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 root
`int`	`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.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- 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

Class RawHierarchyTree

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

RawHierarchyTree

Method Detail

setCopyNumber

getCopyNumber

hasCopyNumber

getName

getParent

getSubclasses

getSubclassbyName

getSizeofChildren

getSizeofSubclasses

initWordOccurrence

getWordOccurrenceSize

getWordOccurrence

releaseWordOccurrence

getLeaveCount

getGenusNodeCount

isSingleton

getNonSingletonLeaveCount

getTaxonomy

setGenusIndex

getGenusIndex

getNodeMap