Package edu.msu.cme.rdp.classifier.train
Class RawHierarchyTree
java.lang.Object
edu.msu.cme.rdp.classifier.train.RawHierarchyTree
A RawHierarchyTree holds the raw taxon and sequences information.
A RawHierarchyTree can only have one type of children:
child treenodes or child sequences.
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Constructor Summary
ConstructorsConstructorDescriptionRawHierarchyTree
(String n, RawHierarchyTree p, Taxonomy tax) Creates new RawHierarchyTree given the name and its parent. -
Method Summary
Modifier and TypeMethodDescriptionfloat
int
Returns the genus index of this treenode.int
int
Counts the number of sequence leaves below this tree.getName()
Gets the name of the treenode.void
getNodeMap
(String level, HashMap<String, RawHierarchyTree> nodeMap) get all the lowest level nodes in given hierarchy level starting from the given rootint
Counts the number of non-singleton sequence leaves below this tree.Gets the parent treenode.int
Gets the size of the children, either taxon children or sequence leaves.int
Gets the size of the child treenodes.Gets the child treenode with the given name.Gets the array of the subclasses if any.Returns the taxon object of this treenode.int
getWordOccurrence
(int wordIndex) Gets the word occurrence for the given word index.int
Returns the size of the array wordOccurrence.boolean
void
initWordOccurrence
(LineageSequence pSeq, float[] wordPriorArr) This method initiates the word occurrences from a sequence for the lowest level of the hierarchy tree.boolean
void
Resets the array wordOccurrence to null.protected void
setCopyNumber
(float c) void
setGenusIndex
(int i) Sets the genus index of this treenode.
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Constructor Details
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RawHierarchyTree
Creates new RawHierarchyTree given the name and its parent. Note: a RawHierarchyTree can only have one type of children: child treenodes or child sequences. Usually the lowest ranked nodes contain the sequence leaves.
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Method Details
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setCopyNumber
protected void setCopyNumber(float c) -
getCopyNumber
public float getCopyNumber() -
hasCopyNumber
public boolean hasCopyNumber() -
getName
Gets the name of the treenode. -
getParent
Gets the parent treenode. -
getSubclasses
Gets the array of the subclasses if any. -
getSubclassbyName
Gets the child treenode with the given name. -
getSizeofChildren
public int getSizeofChildren()Gets the size of the children, either taxon children or sequence leaves. -
getSizeofSubclasses
public int getSizeofSubclasses()Gets the size of the child treenodes. -
initWordOccurrence
This method initiates the word occurrences from a sequence for the lowest level of the hierarchy tree. Duplicate words from one sequence will be count only once.- Throws:
IOException
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getWordOccurrenceSize
public int getWordOccurrenceSize()Returns the size of the array wordOccurrence. -
getWordOccurrence
public int getWordOccurrence(int wordIndex) Gets the word occurrence for the given word index. -
releaseWordOccurrence
public void releaseWordOccurrence()Resets the array wordOccurrence to null. -
getLeaveCount
public int getLeaveCount()Counts the number of sequence leaves below this tree. -
getGenusNodeCount
public int getGenusNodeCount() -
isSingleton
public boolean isSingleton() -
getNonSingletonLeaveCount
public int getNonSingletonLeaveCount()Counts the number of non-singleton sequence leaves below this tree. -
getTaxonomy
Returns the taxon object of this treenode. -
setGenusIndex
public void setGenusIndex(int i) Sets the genus index of this treenode. -
getGenusIndex
public int getGenusIndex()Returns the genus index of this treenode. -
getNodeMap
get all the lowest level nodes in given hierarchy level starting from the given root
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