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