Package edu.msu.cme.rdp.classifier.train
Class TreeFactory
java.lang.Object
edu.msu.cme.rdp.classifier.train.TreeFactory
A TreeFactory reads the raw taxonomic information and creates the RawHierarchyTree nodes.
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Constructor Summary
ConstructorsConstructorDescriptionTreeFactory
(Reader taxReader, int trainsetNo, String version, String modification) Creates new TreeFactory. -
Method Summary
Modifier and TypeMethodDescriptiongetRoot()
Gets the root of the treevoid
parseCopyNumberFile
(String cnFile) parse the copy number file first step, take the copy number info from the lowest rank taxa, then calculate the copy number of the parent taxa based on the immediate children second step, for any taxon without copy number info, uses thevoid
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Constructor Details
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TreeFactory
public TreeFactory(Reader taxReader, int trainsetNo, String version, String modification) throws IOException, NameRankDupException Creates new TreeFactory.- Throws:
IOException
NameRankDupException
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Method Details
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parseSequenceFile
- Throws:
IOException
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parseCopyNumberFile
parse the copy number file first step, take the copy number info from the lowest rank taxa, then calculate the copy number of the parent taxa based on the immediate children second step, for any taxon without copy number info, uses the- Parameters:
cnFile
-- Throws:
IOException
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getRoot
Gets the root of the tree
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