Class TreeFactory
- java.lang.Object
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- edu.msu.cme.rdp.classifier.train.validation.TreeFactory
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public class TreeFactory extends java.lang.Object
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Constructor Summary
Constructors Constructor Description TreeFactory(java.io.Reader taxReader)
Creates new TreeFactory
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description HierarchyTree
addSequence(LineageSequence pSeq)
For the given sequence name, its ancestors, and the sequence, creates a HierarchyTree for each ancestor, If the root does not exist, creates the root with a null parent.HierarchyTree
addSequence(LineageSequence pSeq, boolean initWordOccurrence)
void
buildTree()
build the taxonomic tree without sequences attached to itvoid
calculateWordPrior()
void
displayTreePhylo(HierarchyTree root, java.lang.String index, int indent)
display the phylogenetic tree for each node, display the index and the name for each sequence, diaplay the name and the descriptionjava.lang.String
getLowestRank()
java.util.Set<java.lang.String>
getRankSet()
HierarchyTree
getRoot()
Gets the root of the treeTaxonomy
getTaxonomy(java.lang.String seqName, java.lang.String ancestorName, int pid, int index)
float
getWordPrior(int wordIndex)
void
printWordPriors()
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Method Detail
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buildTree
public void buildTree()
build the taxonomic tree without sequences attached to it
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addSequence
public HierarchyTree addSequence(LineageSequence pSeq) throws java.io.IOException
For the given sequence name, its ancestors, and the sequence, creates a HierarchyTree for each ancestor, If the root does not exist, creates the root with a null parent. If the root is already exist, checks the ParsedSequence to see if its oldest ancestor is the same as the previous root.- Throws:
java.io.IOException
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addSequence
public HierarchyTree addSequence(LineageSequence pSeq, boolean initWordOccurrence) throws java.io.IOException
- Throws:
java.io.IOException
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getTaxonomy
public Taxonomy getTaxonomy(java.lang.String seqName, java.lang.String ancestorName, int pid, int index)
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getRoot
public HierarchyTree getRoot()
Gets the root of the tree
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getRankSet
public java.util.Set<java.lang.String> getRankSet()
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getLowestRank
public java.lang.String getLowestRank()
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displayTreePhylo
public void displayTreePhylo(HierarchyTree root, java.lang.String index, int indent)
display the phylogenetic tree for each node, display the index and the name for each sequence, diaplay the name and the description
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calculateWordPrior
public void calculateWordPrior()
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printWordPriors
public void printWordPriors() throws java.io.IOException
- Throws:
java.io.IOException
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getWordPrior
public float getWordPrior(int wordIndex)
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