public class HierarchyTree
extends java.lang.Object
Constructor and Description |
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HierarchyTree(java.lang.String n,
HierarchyTree p,
Taxonomy tax)
Creates new HierarchyTree given the name and its parent
|
Modifier and Type | Method and Description |
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void |
changeParentSeqCount(int i) |
void |
createWordOccurrenceFromSubclasses()
creates the word occurrence array from its children if the word occurrence
for this node does not exist
|
java.util.Collection |
getLeaves()
Gets the array of Sequenceleaves if any
|
int |
getMissCount() |
java.lang.String |
getName()
Gets the name of the treenode
|
void |
getNodeList(java.lang.String level,
java.util.List nodeList)
get all the lowest level nodes in given hierarchy level starting from the given root
|
void |
getNodeMap(java.lang.String level,
java.util.HashMap<java.lang.String,HierarchyTree> nodeMap)
get all the lowest level nodes in given hierarchy level starting from the given root
|
int |
getNumberofUniqueWords() |
int |
getNumOfLeaves()
Counts the number of sequence leaves below this tree
|
int |
getNumTotalTestedseq() |
HierarchyTree |
getParent()
Gets the parent treenode
|
int |
getSizeofChildren()
Gets the size of the children
|
int |
getSizeofLeaves()
Gets the size of sequence leaves directly belong to this tree, not
including the hidden leaves
|
int |
getSizeofSubclasses()
Gets the size of the subclasses
|
HierarchyTree |
getSubclassbyName(java.lang.String n)
Gets the subclass with the given name
|
java.util.Collection<HierarchyTree> |
getSubclasses()
Gets the array of the subclasses if any
|
Taxonomy |
getTaxonomy() |
int |
getTotalSeqs() |
int |
getWordOccurrence(int wordIndex)
Gets the word occurrence for the given word index
|
int |
getWordOccurrenceSize() |
void |
hideSeq(edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator iterator)
This method hides a sequence by removing the words of that sequence
from the total wordOccurrence
|
void |
incMissCount() |
void |
incNumTotalTestedseq() |
void |
increTotalSeqs() |
void |
initWordOccurrence(LineageSequence pSeq,
float[] wordPriorArr,
boolean initWordOccurrence)
This method initiate the word occurrence from the sequences for the
lowest level of the hierarchy tree
|
boolean |
isSingleton() |
boolean |
isWordOccurDone() |
void |
unhideSeq(edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator iterator)
This method initiate the word occurrence from the sequences for the
lowest level of the hierarchy tree
|
public HierarchyTree(java.lang.String n, HierarchyTree p, Taxonomy tax)
public java.lang.String getName()
public HierarchyTree getParent()
public java.util.Collection<HierarchyTree> getSubclasses()
public java.util.Collection getLeaves()
public HierarchyTree getSubclassbyName(java.lang.String n)
public int getSizeofChildren()
public int getSizeofSubclasses()
public int getSizeofLeaves()
public void initWordOccurrence(LineageSequence pSeq, float[] wordPriorArr, boolean initWordOccurrence) throws java.io.IOException
java.io.IOException
public void unhideSeq(edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator iterator) throws java.io.IOException
java.io.IOException
public void hideSeq(edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator iterator) throws java.io.IOException
java.io.IOException
public void changeParentSeqCount(int i)
public boolean isWordOccurDone()
public int getWordOccurrenceSize()
public int getNumberofUniqueWords()
public void createWordOccurrenceFromSubclasses()
public int getWordOccurrence(int wordIndex)
public int getNumOfLeaves()
public void increTotalSeqs()
public int getTotalSeqs()
public int getMissCount()
public int getNumTotalTestedseq()
public void incNumTotalTestedseq()
public void incMissCount()
public Taxonomy getTaxonomy()
public boolean isSingleton()
public void getNodeList(java.lang.String level, java.util.List nodeList)
public void getNodeMap(java.lang.String level, java.util.HashMap<java.lang.String,HierarchyTree> nodeMap)