUNCTION_STR	"molecular_function"
public static final String	UNASSIGNED_STR	"unassigned"

org.forester.go.GoRelationship

Modifier and Type	Constant Field	Value
public static final String	HAS_PART_STR	"has_part"
public static final String	NEGATIVELY_REGULATES_STR	"negatively_regulates"
public static final String	OCCURS_IN_STR	"occurs_in"
public static final String	PART_OF_STR	"part_of"
public static final String	POSITIVELY_REGULATES_STR	"positively_regulates"
public static final String	REGULATES_STR	"regulates"

org.forester.go.GoSubset

Modifier and Type	Constant Field	Value
public static final String	GOSLIM_ASPERGILLUS_STR	"goslim_aspergillus"
public static final String	GOSLIM_CANDIDA_STR	"goslim_candida"
public static final String	GOSLIM_GENERIC_STR	"goslim_generic"
public static final String	GOSLIM_GOA_STR	"goslim_goa"
public static final String	GOSLIM_PIR_STR	"goslim_pir"
public static final String	GOSLIM_PLANT_STR	"goslim_plant"
public static final String	GOSLIM_POMBE_STR	"goslim_pombe"
public static final String	GOSLIM_YEAST_STR	"goslim_yeast"
public static final String	GOSUBSET_PROK_STR	"gosubset_prok"

org.forester.go.GoXRef

Modifier and Type	Constant Field	Value
public static final String	ARACYC_STR	"AraCyc"
public static final String	CORUM_STR	"CORUM"
public static final String	EC_STR	"EC"
public static final String	GOC_STR	"GOC"
public static final String	IMG_STR	"IMG"
public static final String	KEGG_STR	"KEGG"
public static final String	META_CYC_STR	"MetaCyc"
public static final String	NIF_SUBCELLULAR_STR	"NIF_Subcellular"
public static final String	PMID_STR	"PMID"
public static final String	PO_STR	"PO"
public static final String	REACTOME_STR	"Reactome"
public static final String	RESID_STR	"RESID"
public static final String	RHEA_STR	"RHEA"
public static final String	SABIO_RK_STR	"SABIO-RK"
public static final String	TC_STR	"TC"
public static final String	UM_BBD_ENZYME_ID_STR	"UM-BBD_enzymeID"
public static final String	UM_BBD_PATHWAY_ID_STR	"UM-BBD_pathwayID"
public static final String	UM_BBD_REACTIONID_STR	"UM-BBD_reactionID"
public static final String	UNIPATHWAY_STR	"UniPathway"
public static final String	WIKIPEDIA_STR	"Wikipedia"
public static final String	XX_STR	"XX"

org.forester.io.parsers.nexus.NexusConstants

Modifier and Type	Constant Field	Value
public static final String	BEGIN_CHARACTERS	"Begin Characters;"
public static final String	BEGIN_DATA	"Begin Data;"
public static final String	BEGIN_TAXA	"Begin Taxa;"
public static final String	BEGIN_TREES	"Begin Trees;"
public static final String	CHARSTATELABELS	"CharStateLabels"
public static final String	DATATYPE	"DataType"
public static final String	DIMENSIONS	"Dimensions"
public static final String	END	"End;"
public static final String	FORMAT	"Format"
public static final String	MATRIX	"Matrix"
public static final String	NCHAR	"NChar"
public static final String	NEXUS	"#NEXUS"
public static final String	NTAX	"NTax"
public static final String	STANDARD	"Standard"
public static final String	SYMBOLS	"Symbols"
public static final String	TAXLABELS	"TaxLabels"
public static final String	TRANSLATE	"Translate"
public static final String	TREE	"Tree"
public static final String	UTREE	"UTREE"

org.forester.io.parsers.nhx.NHXParser

Modifier and Type	Constant Field	Value
public static final boolean	REPLACE_UNDERSCORES_DEFAULT	false

org.forester.io.parsers.nhx.NHXtags

Modifier and Type	Constant Field	Value
public static final String	DOMAIN_STRUCTURE	"DS="
public static final String	GENE_NAME	"GN="
public static final String	IS_DUPLICATION	"D="
public static final String	SEQUENCE_ACCESSION	"AC="
public static final String	SPECIES_NAME	"S="
public static final String	SUPPORT	"B="
public static final String	TAXONOMY_ID	"T="

org.forester.io.parsers.phyloxml.PhyloXmlMapping

Modifier and Type	Constant Field	Value
public static final String	ACCESSION	"accession"
public static final String	ACCESSION_COMMENT_ATTR	"comment"
public static final String	ACCESSION_SOURCE_ATTR	"source"
public static final String	ANNOTATION	"annotation"
public static final String	ANNOTATION_DESC	"desc"
public static final String	ANNOTATION_EVIDENCE_ATTR	"evidence"
public static final String	ANNOTATION_REF_ATTR	"ref"
public static final String	ANNOTATION_SOURCE_ATTR	"source"
public static final String	ANNOTATION_TYPE_ATTR	"type"
public static final String	BINARY_CHARACTER	"bc"
public static final String	BINARY_CHARACTERS	"binary_characters"
public static final String	BINARY_CHARACTERS_GAINED	"gained"
public static final String	BINARY_CHARACTERS_GAINED_COUNT_ATTR	"gained_count"
public static final String	BINARY_CHARACTERS_LOST	"lost"
public static final String	BINARY_CHARACTERS_LOST_COUNT_ATTR	"lost_count"
public static final String	BINARY_CHARACTERS_PRESENT	"present"
public static final String	BINARY_CHARACTERS_PRESENT_COUNT_ATTR	"present_count"
public static final String	BINARY_CHARACTERS_TYPE_ATTR	"type"
public static final String	BRANCH_LENGTH	"branch_length"
public static final String	CLADE	"clade"
public static final String	CLADE_DATE	"date"
public static final String	CLADE_DATE_DESC	"desc"
public static final String	CLADE_DATE_MAX	"maximum"
public static final String	CLADE_DATE_MIN	"minimum"
public static final String	CLADE_DATE_UNIT	"unit"
public static final String	CLADE_DATE_VALUE	"value"
public static final String	COLOR	"color"
public static final String	COLOR_BLUE	"blue"
public static final String	COLOR_GREEN	"green"
public static final String	COLOR_RED	"red"
public static final String	CONFIDENCE	"confidence"
public static final String	CONFIDENCE_SD_ATTR	"stddev"
public static final String	CONFIDENCE_TYPE_ATTR	"type"
public static final String	DISTRIBUTION	"distribution"
public static final String	DISTRIBUTION_DESC	"desc"
public static final String	EVENT_DUPLICATIONS	"duplications"
public static final String	EVENT_LOSSES	"losses"
public static final String	EVENT_SPECIATIONS	"speciations"
public static final String	EVENT_TYPE	"type"
public static final String	EVENTS	"events"
public static final String	ID_REF	"id_ref"
public static final String	IDENTIFIER	"id"
public static final String	IDENTIFIER_PROVIDER_ATTR	"provider"
public static final String	NODE_COLLAPSE	"collapse"
public static final String	NODE_NAME	"name"
public static final String	PHYLOGENY	"phylogeny"
public static final String	PHYLOGENY_BRANCHLENGTH_UNIT_ATTR	"branch_length_unit"
public static final String	PHYLOGENY_DESCRIPTION	"description"
public static final String	PHYLOGENY_IS_REROOTABLE_ATTR	"rerootable"
public static final String	PHYLOGENY_IS_ROOTED_ATTR	"rooted"
public static final String	PHYLOGENY_NAME	"name"
public static final String	PHYLOGENY_TYPE_ATTR	"type"
public static final String	POINT	"point"
public static final String	POINT_ALTITUDE	"alt"
public static final String	POINT_ALTITUDE_UNIT_ATTR	"alt_unit"
public static final String	POINT_GEODETIC_DATUM	"geodetic_datum"
public static final String	POINT_LATITUDE	"lat"
public static final String	POINT_LONGITUDE	"long"
public static final String	POLYGON	"polygon"
public static final String	PROPERTY	"property"
public static final String	PROPERTY_APPLIES_TO	"applies_to"
public static final String	PROPERTY_DATATYPE	"datatype"
public static final String	PROPERTY_REF	"ref"
public static final String	PROPERTY_UNIT	"unit"
public static final String	REFERENCE	"reference"
public static final String	REFERENCE_DESC	"desc"
public static final String	REFERENCE_DOI_ATTR	"doi"
public static final String	SEQUENCE	"sequence"
public static final String	SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN	"domain"
public static final String	SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH	"length"
public static final String	SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE	"confidence"
public static final String	SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM	"from"
public static final String	SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO	"to"
public static final String	SEQUENCE_DOMAIN_ARCHITECURE	"domain_architecture"
public static final String	SEQUENCE_GENE_NAME	"gene_name"
public static final String	SEQUENCE_LOCATION	"location"
public static final String	SEQUENCE_MOL_SEQ	"mol_seq"
public static final String	SEQUENCE_MOL_SEQ_ALIGNED_ATTR	"is_aligned"
public static final String	SEQUENCE_NAME	"name"
public static final String	SEQUENCE_RELATION	"sequence_relation"
public static final String	SEQUENCE_RELATION_DISTANCE	"distance"
public static final String	SEQUENCE_RELATION_ID_REF0	"id_ref_0"
public static final String	SEQUENCE_RELATION_ID_REF1	"id_ref_1"
public static final String	SEQUENCE_RELATION_TYPE	"type"
public static final String	SEQUENCE_SOURCE_ID	"id_source"
public static final String	SEQUENCE_SYMBOL	"symbol"
public static final String	SEQUENCE_TYPE	"type"
public static final String	SEQUENCE_X_REFS	"cross_references"
public static final String	TAXONOMY	"taxonomy"
public static final String	TAXONOMY_AUTHORITY	"authority"
public static final String	TAXONOMY_CODE	"code"
public static final String	TAXONOMY_COMMON_NAME	"common_name"
public static final String	TAXONOMY_RANK	"rank"
public static final String	TAXONOMY_SCIENTIFIC_NAME	"scientific_name"
public static final String	TAXONOMY_SYNONYM	"synonym"
public static final String	TYPE_ATTR	"type"
public static final String	URI	"uri"
public static final String	URI_DESC_ATTR	"desc"
public static final String	WIDTH	"width"

org.forester.io.parsers.phyloxml.PhyloXmlParser

Modifier and Type	Constant Field	Value
public static final String	APACHE_FEATURES_VALIDATION_SCHEMA	"http://apache.org/xml/features/validation/schema"
public static final String	APACHE_FEATURES_VALIDATION_SCHEMA_FULL	"http://apache.org/xml/features/validation/schema-full-checking"
public static final String	APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION	"http://apache.org/xml/properties/schema/external-schemaLocation"
public static final String	JAXP_SCHEMA_LANGUAGE	"http://java.sun.com/xml/jaxp/properties/schemaLanguage"
public static final String	JAXP_SCHEMA_SOURCE	"http://java.sun.com/xml/jaxp/properties/schemaSource"
public static final String	SAX_FEATURES_VALIDATION	"http://xml.org/sax/features/validation"
public static final String	W3C_XML_SCHEMA	"http://www.w3.org/2001/XMLSchema"

org.forester.io.parsers.phyloxml.PhyloXmlUtil

Modifier and Type	Constant Field	Value
public static final String	OTHER	"other"
public static final int	ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT	9
public static final String	SEQ_TYPE_DNA	"dna"
public static final String	SEQ_TYPE_PROTEIN	"protein"
public static final String	SEQ_TYPE_RNA	"rna"
public static final String	UNIPROT_TAX_PROVIDER	"uniprot"
public static final String	UNKNOWN	"unknown"
public static final String	VECTOR_PROPERTY_REF	"vector:index="
public static final String	VECTOR_PROPERTY_TYPE	"xsd:decimal"

org.forester.io.parsers.phyloxml.XmlElement

Modifier and Type	Constant Field	Value
public static final boolean	DEBUG	false

org.forester.io.parsers.tol.TolParser

Modifier and Type	Constant Field	Value
public static final String	APACHE_FEATURES_VALIDATION_SCHEMA	"http://apache.org/xml/features/validation/schema"
public static final String	APACHE_FEATURES_VALIDATION_SCHEMA_FULL	"http://apache.org/xml/features/validation/schema-full-checking"
public static final String	APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION	"http://apache.org/xml/properties/schema/external-schemaLocation"
public static final String	JAXP_SCHEMA_LANGUAGE	"http://java.sun.com/xml/jaxp/properties/schemaLanguage"
public static final String	JAXP_SCHEMA_SOURCE	"http://java.sun.com/xml/jaxp/properties/schemaSource"
public static final String	SAX_FEATURES_VALIDATION	"http://xml.org/sax/features/validation"
public static final String	W3C_XML_SCHEMA	"http://www.w3.org/2001/XMLSchema"

org.forester.io.parsers.tol.TolXmlMapping

Modifier and Type	Constant Field	Value
public static final String	AUTHDATE	"AUTHDATE"
public static final String	AUTHORITY	"AUTHORITY"
public static final String	CLADE	"NODE"
public static final String	NODE_ID_ATTR	"ID"
public static final String	NODE_ITALICIZENAME_ATTR	"ITALICIZENAME"
public static final String	OTHERNAME	"OTHERNAME"
public static final String	OTHERNAME_NAME	"NAME"
public static final String	OTHERNAMES	"OTHERNAMES"
public static final String	PHYLOGENY	"TREE"
public static final String	TAXONOMY_NAME	"NAME"
public static final String	TOL_TAXONOMY_ID_TYPE	"tol"

org.forester.io.parsers.util.ParserUtils

Modifier and Type	Constant Field	Value
public static final String	TAX_CODE	"(?:[A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA"
public static final String	TAX_CODE_LO	"(?:[A-Z]{5})|RAT|PIG|PEA"

org.forester.io.writers.PhylogenyWriter

Modifier and Type	Constant Field	Value
public static final boolean	INDENT_PHYLOXML_DEAFULT	true
public static final String	PHYLO_XML_END	"</phyloxml>"
public static final String	PHYLO_XML_INTENDATION_BASE	" "
public static final String	PHYLO_XML_NAMESPACE_LINE	"<phyloxml xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd\" xmlns=\"http://www.phyloxml.org\">"
public static final String	PHYLO_XML_VERSION_ENCODING_LINE	"<?xml version=\"1.0\" encoding=\"UTF-8\"?>"

org.forester.pccx.BranchLengthBasedScoringMethod

Modifier and Type	Constant Field	Value
public static final double	MIN_ALLOWED_BL_VALUE	0.001

org.forester.pccx.LogBranchLengthBasedScoringMethod

Modifier and Type	Constant Field	Value
public static final double	MAX_ALLOWED_BL_VALUE	1.0
public static final double	MIN_ALLOWED_BL_VALUE	1.0E-4

org.forester.phylogeny.Phylogeny

Modifier and Type	Constant Field	Value
public static final boolean	ALLOW_MULTIPLE_PARENTS_DEFAULT	false

org.forester.phylogeny.data.BinaryCharacters

Modifier and Type	Constant Field	Value
public static final int	COUNT_DEFAULT	-1

org.forester.phylogeny.data.BranchWidth

Modifier and Type	Constant Field	Value
public static final double	BRANCH_WIDTH_DEFAULT_VALUE	1.0

org.forester.phylogeny.data.Confidence

Modifier and Type	Constant Field	Value
public static final int	CONFIDENCE_DEFAULT_VALUE	-9999

org.forester.phylogeny.data.DomainArchitecture

Modifier and Type	Constant Field	Value
public static final String	NHX_SEPARATOR	">"

org.forester.phylogeny.data.Event

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_VALUE	-1

org.forester.phylogeny.data.NodeVisualData

Modifier and Type	Constant Field	Value
public static final String	APTX_VISUALIZATION_REF	"style:"
public static final int	DEFAULT_SIZE	-1
public static final String	FONT_COLOR_REF	"style:font_color"
public static final String	FONT_COLOR_TYPE	"xsd:token"
public static final String	FONT_REF	"style:font"
public static final String	FONT_SIZE_REF	"style:font_size"
public static final String	FONT_SIZE_TYPE	"xsd:unsignedByte"
public static final String	FONT_STYLE_BOLD	"bold"
public static final String	FONT_STYLE_BOLD_ITALIC	"bold_italic"
public static final String	FONT_STYLE_ITALIC	"italic"
public static final String	FONT_STYLE_PLAIN	"plain"
public static final String	FONT_STYLE_REF	"style:font_style"
public static final String	FONT_STYLE_TYPE	"xsd:token"
public static final String	FONT_TYPE	"xsd:token"
public static final String	NODE_COLOR_REF	"style:node_color"
public static final String	NODE_COLOR_TYPE	"xsd:token"
public static final String	NODE_FILL_GRADIENT	"gradient"
public static final String	NODE_FILL_NONE	"none"
public static final String	NODE_FILL_SOLID	"solid"
public static final String	NODE_FILL_TYPE_REF	"style:node_fill_type"
public static final String	NODE_FILL_TYPE_TYPE	"xsd:token"
public static final String	NODE_SHAPE_CIRCLE	"circle"
public static final String	NODE_SHAPE_RECTANGLE	"rectangle"
public static final String	NODE_SHAPE_REF	"style:node_shape"
public static final String	NODE_SHAPE_TYPE	"xsd:token"
public static final String	NODE_SIZE_REF	"style:node_size"
public static final String	NODE_SIZE_TYPE	"xsd:float"
public static final String	NODE_TRANSPARENCY_REF	"style:node_transparency"
public static final String	NODE_TRANSPARENCY_TYPE	"xsd:float"

org.forester.phylogeny.data.PhylogenyDataUtil

Modifier and Type	Constant Field	Value
public static final double	BRANCH_LENGTH_DEFAULT	-1024.0

org.forester.phylogeny.data.Point

Modifier and Type	Constant Field	Value
public static final String	UNKNOWN_GEODETIC_DATUM	"?"

org.forester.phylogeny.data.ProteinDomain

Modifier and Type	Constant Field	Value
public static final double	CONFIDENCE_DEFAULT	-1.0
public static final String	IDENTIFIER_DEFAULT	""

org.forester.phylogeny.data.SequenceRelation

Modifier and Type	Constant Field	Value
public static final String	SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY	"one_to_one_orthology"
public static final String	SEQUENCE_RELATION_TYPE_ORTHOLOGY	"orthology"
public static final String	SEQUENCE_RELATION_TYPE_OTHER	"other"
public static final String	SEQUENCE_RELATION_TYPE_PARALOGY	"paralogy"
public static final String	SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY	"super_orthology"
public static final String	SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY	"ultra_paralogy"
public static final String	SEQUENCE_RELATION_TYPE_UNKNOWN	"unknown"
public static final String	SEQUENCE_RELATION_TYPE_XENOLOGY	"xenology"

org.forester.protein.BinaryDomainCombination

Modifier and Type	Constant Field	Value
public static final String	SEPARATOR	"="

org.forester.rio.RIO

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_RANGE	-1

org.forester.sequence.MolecularSequence

Modifier and Type	Constant Field	Value
public static final String	AA_REGEXP	"[^ARNDBCQEZGHILKMFPSTWYVXUO\\-\\*]"
public static final String	DNA_REGEXP	"[^ACGTRYMKWSN\\-\\*]"
public static final char	GAP	45
public static final String	RNA_REGEXP	"[^ACGURYMKWSN\\-\\*]"
public static final char	TERMINATE	42
public static final char	UNSPECIFIED_AA	88
public static final char	UNSPECIFIED_NUC	78

org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

Modifier and Type	Constant Field	Value
public static final double	MAX_SIMILARITY_SCORE	1.0
public static final double	MIN_SIMILARITY_SCORE	0.0

org.forester.surfacing.DomainSimilarity

Modifier and Type	Constant Field	Value
public static final String	SPECIES_SEPARATOR	" "

org.forester.surfacing.SurfacingConstants

Modifier and Type	Constant Field	Value
public static final String	AMIGO_LINK	"http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&query="
public static final String	EOL_LINK	"http://www.eol.org/search?q="
public static final String	GO_LINK	"http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&query="
public static final String	GOOGLE_SCHOLAR_SEARCH	"http://scholar.google.com/scholar?q="
public static final String	GOOGLE_WEB_SEARCH_LINK	"http://www.google.com/search?q="
public static final String	NONE	"[none]"
public static final String	PFAM_FAMILY_ID_LINK	"http://pfam.xfam.org/family/"
public static final String	UNIPROT_TAXONOMY_ID_LINK	"http://www.uniprot.org/taxonomy/"

org.forester.util.DescriptiveStatistics

Modifier and Type	Constant Field	Value
public static final String	PLUS_MINUS	"\u00b1"

org.forester.util.ForesterConstants

Modifier and Type	Constant Field	Value
public static final String	FORESTER_DATE	"150513"
public static final String	FORESTER_VERSION	"1.039"
public static final String	LOCAL_PHYLOXML_XSD_RESOURCE	"resources/phyloxml.xsd"
public static final String	PHYLO_XML_LOCATION	"http://www.phyloxml.org"
public static final String	PHYLO_XML_REFERENCE	"Han MV and Zmasek CM (2009): \"phyloXML: XML for evolutionary biology and comparative genomics\", BMC Bioinformatics 10:356"
public static final String	PHYLO_XML_SUFFIX	".xml"
public static final String	PHYLO_XML_VERSION	"1.10"
public static final String	PHYLO_XML_XSD	"phyloxml.xsd"
public static final boolean	RELEASE	false
public static final String	UTF8	"UTF-8"
public static final String	XML_SCHEMA_INSTANCE	"http://www.w3.org/2001/XMLSchema-instance"

org.forester.util.ForesterUtil

Modifier and Type	Constant Field	Value
public static final String	NCBI_GI	"http://www.ncbi.nlm.nih.gov/protein/gi:"
public static final String	NCBI_NUCCORE	"http://www.ncbi.nlm.nih.gov/nuccore/"
public static final String	NCBI_PROTEIN	"http://www.ncbi.nlm.nih.gov/protein/"
public static final String	PDB	"http://www.pdb.org/pdb/explore/explore.do?pdbId="
public static final String	UNIPROT_KB	"http://www.uniprot.org/uniprot/"
public static final double	ZERO_DIFF	1.0E-9

org.forester.util.SequenceAccessionTools

Modifier and Type	Constant Field	Value
public static final String	UNIPROT_KB_BASE_PATTERN_STR	"((?:[OPQ][0-9][A-Z0-9]{3}[0-9])|(?:[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}))"

org.forester.ws.seqdb.SequenceDbWsTools

Modifier and Type	Constant Field	Value
public static final String	BASE_UNIPROT_URL	"http://www.uniprot.org/"
public static final int	DEFAULT_LINES_TO_RETURN	4000
public static final String	EMBL_DBS_REFSEQ_N	"refseqn"
public static final String	EMBL_DBS_REFSEQ_P	"refseqp"
public static final String	EMBL_EMBL	"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=EMBL&style=raw&id="
public static final String	EMBL_GENBANK	"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id="
public static final String	EMBL_REFSEQ	"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id="

org.forester.ws.seqdb.UniProtTaxonomy

Modifier and Type	Constant Field	Value
public static final String	ARCHAEA	"Archaea"
public static final String	BACTERIA	"Bacteria"
public static final String	CELLULAR_ORGANISMS	"cellular organisms"
public static final String	EUKARYOTA	"Eukaryota"
public static final String	VIRUSES	"Viruses"
public static final String	X	"x"