Uses of Class
org.forester.phylogeny.PhylogenyNode
Packages that use PhylogenyNode
Package
Description
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Uses of PhylogenyNode in org.forester.archaeopteryx
Methods in org.forester.archaeopteryx with parameters of type PhylogenyNodeModifier and TypeMethodDescriptionstatic final String
TreePanelUtil.createUriForSeqWeb
(PhylogenyNode node, Configuration conf, TreePanel tp) TreePanelUtil.createUrisForPdbWeb
(PhylogenyNode node, List<Accession> pdb_accs, Configuration configuration, TreePanel treePanel) AptxUtil.obtainAllDistinctTaxonomies
(PhylogenyNode node) TreePanelUtil.obtainDistinctTaxonomies
(PhylogenyNode node) Returns the set of distinct taxonomies of all external nodes of node.static final void
TreePanelUtil.showExtDescNodeDataUserSelectedHelper
(org.forester.archaeopteryx.ControlPanel cp, PhylogenyNode node, List<String> data) -
Uses of PhylogenyNode in org.forester.archaeopteryx.tools
Methods in org.forester.archaeopteryx.tools with parameters of type PhylogenyNodeModifier and TypeMethodDescriptionstatic final boolean
Blast.isContainsQueryForBlast
(PhylogenyNode node) static final String
Blast.obtainQueryForBlast
(PhylogenyNode node) -
Uses of PhylogenyNode in org.forester.io.parsers.nhx
Methods in org.forester.io.parsers.nhx with parameters of type PhylogenyNodeModifier and TypeMethodDescriptionstatic final void
NHXParser.parseNHX
(String s, PhylogenyNode node_to_annotate, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean replace_underscores, boolean allow_errors_in_distance_to_parent, boolean replace_bell) -
Uses of PhylogenyNode in org.forester.io.parsers.util
Methods in org.forester.io.parsers.util with parameters of type PhylogenyNodeModifier and TypeMethodDescriptionstatic final String
ParserUtils.extractTaxonomyDataFromNodeName
(PhylogenyNode node, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) -
Uses of PhylogenyNode in org.forester.io.writers
Methods in org.forester.io.writers with parameters of type PhylogenyNodeModifier and TypeMethodDescriptionstatic void
PhyloXmlNodeWriter.toPhyloXml
(Writer w, PhylogenyNode node, int level, String indentation) -
Uses of PhylogenyNode in org.forester.pccx
Methods in org.forester.pccx with parameters of type PhylogenyNodeModifier and TypeMethodDescriptionvoid
BranchCountingBasedScoringMethod.calculateScoreForExternalNode
(SortedMap<PhylogenyNode, Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options) 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.Method parameters in org.forester.pccx with type arguments of type PhylogenyNodeModifier and TypeMethodDescriptionvoid
BranchCountingBasedScoringMethod.calculateScoreForExternalNode
(SortedMap<PhylogenyNode, Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options) 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. -
Uses of PhylogenyNode in org.forester.phylogeny
Methods in org.forester.phylogeny that return PhylogenyNodeModifier and TypeMethodDescriptionstatic final PhylogenyNode
PhylogenyMethods.calculateLCA
(PhylogenyNode node1, PhylogenyNode node2) Returns the LCA of PhylogenyNodes node1 and node2.static final PhylogenyNode
PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder
(PhylogenyNode node1, PhylogenyNode node2) Returns the LCA of PhylogenyNodes node1 and node2.static PhylogenyNode
PhylogenyMethods.calculateNodeWithMaxDistanceToRoot
(Phylogeny phy) final PhylogenyNode
PhylogenyNode.copyNodeData()
Returns a new PhylogenyNode which has its data copied from this PhylogenyNode.final PhylogenyNode
PhylogenyNode.copyNodeDataShallow()
Returns a new PhylogenyNode which has the same data as this PhylogenyNode.static PhylogenyNode
PhylogenyNode.createInstanceFromNhxString
(String nhx) static PhylogenyNode
PhylogenyNode.createInstanceFromNhxString
(String nhx, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) static PhylogenyNode
PhylogenyNode.createInstanceFromNhxString
(String nhx, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean replace_underscores) final PhylogenyNode
PhylogenyNode.getChildNode
(int i) This return child node n of this node.final PhylogenyNode
PhylogenyNode.getChildNode1()
Convenience method.final PhylogenyNode
PhylogenyNode.getChildNode2()
Convenience method.PhylogenyBranch.getConnectedNode
(PhylogenyNode node) final PhylogenyNode
PhylogenyNode.getFirstChildNode()
Convenience method.Phylogeny.getFirstExternalNode()
Returns the first external PhylogenyNode.PhylogenyBranch.getFirstNode()
static PhylogenyNode
PhylogenyMethods.getFurthestDescendant
(PhylogenyNode node) final PhylogenyNode
PhylogenyNode.getLastChildNode()
Convenience method.final PhylogenyNode
PhylogenyNode.getLink()
Returns a refernce to the linked PhylogenyNode of this PhylogenyNode.final PhylogenyNode
PhylogenyNode.getNextExternalNode()
Returns a refernce to the next external PhylogenyNode of this PhylogenyNode.final PhylogenyNode
PhylogenyNode.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes()
Phylogeny.getNode
(long id) Finds the PhylogenyNode of this Phylogeny which has a matching ID number.Returns a PhylogenyNode of this Phylogeny which has a matching name.Phylogeny.getNodeViaSequenceName
(String seq_name) Phylogeny.getNodeViaTaxonomyCode
(String taxonomy_code) final PhylogenyNode
PhylogenyNode.getParent()
Returns a refernce to the parent PhylogenyNode of this PhylogenyNode.final PhylogenyNode
PhylogenyNode.getPreviousExternalNode()
Returns a refernce to the next external PhylogenyNode of this PhylogenyNode.Phylogeny.getRoot()
Returns the root PhylogenyNode of this Phylogeny.PhylogenyBranch.getSecondNode()
Methods in org.forester.phylogeny that return types with arguments of type PhylogenyNodeModifier and TypeMethodDescriptionstatic final HashMap
<String, PhylogenyNode> PhylogenyMethods.createNameToExtNodeMap
(Phylogeny phy) static final List
<List<PhylogenyNode>> PhylogenyMethods.divideIntoSubTrees
(Phylogeny phy, double min_distance_to_root) static List
<PhylogenyNode> PhylogenyMethods.getAllDescendants
(PhylogenyNode node) final List
<PhylogenyNode> PhylogenyNode.getAllDescendants()
final List
<PhylogenyNode> PhylogenyNode.getAllExternalDescendants()
Returns a List containing references to all external children of this PhylogenyNode.final List
<PhylogenyNode> PhylogenyNode.getDescendants()
Phylogeny.getExternalNodes()
Warning.Returns a List with references to all Nodes of this Phylogeny which have a matching name.Phylogeny.getNodesViaGeneName
(String seq_name) Phylogeny.getNodesViaSequenceName
(String seq_name) Phylogeny.getNodesViaSequenceSymbol
(String seq_name) Phylogeny.getNodesViaTaxonomyCode
(String taxonomy_code) Phylogeny.getNodesWithMatchingSpecies
(String specname) Returns a Vector with references to all Nodes of this Phylogeny which have a matching species name.Phylogeny.getParalogousNodes
(PhylogenyNode n, String[] taxonomyCodeRange) Returns all paralogs of the external PhylogenyNode n of this Phylogeny.static List
<PhylogenyNode> PhylogenyMethods.obtainAllNodesAsList
(Phylogeny phy) 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 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.Methods in org.forester.phylogeny with parameters of type PhylogenyNodeModifier and TypeMethodDescriptionvoid
Phylogeny.addAsChild
(PhylogenyNode parent) Adds this Phylogeny to the list of child nodes of PhylogenyNode parent and sets the parent of this to parent.final void
PhylogenyNode.addAsChild
(PhylogenyNode node) Adds PhylogenyNode n to the list of child nodes and sets the _parent of n to this.void
Phylogeny.addAsSibling
(PhylogenyNode sibling) static double
PhylogenyMethods.calculateDistance
(PhylogenyNode node1, PhylogenyNode node2) Calculates the distance between PhylogenyNodes node1 and node2.static final PhylogenyNode
PhylogenyMethods.calculateLCA
(PhylogenyNode node1, PhylogenyNode node2) Returns the LCA of PhylogenyNodes node1 and node2.static final PhylogenyNode
PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder
(PhylogenyNode node1, PhylogenyNode node2) Returns the LCA of PhylogenyNodes node1 and node2.static short
PhylogenyMethods.calculateMaxBranchesToLeaf
(PhylogenyNode node) static int
PhylogenyMethods.calculateNumberOfExternalNodesWithoutTaxonomy
(PhylogenyNode node) double
Phylogeny.calculateSubtreeHeight
(PhylogenyNode n) This calculates the height of the subtree emanating at n for rooted, tree-shaped phylogeniesstatic final void
PhylogenyMethods.collapseSubtreeStructure
(PhylogenyNode n) final int
PhylogenyNode.compareTo
(PhylogenyNode o) Phylogeny.copy
(PhylogenyNode source) Returns a deep copy of this Phylogeny.Phylogeny.copyShallow
(PhylogenyNode source) static final void
PhylogenyMethods.deleteNonOrthologousExternalNodes
(Phylogeny phy, PhylogenyNode n) void
Phylogeny.deleteSubtree
(PhylogenyNode remove_us, boolean collapse_resulting_node_with_one_desc) Need to call clearHashIdToNodeMap() afterwards (not done automatically to allow client multiple deletions in linear time).static List
<PhylogenyNode> PhylogenyMethods.getAllDescendants
(PhylogenyNode node) static Color
PhylogenyMethods.getBranchColorValue
(PhylogenyNode node) Convenience methodstatic double
PhylogenyMethods.getBranchWidthValue
(PhylogenyNode node) Convenience methodfinal int
PhylogenyNode.getChildNodeIndex
(PhylogenyNode parent) This gets the child node index of this node, given that parent is its parentstatic double
PhylogenyMethods.getConfidenceValue
(PhylogenyNode node) Convenience methodstatic double[]
PhylogenyMethods.getConfidenceValuesAsArray
(PhylogenyNode node) Convenience methodPhylogenyBranch.getConnectedNode
(PhylogenyNode node) static final Event
PhylogenyMethods.getEventAtLCA
(PhylogenyNode n1, PhylogenyNode n2) static Taxonomy
PhylogenyMethods.getExternalDescendantsTaxonomy
(PhylogenyNode node) Returns taxonomy t if all external descendants have the same taxonomy t, null otherwise.static PhylogenyNode
PhylogenyMethods.getFurthestDescendant
(PhylogenyNode node) Phylogeny.getParalogousNodes
(PhylogenyNode n, String[] taxonomyCodeRange) Returns all paralogs of the external PhylogenyNode n of this Phylogeny.static String
PhylogenyMethods.getSpecies
(PhylogenyNode node) Convenience method for display purposes.static String
PhylogenyMethods.getTaxonomyIdentifier
(PhylogenyNode node) Convenience method for display purposes.static final boolean
PhylogenyMethods.isAllDecendentsAreDuplications
(PhylogenyNode n) boolean
PhylogenyBranch.isDirectionTowards
(PhylogenyNode node) static boolean
PhylogenyMethods.isHasExternalDescendant
(PhylogenyNode node) PhylogenyMethods.obtainDistinctTaxonomyCounts
(PhylogenyNode node) Returns a map of distinct taxonomies of all external nodes of node.static void
PhylogenyMethods.orderAppearance
(PhylogenyNode n, boolean order, boolean order_ext_alphabetically, PhylogenyMethods.DESCENDANT_SORT_PRIORITY pri) Arranges the order of childern for each node of this Phylogeny in such a way that either the branch with more children is on top (right) or on bottom (left), dependent on the value of boolean order.final void
PhylogenyNode.removeChildNode
(PhylogenyNode remove_me) static void
PhylogenyMethods.removeNode
(PhylogenyNode remove_me, Phylogeny phylogeny) void
Phylogeny.reRoot
(PhylogenyNode n) Places the root of this Phylogeny on the parent branch PhylogenyNode n.void
Phylogeny.reRoot
(PhylogenyNode n, double distance_n_to_parent) static void
PhylogenyMethods.setBootstrapConfidence
(PhylogenyNode node, double bootstrap_confidence_value) Convenience method.static void
PhylogenyMethods.setBranchColorValue
(PhylogenyNode node, Color color) static void
PhylogenyMethods.setBranchWidthValue
(PhylogenyNode node, double branch_width_value) Convenience methodfinal void
PhylogenyNode.setChild1
(PhylogenyNode n) Sets the first child PhylogenyNode of this PhylogenyNode to n.final void
PhylogenyNode.setChild2
(PhylogenyNode n) Sets the second child PhylogenyNode of this PhylogenyNode to n.final void
PhylogenyNode.setChildNode
(int i, PhylogenyNode node) Inserts PhylogenyNode n at the specified position i into the list of child nodes.static void
PhylogenyMethods.setConfidence
(PhylogenyNode node, double confidence_value) Convenience method.static void
PhylogenyMethods.setConfidence
(PhylogenyNode node, double confidence_value, String type) Convenience method.void
PhylogenyBranch.setDirectionTowards
(PhylogenyNode node) final void
PhylogenyNode.setLink
(PhylogenyNode n) Sets the linked PhylogenyNode of this PhylogenyNode to n.final void
PhylogenyNode.setParent
(PhylogenyNode n) Sets the _parent PhylogenyNode of this PhylogenyNode to n.void
Phylogeny.setRoot
(PhylogenyNode n) static void
PhylogenyMethods.setScientificName
(PhylogenyNode node, String scientific_name) static void
PhylogenyMethods.setTaxonomyCode
(PhylogenyNode node, String taxonomy_code) Convenience method to set the taxonomy code of a phylogeny node.static final void
PhylogenyMethods.sortNodeDescendents
(PhylogenyNode node, PhylogenyMethods.DESCENDANT_SORT_PRIORITY pri) Method parameters in org.forester.phylogeny with type arguments of type PhylogenyNodeModifier and TypeMethodDescriptionvoid
Phylogeny.setIdToNodeMap
(HashMap<Long, PhylogenyNode> idhash) Constructors in org.forester.phylogeny with parameters of type PhylogenyNodeModifierConstructorDescriptionPhylogenyBranch
(PhylogenyNode first_node, PhylogenyNode second_node) PhylogenyBranch
(PhylogenyNode first_node, PhylogenyNode second_node, boolean direction_towards_first) -
Uses of PhylogenyNode in org.forester.phylogeny.iterators
Methods in org.forester.phylogeny.iterators that return PhylogenyNodeModifier and TypeMethodDescriptionfinal PhylogenyNode
PostOrderStackObject.getNode()
ExternalForwardIterator.next()
LevelOrderTreeIterator.next()
Returns the next PhylogenyNode.PhylogenyNodeIterator.next()
final PhylogenyNode
PostorderTreeIterator.next()
Advances the Iterator by one.final PhylogenyNode
PreorderTreeIterator.next()
Advances the Iterator by one.Constructors in org.forester.phylogeny.iterators with parameters of type PhylogenyNodeModifierConstructorDescriptionCreates a new LevelOrderTreeIterator for iterating over all the child nodes of PhylogenyNode node (including node itself).PostOrderStackObject
(PhylogenyNode n, int i) -
Uses of PhylogenyNode in org.forester.rio
Methods in org.forester.rio that return types with arguments of type PhylogenyNode -
Uses of PhylogenyNode in org.forester.sdi
Methods in org.forester.sdi that return types with arguments of type PhylogenyNodeModifier and TypeMethodDescriptionGSDII.getStrippedExternalGeneTreeNodes()
GSDIR.getStrippedExternalGeneTreeNodes()
GSDI.getStrippedSpeciesTreeNodes()
GSDII.getStrippedSpeciesTreeNodes()
GSDIR.getStrippedSpeciesTreeNodes()
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Uses of PhylogenyNode in org.forester.tools
Method parameters in org.forester.tools with type arguments of type PhylogenyNodeConstructor parameters in org.forester.tools with type arguments of type PhylogenyNodeModifierConstructorDescriptionTreeSplitMatrix
(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 PhylogenyNode in org.forester.util
Methods in org.forester.util with parameters of type PhylogenyNodeModifier and TypeMethodDescriptionstatic final void
ForesterUtil.ensurePresenceOfDate
(PhylogenyNode node) static final void
ForesterUtil.ensurePresenceOfDistribution
(PhylogenyNode node) static void
ForesterUtil.ensurePresenceOfSequence
(PhylogenyNode node) static void
ForesterUtil.ensurePresenceOfTaxonomy
(PhylogenyNode node) static final Accession
SequenceAccessionTools.obtainAccessorFromDataFields
(PhylogenyNode n) static final Accession
SequenceAccessionTools.obtainFromSeqAccession
(PhylogenyNode n) static final String
SequenceAccessionTools.obtainGenbankAccessorFromDataFields
(PhylogenyNode n) static final String
SequenceAccessionTools.obtainGiNumberFromDataFields
(PhylogenyNode n) static final String
SequenceAccessionTools.obtainRefSeqAccessorFromDataFields
(PhylogenyNode n) static final String
SequenceAccessionTools.obtainUniProtAccessorFromDataFields
(PhylogenyNode n) -
Uses of PhylogenyNode in org.forester.ws.seqdb
Methods in org.forester.ws.seqdb with parameters of type PhylogenyNodeModifier and TypeMethodDescriptionstatic final Accession
SequenceDbWsTools.obtainSeqAccession
(PhylogenyNode node) static final void
SequenceDbWsTools.obtainSeqInformation
(boolean allow_to_set_taxonomic_data, int lines_to_return, SortedSet<String> not_found, PhylogenyNode node) static final void
SequenceDbWsTools.obtainSeqInformation
(boolean allow_to_set_taxonomic_data, SortedSet<String> not_found, PhylogenyNode node) static final void
SequenceDbWsTools.obtainSeqInformation
(PhylogenyNode node)