Uses of Class
org.forester.phylogeny.Phylogeny
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Uses of Phylogeny in org.biojava.nbio.phylo
Methods in org.biojava.nbio.phylo that return Phylogeny Modifier and Type Method Description static Phylogeny
TreeConstructor. distanceTree(BasicSymmetricalDistanceMatrix distM, TreeConstructorType constructor)
Methods in org.biojava.nbio.phylo with parameters of type Phylogeny Modifier and Type Method Description static double
DistanceTreeEvaluator. evaluate(Phylogeny tree, DistanceMatrix matrix)
Evaluate the goodness of fit of a given tree to the original distance matrix.static java.lang.String
ForesterWrapper. getNewickString(Phylogeny phylo, boolean writeDistances)
Convert a Phylogenetic tree to its Newick representation, so that it can be exported to an external application. -
Uses of Phylogeny in org.biojava.nbio.structure.align.multiple.util
Methods in org.biojava.nbio.structure.align.multiple.util that return Phylogeny Modifier and Type Method Description static Phylogeny
MultipleAlignmentTools. getHSDMTree(MultipleAlignment msta)
Calculate a phylogenetic tree of the MultipleAlignment using dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for distantly related proteins, structure-derived) and the Neighbor Joining algorithm from forester.static Phylogeny
MultipleAlignmentTools. getKimuraTree(MultipleAlignment msta)
Calculate a phylogenetic tree of the MultipleAlignment using Kimura distances and the Neighbor Joining algorithm from forester.static Phylogeny
MultipleAlignmentTools. getStructuralTree(MultipleAlignment msta)
Calculate a phylogenetic tree of the MultipleAlignment using RMSD distances and the Neighbor Joining algorithm from forester. -
Uses of Phylogeny in org.forester.analysis
Methods in org.forester.analysis with parameters of type Phylogeny Modifier and Type Method Description static void
AncestralTaxonomyInference. inferTaxonomyFromDescendents(Phylogeny phy)
Constructors in org.forester.analysis with parameters of type Phylogeny Constructor Description TaxonomyDataManager(MainFrameApplication mf, TreePanel treepanel, Phylogeny phy)
TaxonomyDataManager(MainFrameApplication mf, TreePanel treepanel, Phylogeny phy, boolean delete, boolean allow_simple_name)
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Uses of Phylogeny in org.forester.application
Methods in org.forester.application with parameters of type Phylogeny Modifier and Type Method 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 Description Phylogeny
TreePanel. getPhylogeny()
Get a pointer to the phylogenystatic Phylogeny[]
AptxUtil. readPhylogeniesFromUrl(java.net.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 Description void
MainPanel. addPhylogenyInNewTab(Phylogeny phy, Configuration config, java.lang.String default_name, java.lang.String full_path)
static MainFrame
Archaeopteryx. createApplication(Phylogeny phylogeny)
static MainFrame
Archaeopteryx. createApplication(Phylogeny[] phylogenies)
static MainFrame
Archaeopteryx. createApplication(Phylogeny[] phylogenies, java.lang.String config_file_name, java.lang.String title)
static MainFrame
Archaeopteryx. createApplication(Phylogeny phylogeny, Configuration config, java.lang.String title)
static MainFrameApplication
MainFrameApplication. createInstance(Phylogeny[] phys, Configuration config)
static MainFrame
MainFrameApplication. createInstance(Phylogeny[] phys, Configuration config, java.lang.String title, java.io.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, java.io.File outfile, int width, int height, AptxUtil.GraphicsExportType type, Configuration config)
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Uses of Phylogeny in org.forester.archaeopteryx.tools
Constructors in org.forester.archaeopteryx.tools with parameters of type Phylogeny Constructor Description AncestralTaxonomyInferrer(MainFrame mf, TreePanel treepanel, Phylogeny phy)
SequenceDataRetriver(MainFrameApplication mf, TreePanel treepanel, Phylogeny phy)
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Uses of Phylogeny in org.forester.archaeopteryx.webservices
Methods in org.forester.archaeopteryx.webservices with parameters of type Phylogeny Modifier and Type Method Description static void
WebserviceUtil. processInstructions(PhylogeniesWebserviceClient client, Phylogeny phylogeny)
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Uses of Phylogeny in org.forester.development
Methods in org.forester.development that return Phylogeny Modifier and Type Method 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 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 Description Phylogeny
NeighborJoining. execute(BasicSymmetricalDistanceMatrix distance)
Phylogeny
NeighborJoiningF. 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 Description java.util.List<Phylogeny>
NeighborJoining. execute(java.util.List<BasicSymmetricalDistanceMatrix> distances_list)
java.util.List<Phylogeny>
NeighborJoiningF. execute(java.util.List<BasicSymmetricalDistanceMatrix> distances_list)
java.util.List<Phylogeny>
NeighborJoiningR. execute(java.util.List<BasicSymmetricalDistanceMatrix> distances_list)
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Uses of Phylogeny in org.forester.evoinference.parsimony
Methods in org.forester.evoinference.parsimony with parameters of type Phylogeny Modifier and Type Method Description void
DolloParsimony. execute(Phylogeny p, CharacterStateMatrix<CharacterStateMatrix.BinaryStates> 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)
void
SankoffParsimony. execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix)
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Uses of Phylogeny in org.forester.io.parsers
Methods in org.forester.io.parsers that return Phylogeny Modifier and Type Method Description Phylogeny
IteratingPhylogenyParser. next()
Phylogeny[]
PhylogenyParser. parse()
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Uses of Phylogeny in org.forester.io.parsers.nexus
Methods in org.forester.io.parsers.nexus that return Phylogeny Modifier and Type Method Description Phylogeny
NexusPhylogeniesParser. next()
Phylogeny[]
NexusPhylogeniesParser. parse()
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Uses of Phylogeny in org.forester.io.parsers.nhx
Methods in org.forester.io.parsers.nhx that return Phylogeny Modifier and Type Method Description Phylogeny
NHXParser. next()
Phylogeny[]
NHXParser. parse()
static Phylogeny[]
NHXParser. parse(java.lang.Object nhx_source)
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Uses of Phylogeny in org.forester.io.parsers.phyloxml
Methods in org.forester.io.parsers.phyloxml that return Phylogeny Modifier and Type Method Description Phylogeny[]
PhyloXmlParser. parse()
Methods in org.forester.io.parsers.phyloxml with parameters of type Phylogeny Modifier and Type Method Description static java.util.Map<java.lang.String,Sequence>
PhyloXmlHandler. getSequenceMapByIdForPhylogeny(Phylogeny ph)
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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 Description static PhylogenyDataPhyloXmlParser
SequenceRelationParser. getInstance(Phylogeny phylogeny)
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Uses of Phylogeny in org.forester.io.parsers.tol
Methods in org.forester.io.parsers.tol that return Phylogeny Modifier and Type Method Description Phylogeny[]
TolParser. parse()
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Uses of Phylogeny in org.forester.io.parsers.util
Methods in org.forester.io.parsers.util that return Phylogeny Modifier and Type Method Description static Phylogeny[]
ParserUtils. readPhylogenies(java.io.File file)
static Phylogeny[]
ParserUtils. readPhylogenies(java.lang.String file_name)
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Uses of Phylogeny in org.forester.io.writers
Methods in org.forester.io.writers with parameters of type Phylogeny Modifier and Type Method Description void
PhylogenyWriter. toNewHampshire(Phylogeny[] trees, boolean write_distance_to_parent, java.io.File out_file, java.lang.String separator)
java.lang.StringBuffer
PhylogenyWriter. toNewHampshire(Phylogeny tree, boolean nh_write_distance_to_parent)
void
PhylogenyWriter. toNewHampshire(Phylogeny tree, boolean write_distance_to_parent, java.io.File out_file)
java.lang.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, java.io.File out_file)
java.lang.StringBuffer
PhylogenyWriter. toNewHampshireX(Phylogeny tree)
void
PhylogenyWriter. toNewHampshireX(Phylogeny[] trees, java.io.File out_file, java.lang.String separator)
void
PhylogenyWriter. toNewHampshireX(Phylogeny tree, java.io.File out_file)
void
PhylogenyWriter. toNexus(java.io.File out_file, Phylogeny tree, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
java.lang.StringBuffer
PhylogenyWriter. toNexus(Phylogeny tree, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
void
PhylogenyWriter. toPhyloXML(java.io.File out_file, Phylogeny tree, int phyloxml_level)
void
PhylogenyWriter. toPhyloXML(java.io.Writer writer, Phylogeny[] trees, int phyloxml_level, java.lang.String separator)
void
PhylogenyWriter. toPhyloXML(java.io.Writer writer, Phylogeny tree, int phyloxml_level)
void
PhylogenyWriter. toPhyloXML(Phylogeny[] trees, int phyloxml_level, java.io.File out_file, java.lang.String separator)
java.lang.StringBuffer
PhylogenyWriter. toPhyloXML(Phylogeny tree, int phyloxml_level)
void
PhylogenyWriter. toPhyloXML(Phylogeny phy, int phyloxml_level, java.io.File out_file)
static void
PhylogenyWriter. writeNexusTaxaBlock(java.io.Writer writer, Phylogeny tree)
Method parameters in org.forester.io.writers with type arguments of type Phylogeny Modifier and Type Method Description void
PhylogenyWriter. toNewHampshire(java.util.List<Phylogeny> trees, boolean write_distance_to_parent, java.io.File out_file, java.lang.String separator)
void
PhylogenyWriter. toNewHampshireX(java.util.List<Phylogeny> trees, java.io.File out_file, java.lang.String separator)
void
PhylogenyWriter. toPhyloXML(java.io.File out_file, java.util.List<Phylogeny> trees, int phyloxml_level, java.lang.String separator)
void
PhylogenyWriter. toPhyloXML(java.io.Writer writer, java.util.List<Phylogeny> trees, int phyloxml_level, java.lang.String separator)
static void
PhylogenyWriter. writeNexusTreesBlock(java.io.Writer writer, java.util.List<Phylogeny> trees, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
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Uses of Phylogeny in org.forester.msa_compactor
Methods in org.forester.msa_compactor that return Phylogeny Modifier and Type Method Description Phylogeny
MsaCompactor. calcTree()
Methods in org.forester.msa_compactor with parameters of type Phylogeny Modifier and Type Method Description void
MsaCompactor. displayTree(Phylogeny phy)
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Uses of Phylogeny in org.forester.pccx
Methods in org.forester.pccx with parameters of type Phylogeny Modifier and Type Method Description void
BranchCountingBasedScoringMethod. calculateScoreForExternalNode(java.util.SortedMap<PhylogenyNode,java.lang.Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options)
void
ScoringMethodForExternalNode. calculateScoreForExternalNode(java.util.SortedMap<PhylogenyNode,java.lang.Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options)
This calculates the coverage score for one external node.double
BranchCountingBasedScoringMethod. getNormalizationFactor(Phylogeny phylogeny)
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.Method parameters in org.forester.pccx with type arguments of type Phylogeny Modifier and Type Method Description Coverage
CoverageCalculationMethod. calculateCoverage(java.util.List<Phylogeny> phylogenies, java.util.List<java.lang.String> names, CoverageCalculationOptions options, boolean annotate_phylogenies)
Coverage
CoverageCalculator. calculateCoverage(java.util.List<Phylogeny> phylogenies, java.util.List<java.lang.String> names, boolean annotate_phylogenies)
Coverage
ExternalNodeBasedCoverageMethod. calculateCoverage(java.util.List<Phylogeny> phylogenies, java.util.List<java.lang.String> names, CoverageCalculationOptions options, boolean annotate_phylogenies)
java.util.List<java.lang.String>
BasicExternalNodeBasedCoverageExtender. find(java.util.List<Phylogeny> phylogenies, java.util.List<java.lang.String> already_covered, int number_names_to_find, CoverageCalculationOptions options, java.io.PrintStream out)
java.util.List<java.lang.String>
CoverageExtender. find(java.util.List<Phylogeny> phylogenies, java.util.List<java.lang.String> already_covered, int number_names_to_find, CoverageCalculationOptions options, java.io.PrintStream out)
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Uses of Phylogeny in org.forester.phylogeny
Methods in org.forester.phylogeny that return Phylogeny Modifier and Type Method 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(java.lang.String nhx)
static Phylogeny[]
PhylogenyMethods. readPhylogenies(PhylogenyParser parser, java.io.File file)
static Phylogeny[]
PhylogenyMethods. readPhylogenies(PhylogenyParser parser, java.util.List<java.io.File> files)
Methods in org.forester.phylogeny with parameters of type Phylogeny Modifier and Type Method Description static void
PhylogenyMethods. addMolecularSeqsToTree(Phylogeny phy, Msa msa)
static DescriptiveStatistics
PhylogenyMethods. calculateBranchLengthStatistics(Phylogeny phy)
static java.util.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 java.util.HashMap<java.lang.String,PhylogenyNode>
PhylogenyMethods. createNameToExtNodeMap(Phylogeny phy)
static void
PhylogenyMethods. deleteExternalNodesNegativeSelection(java.lang.String[] node_names_to_delete, Phylogeny p)
static void
PhylogenyMethods. deleteExternalNodesNegativeSelection(java.util.Set<java.lang.Long> to_delete, Phylogeny phy)
static java.util.List<java.lang.String>
PhylogenyMethods. deleteExternalNodesPositiveSelection(java.lang.String[] node_names_to_keep, Phylogeny p)
static void
PhylogenyMethods. deleteExternalNodesPositiveSelectionT(java.util.List<Taxonomy> species_to_keep, Phylogeny phy)
static void
PhylogenyMethods. deleteInternalNodesWithOnlyOneDescendent(Phylogeny phy)
static void
PhylogenyMethods. deleteNonOrthologousExternalNodes(Phylogeny phy, PhylogenyNode n)
static java.util.List<java.util.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 java.util.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 java.util.List<PhylogenyNode>
PhylogenyMethods. searchData(java.lang.String query, Phylogeny phy, boolean case_sensitive, boolean partial, boolean regex, boolean search_domains, double domains_confidence_threshold)
static java.util.List<PhylogenyNode>
PhylogenyMethods. searchDataLogicalAnd(java.lang.String[] queries, Phylogeny phy, boolean case_sensitive, boolean partial, boolean search_domains, double domains_confidence_threshold)
static void
PhylogenyMethods. setAllIndicatorsToZero(Phylogeny phy)
static java.util.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, java.lang.String confidence_type)
static void
PhylogenyMethods. transferNodeNameToField(Phylogeny phy, PhylogenyMethods.PhylogenyNodeField field, boolean external_only)
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Uses of Phylogeny in org.forester.phylogeny.factories
Methods in org.forester.phylogeny.factories that return Phylogeny Modifier and Type Method Description Phylogeny[]
ParserBasedPhylogenyFactory. create(java.lang.Object source, java.lang.Object parser)
Phylogeny[]
ParserBasedPhylogenyFactory. create(java.lang.Object source, java.lang.Object parser, java.lang.String schema_location)
Phylogeny[]
PhylogenyFactory. create(java.lang.Object source, java.lang.Object creator)
This must create a Phylogeny from source (e.g. -
Uses of Phylogeny in org.forester.phylogeny.iterators
Constructors in org.forester.phylogeny.iterators with parameters of type Phylogeny Constructor Description ExternalForwardIterator(Phylogeny phylogeny)
Constructor for ExternalForwardIterator.LevelOrderTreeIterator(Phylogeny phylogeny)
Creates a new LevelOrderTreeIterator for iterating over all the nodes of Phylogeny phylogenyPostorderTreeIterator(Phylogeny tree)
PreorderTreeIterator(Phylogeny tree)
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Uses of Phylogeny in org.forester.rio
Methods in org.forester.rio that return Phylogeny Modifier and Type Method Description Phylogeny[]
RIO. getAnalyzedGeneTrees()
Phylogeny
RIO. getMinDuplicationsGeneTree()
Phylogeny
RIO. getSpeciesTree()
Methods in org.forester.rio with parameters of type Phylogeny Modifier and Type Method Description static IntMatrix
RIO. calculateOrthologTable(Phylogeny[] analyzed_gene_trees, boolean sort)
static RIO
RIO. executeAnalysis(java.io.File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.String outgroup, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
static RIO
RIO. executeAnalysis(java.io.File gene_trees_file, Phylogeny species_tree, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.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, java.lang.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, java.lang.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, SDIutil.ALGORITHM algorithm, RIO.REROOTING rerooting, java.lang.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, java.lang.String outgroup, int first, int last, boolean produce_log, boolean verbose, boolean transfer_taxonomy)
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Uses of Phylogeny in org.forester.sdi
Methods in org.forester.sdi that return Phylogeny Modifier and Type Method 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, java.io.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 Description static SDIutil.TaxonomyComparisonBase
SDIutil. determineTaxonomyComparisonBase(Phylogeny gene_tree)
static java.util.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, java.io.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 Description static java.util.List<java.lang.Integer>
GSDIR. getIndexesOfShortestTree(java.util.List<Phylogeny> assigned_trees)
Constructors in org.forester.sdi with parameters of type Phylogeny Constructor 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 Description static Phylogeny
SurfacingUtil. createNjTreeBasedOnMatrixToFile(java.io.File nj_tree_outfile, DistanceMatrix distance)
static Phylogeny[]
SurfacingUtil. obtainAndPreProcessIntrees(java.io.File[] intree_files, int number_of_genomes, java.lang.String[][] input_file_properties)
static Phylogeny
SurfacingUtil. obtainFirstIntree(java.io.File intree_file)
Methods in org.forester.surfacing with parameters of type Phylogeny Modifier and Type Method Description static DomainParsimonyCalculator
DomainParsimonyCalculator. createInstance(Phylogeny phylogeny)
static DomainParsimonyCalculator
DomainParsimonyCalculator. createInstance(Phylogeny phylogeny, java.util.List<GenomeWideCombinableDomains> gwcd_list)
static DomainParsimonyCalculator
DomainParsimonyCalculator. createInstance(Phylogeny phylogeny, java.util.List<GenomeWideCombinableDomains> gwcd_list, java.util.Map<java.lang.String,java.util.Set<java.lang.String>> domain_id_to_secondary_features_map)
static java.util.Map<java.lang.String,java.lang.Integer>
SurfacingUtil. createTaxCodeToIdMap(Phylogeny phy)
static void
SurfacingUtil. executeParsimonyAnalysis(long random_number_seed_for_fitch_parsimony, boolean radomize_fitch_parsimony, java.lang.String outfile_name, DomainParsimonyCalculator domain_parsimony, Phylogeny phylogeny, java.util.Map<java.lang.String,java.util.List<GoId>> domain_id_to_go_ids_map, java.util.Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, java.lang.String parameters_str, java.util.Map<java.lang.String,java.util.Set<java.lang.String>>[] domain_id_to_secondary_features_maps, java.util.SortedSet<java.lang.String> positive_filter, boolean output_binary_domain_combinations_for_graphs, java.util.List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch, java.util.List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch, BinaryDomainCombination.DomainCombinationType dc_type, java.util.Map<java.lang.String,DescriptiveStatistics> protein_length_stats_by_dc, java.util.Map<java.lang.String,DescriptiveStatistics> domain_number_stats_by_dc, java.util.Map<java.lang.String,DescriptiveStatistics> domain_length_stats_by_domain, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, boolean write_to_nexus, boolean use_last_in_fitch_parsimony, boolean perform_dc_fich)
static void
SurfacingUtil. executeParsimonyAnalysisForSecondaryFeatures(java.lang.String outfile_name, DomainParsimonyCalculator secondary_features_parsimony, Phylogeny phylogeny, java.lang.String parameters_str, java.util.Map<Species,MappingResults> mapping_results_map, boolean use_last_in_fitch_parsimony)
static int
SurfacingUtil. getNumberOfNodesLackingName(Phylogeny p, java.lang.StringBuilder names)
static java.lang.String
SurfacingUtil. obtainHexColorStringDependingOnTaxonomyGroup(java.lang.String tax_code, Phylogeny phy)
static java.lang.String
SurfacingUtil. obtainTaxonomyGroup(java.lang.String tax_code, Phylogeny species_tree)
void
PairwiseGenomeComparator. performPairwiseComparisons(java.lang.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, java.util.Map<java.lang.String,java.util.List<GoId>> domain_id_to_go_ids_map, java.util.Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, Species[] species, int number_of_genomes, java.util.List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains, PairwiseDomainSimilarityCalculator pw_calc, java.lang.String automated_pairwise_comparison_suffix, boolean verbose, java.lang.String automated_pairwise_comparison_prefix, java.lang.String command_line_prg_name, java.io.File out_dir, boolean write_pairwise_comparisons, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, boolean calc_similarity_scores, Phylogeny phy)
static void
SurfacingUtil. preparePhylogeny(Phylogeny p, DomainParsimonyCalculator domain_parsimony, java.lang.String date_time, java.lang.String method, java.lang.String name, java.lang.String parameters_str)
static void
SurfacingUtil. preparePhylogenyForParsimonyAnalyses(Phylogeny intree, java.lang.String[][] input_file_properties)
java.lang.StringBuffer
DomainSimilarity. toStringBuffer(DomainSimilarity.PRINT_OPTION print_option, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, Phylogeny phy)
static void
SurfacingUtil. writeAllDomainsChangedOnAllSubtrees(Phylogeny p, boolean get_gains, java.lang.String outdir, java.lang.String suffix_for_filename)
static void
SurfacingUtil. writeDomainSimilaritiesToFile(java.lang.StringBuilder html_desc, java.lang.StringBuilder html_title, java.io.Writer simple_tab_writer, java.io.Writer single_writer, java.util.Map<java.lang.Character,java.io.Writer> split_writers, java.util.SortedSet<DomainSimilarity> similarities, boolean treat_as_binary, java.util.List<Species> species_order, DomainSimilarity.PRINT_OPTION print_option, DomainSimilarity.DomainSimilarityScoring scoring, boolean verbose, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, Phylogeny phy, java.util.Set<java.lang.String> pos_filter_doms)
static void
SurfacingUtil. writePhylogenyToFile(Phylogeny phylogeny, java.lang.String filename)
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Uses of Phylogeny in org.forester.tools
Methods in org.forester.tools that return types with arguments of type Phylogeny Modifier and Type Method Description static java.util.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 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 java.util.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 java.lang.String
PhylogenyDecorator. decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.lang.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 java.lang.String
PhylogenyDecorator. decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, java.util.Map<java.lang.String,java.lang.String> intermediate_map, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose)
static void
PhylogenyDecorator. decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> map, boolean picky)
static void
ConfidenceAssessor. evaluate(java.lang.String confidence_type, Phylogeny[] evaluators, Phylogeny target, boolean strict, double value)
static void
ConfidenceAssessor. evaluate(java.lang.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 Description TreeSplitMatrix(Phylogeny evaluator, boolean strict, java.util.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.TreeSplitMatrix(Phylogeny evaluator, boolean strict, Phylogeny target)
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Uses of Phylogeny in org.forester.ws.seqdb
Methods in org.forester.ws.seqdb with parameters of type Phylogeny Modifier and Type Method Description static java.util.SortedSet<java.lang.String>
SequenceDbWsTools. obtainSeqInformation(Phylogeny phy, boolean ext_nodes_only, boolean allow_to_set_taxonomic_data, int lines_to_return)
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