Uses of Class
org.forester.phylogeny.PhylogenyNode
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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)
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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)
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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)
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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)
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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)
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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 phylogeniesstatic 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 methodstatic double
PhylogenyMethods. getBranchWidthValue(PhylogenyNode node)
Convenience methodint
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 methodPhylogenyNode
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 methodvoid
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)
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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)
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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()
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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()
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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)
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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)
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