Uses of Class
org.forester.phylogeny.PhylogenyNode

Packages that use PhylogenyNode

Package	Description
org.forester.archaeopteryx
org.forester.archaeopteryx.tools
org.forester.io.parsers.nhx
org.forester.io.parsers.util
org.forester.io.writers
org.forester.pccx
org.forester.phylogeny
org.forester.phylogeny.iterators
org.forester.rio
org.forester.sdi
org.forester.tools
org.forester.util
org.forester.ws.seqdb

Uses of PhylogenyNode in org.forester.archaeopteryx

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

Modifier and Type	Method	Description
static java.lang.String	TreePanelUtil.createUriForSeqWeb(PhylogenyNode node, Configuration conf, TreePanel tp)
static java.util.List<java.lang.String>	TreePanelUtil.createUrisForPdbWeb(PhylogenyNode node, java.util.List<Accession> pdb_accs, Configuration configuration, TreePanel treePanel)
static java.util.Set<Taxonomy>	AptxUtil.obtainAllDistinctTaxonomies(PhylogenyNode node)
static java.util.Set<Taxonomy>	TreePanelUtil.obtainDistinctTaxonomies(PhylogenyNode node)	Returns the set of distinct taxonomies of all external nodes of node.
static void	TreePanelUtil.showExtDescNodeDataUserSelectedHelper(org.forester.archaeopteryx.ControlPanel cp, PhylogenyNode node, java.util.List<java.lang.String> data)

Uses of PhylogenyNode in org.forester.archaeopteryx.tools

Methods in org.forester.archaeopteryx.tools with parameters of type PhylogenyNode

Modifier and Type	Method	Description
static boolean	Blast.isContainsQueryForBlast(PhylogenyNode node)
static java.lang.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 PhylogenyNode

Modifier and Type	Method	Description
static void	NHXParser.parseNHX(java.lang.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 PhylogenyNode

Modifier and Type	Method	Description
static java.lang.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 PhylogenyNode

Modifier and Type	Method	Description
static void	PhyloXmlNodeWriter.toPhyloXml(java.io.Writer w, PhylogenyNode node, int level, java.lang.String indentation)

Uses of PhylogenyNode in org.forester.pccx

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

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.

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

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.

Uses of PhylogenyNode in org.forester.phylogeny

Methods in org.forester.phylogeny that return PhylogenyNode

Modifier and Type	Method	Description
static PhylogenyNode	PhylogenyMethods.calculateLCA(PhylogenyNode node1, PhylogenyNode node2)	Returns the LCA of PhylogenyNodes node1 and node2.
static PhylogenyNode	PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder(PhylogenyNode node1, PhylogenyNode node2)	Returns the LCA of PhylogenyNodes node1 and node2.
static PhylogenyNode	PhylogenyMethods.calculateNodeWithMaxDistanceToRoot(Phylogeny phy)
PhylogenyNode	PhylogenyNode.copyNodeData()	Returns a new PhylogenyNode which has its data copied from this PhylogenyNode.
PhylogenyNode	PhylogenyNode.copyNodeDataShallow()	Returns a new PhylogenyNode which has the same data as this PhylogenyNode.
static PhylogenyNode	PhylogenyNode.createInstanceFromNhxString(java.lang.String nhx)
static PhylogenyNode	PhylogenyNode.createInstanceFromNhxString(java.lang.String nhx, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
static PhylogenyNode	PhylogenyNode.createInstanceFromNhxString(java.lang.String nhx, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean replace_underscores)
PhylogenyNode	PhylogenyNode.getChildNode(int i)	This return child node n of this node.
PhylogenyNode	PhylogenyNode.getChildNode1()	Convenience method.
PhylogenyNode	PhylogenyNode.getChildNode2()	Convenience method.
PhylogenyNode	PhylogenyBranch.getConnectedNode(PhylogenyNode node)
PhylogenyNode	PhylogenyNode.getFirstChildNode()	Convenience method.
PhylogenyNode	Phylogeny.getFirstExternalNode()	Returns the first external PhylogenyNode.
PhylogenyNode	PhylogenyBranch.getFirstNode()
static PhylogenyNode	PhylogenyMethods.getFurthestDescendant(PhylogenyNode node)
PhylogenyNode	PhylogenyNode.getLastChildNode()	Convenience method.
PhylogenyNode	PhylogenyNode.getLink()	Returns a refernce to the linked PhylogenyNode of this PhylogenyNode.
PhylogenyNode	PhylogenyNode.getNextExternalNode()	Returns a refernce to the next external PhylogenyNode of this PhylogenyNode.
PhylogenyNode	PhylogenyNode.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes()
PhylogenyNode	Phylogeny.getNode(long id)	Finds the PhylogenyNode of this Phylogeny which has a matching ID number.
PhylogenyNode	Phylogeny.getNode(java.lang.String name)	Returns a PhylogenyNode of this Phylogeny which has a matching name.
PhylogenyNode	Phylogeny.getNodeViaSequenceName(java.lang.String seq_name)
PhylogenyNode	Phylogeny.getNodeViaTaxonomyCode(java.lang.String taxonomy_code)
PhylogenyNode	PhylogenyNode.getParent()	Returns a refernce to the parent PhylogenyNode of this PhylogenyNode.
PhylogenyNode	PhylogenyNode.getPreviousExternalNode()	Returns a refernce to the next external PhylogenyNode of this PhylogenyNode.
PhylogenyNode	Phylogeny.getRoot()	Returns the root PhylogenyNode of this Phylogeny.
PhylogenyNode	PhylogenyBranch.getSecondNode()

Methods in org.forester.phylogeny that return types with arguments of type PhylogenyNode

Modifier and Type	Method	Description
static java.util.HashMap<java.lang.String,PhylogenyNode>	PhylogenyMethods.createNameToExtNodeMap(Phylogeny phy)
static java.util.List<java.util.List<PhylogenyNode>>	PhylogenyMethods.divideIntoSubTrees(Phylogeny phy, double min_distance_to_root)
static java.util.List<PhylogenyNode>	PhylogenyMethods.getAllDescendants(PhylogenyNode node)
java.util.List<PhylogenyNode>	PhylogenyNode.getAllDescendants()
java.util.List<PhylogenyNode>	PhylogenyNode.getAllExternalDescendants()	Returns a List containing references to all external children of this PhylogenyNode.
java.util.List<PhylogenyNode>	PhylogenyNode.getDescendants()
java.util.List<PhylogenyNode>	Phylogeny.getExternalNodes()	Warning.
java.util.List<PhylogenyNode>	Phylogeny.getNodes(java.lang.String name)	Returns a List with references to all Nodes of this Phylogeny which have a matching name.
java.util.List<PhylogenyNode>	Phylogeny.getNodesViaGeneName(java.lang.String seq_name)
java.util.List<PhylogenyNode>	Phylogeny.getNodesViaSequenceName(java.lang.String seq_name)
java.util.List<PhylogenyNode>	Phylogeny.getNodesViaSequenceSymbol(java.lang.String seq_name)
java.util.List<PhylogenyNode>	Phylogeny.getNodesViaTaxonomyCode(java.lang.String taxonomy_code)
java.util.List<PhylogenyNode>	Phylogeny.getNodesWithMatchingSpecies(java.lang.String specname)	Returns a Vector with references to all Nodes of this Phylogeny which have a matching species name.
java.util.List<PhylogenyNode>	Phylogeny.getParalogousNodes(PhylogenyNode n, java.lang.String[] taxonomyCodeRange)	Returns all paralogs of the external PhylogenyNode n of this Phylogeny.
static java.util.List<PhylogenyNode>	PhylogenyMethods.obtainAllNodesAsList(Phylogeny phy)
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 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.

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

Modifier and Type	Method	Description
void	Phylogeny.addAsChild(PhylogenyNode parent)	Adds this Phylogeny to the list of child nodes of PhylogenyNode parent and sets the parent of this to parent.
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 PhylogenyNode	PhylogenyMethods.calculateLCA(PhylogenyNode node1, PhylogenyNode node2)	Returns the LCA of PhylogenyNodes node1 and node2.
static 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 phylogenies
static void	PhylogenyMethods.collapseSubtreeStructure(PhylogenyNode n)
int	PhylogenyNode.compareTo(PhylogenyNode o)
Phylogeny	Phylogeny.copy(PhylogenyNode source)	Returns a deep copy of this Phylogeny.
Phylogeny	Phylogeny.copyShallow(PhylogenyNode source)
static 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 java.util.List<PhylogenyNode>	PhylogenyMethods.getAllDescendants(PhylogenyNode node)
static java.awt.Color	PhylogenyMethods.getBranchColorValue(PhylogenyNode node)	Convenience method
static double	PhylogenyMethods.getBranchWidthValue(PhylogenyNode node)	Convenience method
int	PhylogenyNode.getChildNodeIndex(PhylogenyNode parent)	This gets the child node index of this node, given that parent is its parent
static double	PhylogenyMethods.getConfidenceValue(PhylogenyNode node)	Convenience method
static double[]	PhylogenyMethods.getConfidenceValuesAsArray(PhylogenyNode node)	Convenience method
PhylogenyNode	PhylogenyBranch.getConnectedNode(PhylogenyNode node)
static 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)
java.util.List<PhylogenyNode>	Phylogeny.getParalogousNodes(PhylogenyNode n, java.lang.String[] taxonomyCodeRange)	Returns all paralogs of the external PhylogenyNode n of this Phylogeny.
static java.lang.String	PhylogenyMethods.getSpecies(PhylogenyNode node)	Convenience method for display purposes.
static java.lang.String	PhylogenyMethods.getTaxonomyIdentifier(PhylogenyNode node)	Convenience method for display purposes.
static boolean	PhylogenyMethods.isAllDecendentsAreDuplications(PhylogenyNode n)
boolean	PhylogenyBranch.isDirectionTowards(PhylogenyNode node)
static boolean	PhylogenyMethods.isHasExternalDescendant(PhylogenyNode node)
static java.util.Map<Taxonomy,java.lang.Integer>	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.
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, java.awt.Color color)
static void	PhylogenyMethods.setBranchWidthValue(PhylogenyNode node, double branch_width_value)	Convenience method
void	PhylogenyNode.setChild1(PhylogenyNode n)	Sets the first child PhylogenyNode of this PhylogenyNode to n.
void	PhylogenyNode.setChild2(PhylogenyNode n)	Sets the second child PhylogenyNode of this PhylogenyNode to n.
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, java.lang.String type)	Convenience method.
void	PhylogenyBranch.setDirectionTowards(PhylogenyNode node)
void	PhylogenyNode.setLink(PhylogenyNode n)	Sets the linked PhylogenyNode of this PhylogenyNode to n.
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, java.lang.String scientific_name)
static void	PhylogenyMethods.setTaxonomyCode(PhylogenyNode node, java.lang.String taxonomy_code)	Convenience method to set the taxonomy code of a phylogeny node.
static void	PhylogenyMethods.sortNodeDescendents(PhylogenyNode node, PhylogenyMethods.DESCENDANT_SORT_PRIORITY pri)

Method parameters in org.forester.phylogeny with type arguments of type PhylogenyNode

Modifier and Type	Method	Description
void	Phylogeny.setIdToNodeMap(java.util.HashMap<java.lang.Long,PhylogenyNode> idhash)

Constructors in org.forester.phylogeny with parameters of type PhylogenyNode

Constructor	Description
PhylogenyBranch(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 PhylogenyNode

Modifier and Type	Method	Description
PhylogenyNode	PostOrderStackObject.getNode()
PhylogenyNode	ExternalForwardIterator.next()
PhylogenyNode	LevelOrderTreeIterator.next()	Returns the next PhylogenyNode.
PhylogenyNode	PhylogenyNodeIterator.next()
PhylogenyNode	PostorderTreeIterator.next()	Advances the Iterator by one.
PhylogenyNode	PreorderTreeIterator.next()	Advances the Iterator by one.

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

Constructor	Description
LevelOrderTreeIterator(PhylogenyNode node)	Creates a new LevelOrderTreeIterator for iterating over all the child nodes of PhylogenyNode node (including node itself).
PostOrderStackObject(PhylogenyNode n, int i)
PreorderTreeIterator(PhylogenyNode node)

Uses of PhylogenyNode in org.forester.rio

Methods in org.forester.rio that return types with arguments of type PhylogenyNode

Modifier and Type	Method	Description
java.util.List<PhylogenyNode>	RIO.getRemovedGeneTreeNodes()

Uses of PhylogenyNode in org.forester.sdi

Methods in org.forester.sdi that return types with arguments of type PhylogenyNode

Modifier and Type	Method	Description
java.util.Set<PhylogenyNode>	GSDI.getMappedExternalSpeciesTreeNodes()
java.util.Set<PhylogenyNode>	GSDII.getMappedExternalSpeciesTreeNodes()
java.util.Set<PhylogenyNode>	GSDIR.getMappedExternalSpeciesTreeNodes()
java.util.List<PhylogenyNode>	GSDI.getStrippedExternalGeneTreeNodes()
java.util.List<PhylogenyNode>	GSDII.getStrippedExternalGeneTreeNodes()
java.util.List<PhylogenyNode>	GSDIR.getStrippedExternalGeneTreeNodes()
java.util.List<PhylogenyNode>	GSDI.getStrippedSpeciesTreeNodes()
java.util.List<PhylogenyNode>	GSDII.getStrippedSpeciesTreeNodes()
java.util.List<PhylogenyNode>	GSDIR.getStrippedSpeciesTreeNodes()

Uses of PhylogenyNode in org.forester.tools

Method parameters in org.forester.tools with type arguments of type PhylogenyNode

Modifier and Type	Method	Description
boolean	TreeSplitMatrix.match(java.util.Set<PhylogenyNode> query_nodes)

Constructor parameters in org.forester.tools with type arguments of type PhylogenyNode

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.

Uses of PhylogenyNode in org.forester.util

Methods in org.forester.util with parameters of type PhylogenyNode

Modifier and Type	Method	Description
static void	ForesterUtil.ensurePresenceOfDate(PhylogenyNode node)
static void	ForesterUtil.ensurePresenceOfDistribution(PhylogenyNode node)
static void	ForesterUtil.ensurePresenceOfSequence(PhylogenyNode node)
static void	ForesterUtil.ensurePresenceOfTaxonomy(PhylogenyNode node)
static Accession	SequenceAccessionTools.obtainAccessorFromDataFields(PhylogenyNode n)
static Accession	SequenceAccessionTools.obtainFromSeqAccession(PhylogenyNode n)
static java.lang.String	SequenceAccessionTools.obtainGenbankAccessorFromDataFields(PhylogenyNode n)
static java.lang.String	SequenceAccessionTools.obtainGiNumberFromDataFields(PhylogenyNode n)
static java.lang.String	SequenceAccessionTools.obtainRefSeqAccessorFromDataFields(PhylogenyNode n)
static java.lang.String	SequenceAccessionTools.obtainUniProtAccessorFromDataFields(PhylogenyNode n)

Uses of PhylogenyNode in org.forester.ws.seqdb

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

Modifier and Type	Method	Description
static Accession	SequenceDbWsTools.obtainSeqAccession(PhylogenyNode node)
static void	SequenceDbWsTools.obtainSeqInformation(boolean allow_to_set_taxonomic_data, int lines_to_return, java.util.SortedSet<java.lang.String> not_found, PhylogenyNode node)
static void	SequenceDbWsTools.obtainSeqInformation(boolean allow_to_set_taxonomic_data, java.util.SortedSet<java.lang.String> not_found, PhylogenyNode node)
static void	SequenceDbWsTools.obtainSeqInformation(PhylogenyNode node)