Package edu.msu.cme.rdp.classifier.io

Examples of edu.msu.cme.rdp.classifier.io.TreeFileParser

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        if (!(isProbIndexArrDone || isGenusWordProbListDone || isWordPriorArrDone)) {
            throw new IllegalStateException("Error: The bergeyTree file should be read after "
                    + "at least one of the other training files");
        }

        TreeFileParser parser = new TreeFileParser();
        rootTree = parser.createTree(reader, hierarchyVersion);

        createGenusNodeList(rootTree);

        logLeaveCountArr = new float[genusNodeList.size()];

        for (HierarchyTree node : genusNodeList) {
            logLeaveCountArr[node.getGenusIndex()] = (float) Math.log(node.getLeaveCount() + 1);
        }
        this.trainRank = parser.getTrainRank();
        isTreeDone = true;
    }
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  }
 
  /** Test of parseTreeFile method, of class classification.TrainingFileParser. */
  public void testParseTreeFile() throws Exception{
    System.out.println("testParseTreeFile");
    TreeFileParser parser = new TreeFileParser();
    InputStream dstream = System.class.getResourceAsStream("/test/classifier/testTreeFile.xml");
    HierarchyVersion hVersion = null;
   
    Reader in =  new InputStreamReader( dstream );
    HierarchyTree root = parser.createTree(in, null);
    assertEquals(root.getName(), "BACTERIA");
    assertEquals(root.getLeaveCount(), 4123);
    assertEquals(root.getSizeofSubclasses(), 3);
    //displayTrainingTree(root);
   
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Related Classes of edu.msu.cme.rdp.classifier.io.TreeFileParser

  • edu.msu.cme.rdp.classifier.HierarchyTree
  • edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParserTest
  • edu.msu.cme.rdp.classifier.TrainingInfo
  • edu.msu.cme.rdp.classifier.utils.HierarchyVersion
  • org.xml.sax.InputSource
  • java.io.BufferedReader
  • javax.xml.parsers.SAXParser
  • javax.xml.parsers.SAXParserFactory
  • java.io.StringReader
  • org.xml.sax.SAXException
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