Package edu.msu.cme.rdp.classifier.train

Class TreeFactory

  • public class TreeFactory
extends java.lang.Object
    A TreeFactory reads the raw taxonomic information and creates the RawHierarchyTree nodes.

    • Constructor Summary

      Constructors 
      Constructor Description
      TreeFactory​(java.io.Reader taxReader, int trainsetNo, java.lang.String version, java.lang.String modification)
      Creates new TreeFactory.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      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)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • TreeFactory

        public TreeFactory​(java.io.Reader taxReader,
                   int trainsetNo,
                   java.lang.String version,
                   java.lang.String modification)
            throws java.io.IOException,
                   NameRankDupException
        Creates new TreeFactory.
        Throws:
        java.io.IOException
        NameRankDupException

    • Method Detail

      • parseSequenceFile

        public void parseSequenceFile​(LineageSequenceParser parser)
                       throws java.io.IOException
        Throws:
        java.io.IOException

      • parseCopyNumberFile

        public void parseCopyNumberFile​(java.lang.String cnFile)
                         throws java.io.IOException
        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:
        java.io.IOException