Package edu.msu.cme.rdp.classifier.io

Class TreeFileParser

  • All Implemented Interfaces:
    org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler
    public class TreeFileParser
extends org.xml.sax.helpers.DefaultHandler
    A parser to parse a reader containing taxonomic training information. Note: The first TreeNode is the root TreeNode.

    • Constructor Summary

      Constructors 
      Constructor Description
      TreeFileParser()
      Creates a new instance of TreeFileParser.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      HierarchyTree createTree​(java.io.Reader in, HierarchyVersion version)
      Reads from a reader that contains the information for each treenode.
      void endElement​(java.lang.String str, java.lang.String str1, java.lang.String str2)  
      void error​(org.xml.sax.SAXParseException e)  
      java.lang.String getTrainRank()  
      void startElement​(java.lang.String namespaceURI, java.lang.String lName, java.lang.String qName, org.xml.sax.Attributes attrs)  

      • Methods inherited from class org.xml.sax.helpers.DefaultHandler

        characters, endDocument, endPrefixMapping, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startDocument, startPrefixMapping, unparsedEntityDecl, warning

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • TreeFileParser

        public TreeFileParser()
        Creates a new instance of TreeFileParser.

    • Method Detail

      • getTrainRank

        public java.lang.String getTrainRank()

      • createTree

        public HierarchyTree createTree​(java.io.Reader in,
                                HierarchyVersion version)
                         throws java.io.IOException,
                                TrainingDataException
        Reads from a reader that contains the information for each treenode. Creates all the HierarchyTrees and returns the root of the trees. Note: The first TreeNode is the root TreeNode. The version information should be obtained from the other files first.
        Throws:
        java.io.IOException
        TrainingDataException

      • startElement

        public void startElement​(java.lang.String namespaceURI,
                         java.lang.String lName,
                         java.lang.String qName,
                         org.xml.sax.Attributes attrs)
                  throws org.xml.sax.SAXException
        Specified by:
        startElement in interface org.xml.sax.ContentHandler
        Overrides:
        startElement in class org.xml.sax.helpers.DefaultHandler
        Throws:
        org.xml.sax.SAXException

      • endElement

        public void endElement​(java.lang.String str,
                       java.lang.String str1,
                       java.lang.String str2)
                throws org.xml.sax.SAXException
        Specified by:
        endElement in interface org.xml.sax.ContentHandler
        Overrides:
        endElement in class org.xml.sax.helpers.DefaultHandler
        Throws:
        org.xml.sax.SAXException

      • error

        public void error​(org.xml.sax.SAXParseException e)
           throws org.xml.sax.SAXException
        Specified by:
        error in interface org.xml.sax.ErrorHandler
        Overrides:
        error in class org.xml.sax.helpers.DefaultHandler
        Throws:
        org.xml.sax.SAXException