Uses of Class
BioinfoFieldExtractor.PhylogenTree

Packages that use PhylogenTree

BioinfoFieldExtractor

Uses of PhylogenTree in BioinfoFieldExtractor

Methods in BioinfoFieldExtractor that return PhylogenTree

PhylogenTree	MultiSequenceAligner.assignTreeAlignments(PhylogenTree root) Assigns the aligned messages sequences to the tree
PhylogenTree	UPGMA.buildTree() This method performs UPGMA algorithm to build a tree with clusters characterizing the closest related elements of the sequence.
PhylogenTree	PhylogenTree.getLeftChild() Returns the left child
PhylogenTree	PhylogenTree.getParent() Returns the parent node
PhylogenTree	PhylogenTree.getRightChild() Returns the right child

Methods in BioinfoFieldExtractor that return types with arguments of type PhylogenTree

java.util.ArrayList<PhylogenTree>

UPGMA.getClusters() Returns the clusters

Methods in BioinfoFieldExtractor with parameters of type PhylogenTree

java.util.ArrayList<java.util.ArrayList<java.lang.Integer>>	MultiSequenceAligner.alignMultipleSequences(java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> list, java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> gaps, PhylogenTree root)
PhylogenTree	MultiSequenceAligner.assignTreeAlignments(PhylogenTree root) Assigns the aligned messages sequences to the tree
void	UPGMA.clusterTrees(PhylogenTree root) Cluster "closely-related" trees into clusters
float	UPGMA.findDistance(PhylogenTree tree1, PhylogenTree tree2) Returns the distance between two clusters
static void	BioTester.printCluster(PhylogenTree t)
void	PhylogenTree.setLeftChild(PhylogenTree l) Sets the left child
void	PhylogenTree.setParent(PhylogenTree p) Sets the parent
void	PhylogenTree.setRightChild(PhylogenTree r) Sets the right child