public class TreeFactory
extends java.lang.Object
Constructor and Description |
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TreeFactory(java.io.Reader taxReader,
int trainsetNo,
java.lang.String version,
java.lang.String modification)
Creates new TreeFactory.
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Modifier and Type | Method and Description |
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RawHierarchyTree |
getRoot()
Gets the root of the tree
|
void |
parseCopyNumberFile(java.lang.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 the
|
void |
parseSequenceFile(LineageSequenceParser parser) |
public TreeFactory(java.io.Reader taxReader, int trainsetNo, java.lang.String version, java.lang.String modification) throws java.io.IOException, NameRankDupException
java.io.IOException
NameRankDupException
public void parseSequenceFile(LineageSequenceParser parser) throws java.io.IOException
java.io.IOException
public void parseCopyNumberFile(java.lang.String cnFile) throws java.io.IOException
cnFile
- java.io.IOException
public RawHierarchyTree getRoot()