Package edu.msu.cme.rdp.classifier
Class HierarchyTree
java.lang.Object
edu.msu.cme.rdp.classifier.HierarchyTree
A HierarchyTree holds the taxonomic information of a taxon.
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Constructor Summary
ConstructorsConstructorDescriptionHierarchyTree
(String n, int taxid, String rank, int leaves, int gIndex) HierarchyTree
(String n, int taxid, String rank, int leaves, int gIndex, double copyNumber) Creates new HierarchyTree given the taxonomic information. -
Method Summary
Modifier and TypeMethodDescriptionvoid
Adds the parent HierarchyTree, also adds this node to the parent treenode as a child.double
int
Gets the index of the genus treenode in the genusNodeList.int
Gets the size of sequence leaves directly belong to this treenode.getName()
Gets the name of the treenode.Gets the parent treenode.getRank()
Gets the rank of the treenode.int
Gets the list of the child treenodes.Gets the name of the treenode.int
getTaxid()
Gets the taxon id of the treenode.boolean
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Constructor Details
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HierarchyTree
Creates new HierarchyTree given the taxonomic information. -
HierarchyTree
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Method Details
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addParent
Adds the parent HierarchyTree, also adds this node to the parent treenode as a child. -
getName
Gets the name of the treenode. -
getParent
Gets the parent treenode. -
getRank
Gets the rank of the treenode. -
getTaxid
public int getTaxid()Gets the taxon id of the treenode. -
getSubclasses
Gets the name of the treenode. -
getSizeofSubclasses
public int getSizeofSubclasses()Gets the list of the child treenodes. -
getChild
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getLeaveCount
public int getLeaveCount()Gets the size of sequence leaves directly belong to this treenode. -
getGenusIndex
public int getGenusIndex()Gets the index of the genus treenode in the genusNodeList. Returns -1 if not a genus node. -
getCopyNumber
public double getCopyNumber() -
hasCopyNumberInfo
public boolean hasCopyNumberInfo()- Returns:
- true if the taxon has copy number information
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