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