Package edu.msu.cme.rdp.readseq.utils.orientation

Examples of edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator

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            leaveCount = 1;
        } else {
            leaveCount++;
        }

        GoodWordIterator iterator = new GoodWordIterator(pSeq.getSeqString());
        if (wordOccurrence == null) {
            wordOccurrence = new int[iterator.getMask() + 1];
        }

        // create a temporary list and initialize the value to be -1;
        int[] wordList = new int[iterator.getNumofWords()];

        for (int i = 0; i < wordList.length; i++) {
            wordList[i] = -1;
        }

        int numUniqueWords = 0;  // indicate the number of unique words
        // duplicated words in one sequence are only counted once
        while (iterator.hasNext()) {
            int index = iterator.next();  // index is the actual integer representation of the word

            if (!isWordExist(wordList, index)) {
                wordList[numUniqueWords] = index;
                wordOccurrence[index]++;
                numUniqueWords++;
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    }
   
  /* partial sequences with good words only
   */
  public GoodWordIterator getPartialSeqIteratorbyGoodBases(int num_good_bases) throws IOException{
    GoodWordIterator wordIterator = null;
    String sequence = super.getSeqString();
    int size = sequence.length();
    if ( size < num_good_bases) {
        return wordIterator;
    }

    double d = Math.random();
    int loc = (int)Math.round((double)(size * d ) );
    String newSeq = sequence.substring(loc,size) + marker + sequence.substring(0,loc);

    int numGoodBases = 0;

    StringReader in = new StringReader(newSeq);

    int offset = 0;

    int c;
    while ( (c = in.read()) != -1 ){
      if ( numGoodBases == num_good_bases){
        break;
      }
      int charIndex = GoodWordIterator.getCharIndex(c);

      if ( charIndex != -1){
        numGoodBases ++;
      }else {
        numGoodBases = 0;
      }

      offset ++;
    }

    in.close();
    if (numGoodBases == num_good_bases){
      String partialSeq = newSeq.substring(offset - num_good_bases, offset);
      //System.err.println(">" + this.getName() + " " + this.getLineage() + "\n" + partialSeq + " NUM_GOOD_BASES=" + numGoodBases);
      wordIterator = new GoodWordIterator(partialSeq);
       if ( wordIterator.getNumofWords() == 0){
            wordIterator = null;
        }
    }

    return wordIterator;
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        int i = 0;
        Iterator seqIt = seqList.iterator();
        while (seqIt.hasNext()) {
            LineageSequence pSeq = (LineageSequence) seqIt.next();

            GoodWordIterator wordIterator = getPartialSeqIteratorbyWindow(pSeq, window); // full sequence 

            if (wordIterator == null) {
                continue;
            }
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        // at least half of the window size.

        if (seqString.length() < FindWindowFrame.window_size / 2) {
            return null;
        }
        GoodWordIterator wordIterator = new GoodWordIterator(seqString);
        if (wordIterator.getNumofWords() == 0) {
            wordIterator = null;
        }
        return wordIterator;
    }
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            numOfLeaves++;
        }
       
        if ( !initWordOccurrence) return;

        GoodWordIterator iterator = new GoodWordIterator(pSeq.getSeqString());
        if (wordOccurrence == null) {
            wordOccurrence = new short[iterator.getMask() + 1];
        }

        // create a temporary list and initialize the value to be -1;
        int[] wordList = new int[iterator.getNumofWords()];

        for (int i = 0; i < wordList.length; i++) {
            wordList[i] = -1;
        }

        int numUniqueWords = 0;  // indicate the number of unique words
        // duplicated words in one sequence are only counted once
        while (iterator.hasNext()) {
            int index = iterator.next();  // index is the actual integer representation of the word
           
            if (!isWordExist(wordList, index)) {
                wordList[numUniqueWords] = index;
                wordOccurrence[index]++;
                numUniqueWords++;
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        while (parser.hasNext()) {
            LineageSequence pSeq = parser.next();
            if (pSeq.getSeqString().length() == 0) {
                continue;
            }
            GoodWordIterator wordIterator = null;
            if (numGoodBases > 0) {
                wordIterator = pSeq.getPartialSeqIteratorbyGoodBases(numGoodBases);  // test partial sequences with good words only

            } else {
                wordIterator = new GoodWordIterator(pSeq.getSeqString()); // full sequence 
            }

            if (wordIterator == null || wordIterator.getNumofWords() == 0) {
                //System.err.println(pSeq.getSeqName() + " unable to find good subsequence with length " + numGoodBases);
                continue;
            }

            //for leave-one-out testing, we need to remove the word occurrence for
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            totalSeq ++;
          LineageSequence pSeq = parser.next();
          if ( !selectedTestSeqIDs.contains(pSeq.getSeqName()) || pSeq.getSeqString().length() == 0){
              continue;
          }
          GoodWordIterator wordIterator = null ;
          if ( partialLength != null ){
                wordIterator = pSeq.getPartialSeqIteratorbyGoodBases(partialLength.intValue());  // test partial sequences with good words only

          }else {
                wordIterator = new GoodWordIterator(pSeq.getSeqString()); // full sequence
          }

          if (wordIterator == null || wordIterator.getNumofWords() == 0){
            //System.err.println(pSeq.getSeqName() + " unable to find good sequence");
            continue;
          }
       
          List result = dm.getBestClasspath( wordIterator, genusNodeMap, useSeed, min_bootstrap_words);
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        //test hide and unhide sequence 1 which belong to child1
        String seq1 = "AAAAAAAAAGUCACCCCCCCCUGA";     // belong to child1     

        GoodWordIterator seq_iterator = new GoodWordIterator(seq1);
        assertEquals(2, c1.getNumOfLeaves());
        c1.hideSeq(seq_iterator);
        assertEquals(1, c1.getNumOfLeaves());
        assertEquals(1, c2.getNumOfLeaves());
        assertEquals(2, root.getNumOfLeaves());

        assertEquals(0, c1.getWordOccurrence(0)); //AAAAAAAA
        assertEquals(1, c1.getWordOccurrence(2)); //AAAAAAAG
        // assertEquals(2, root.getWordOccurrence(39) );   //AAAAAGUC

        c1.unhideSeq(seq_iterator);
        assertEquals(2, c1.getNumOfLeaves());
        assertEquals(3, root.getNumOfLeaves());

        assertEquals(1, c1.getWordOccurrence(0)); //AAAAAAAA    
        // assertEquals(2, root.getWordOccurrence(65535) );   //CCCCCCCC

        //est hide and unhide sequence 2 which belong to child2
        String seq2 = "AAAAUAAAAAGUCCCCCCCCUG"; // belong to child2
        seq_iterator = new GoodWordIterator(seq2);
        c2.hideSeq(seq_iterator);
        assertEquals(2, c1.getNumOfLeaves());
        assertEquals(0, c2.getNumOfLeaves());
        assertEquals(2, root.getNumOfLeaves());
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        // test the first sequence
        File queryReader = new File(System.class.getResource("/test/classifier/testNBClassifierSet.fasta").getFile());       
        parser = new LineageSequenceParser(queryReader);
        LineageSequence pSeq = parser.next();
        GoodWordIterator iterator = new GoodWordIterator(pSeq.getSeqString());
        NBClassifier classifier = new NBClassifier(factory, iterator.getWordArr(), nodeList, useSeed, min_bootstrap_words);

        assertEquals(pSeq.getSeqName(), "XG1_child1");       
        ValidationClassificationResult result = classifier.assignClass();
        assertEquals("G1", ((HierarchyTree) result.getBestClass()).getName());
        assertTrue(0.1 > result.getPosteriorProb());


        pSeq = parser.next();
        // test the 3rd getSequence()
        pSeq = parser.next();
        assertEquals(pSeq.getSeqName(), "XG2_child1");
        iterator = new GoodWordIterator(pSeq.getSeqString());
        classifier = new NBClassifier(factory, iterator.getWordArr(), nodeList, useSeed, min_bootstrap_words);
        result = classifier.assignClass();
        assertEquals("G2", ((HierarchyTree) result.getBestClass()).getName());
        assertTrue(0.2 > result.getPosteriorProb());


        pSeq = parser.next();
        // test the 5th getSequence()
        pSeq = parser.next();
        assertEquals(pSeq.getSeqName(), "XPh2G6_child1");
        iterator = new GoodWordIterator(pSeq.getSeqString());
        classifier = new NBClassifier(factory, iterator.getWordArr(), nodeList, useSeed, min_bootstrap_words);
        result = classifier.assignClass();
        assertEquals("G1", ((HierarchyTree) result.getBestClass()).getName());
        assertTrue(0.2 > result.getPosteriorProb());

        //test the 8th sequence in G7, it is the same as the 9th sequence in G8
        // the classifier should randomly choose a genus (either G7 or G8) because the score will be tie
        parser.next();
        parser.next();
        pSeq = parser.next();
        assertEquals(pSeq.getSeqName(), "XPh2G7_child1");
        iterator = new GoodWordIterator(pSeq.getSeqString());
        int G7_count = 0;
        int G8_count = 0;
        for ( int run = 0; run < DecisionMaker.NUM_OF_RUNS; run++){
            classifier = new NBClassifier(factory, iterator.getWordArr(), nodeList, useSeed, min_bootstrap_words);
            result = classifier.assignClass();
            if ( ((HierarchyTree) result.getBestClass()).getName().equals("G7")){
                G7_count ++;
            }else if ( ((HierarchyTree) result.getBestClass()).getName().equals("G8")){
                G8_count ++;
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  private String seq = "AAAAAAAAAG-CCCCCCCCUGAGGGUUACnAA";
  private GoodWordIterator wordIt;
 
  public GoodWordIteratorTest(java.lang.String testName) throws IOException{
    super(testName);   
    wordIt = new GoodWordIterator(seq);
  }
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Related Classes of edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator

  • edu.msu.cme.rdp.classifier.train.GoodWordIteratorTest
  • edu.msu.cme.rdp.classifier.train.LineageSequence
  • edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  • edu.msu.cme.rdp.classifier.train.validation.crossvalidate.CrossValidate
  • edu.msu.cme.rdp.classifier.train.validation.GoodWordIteratorTest
  • edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  • edu.msu.cme.rdp.classifier.train.validation.HierarchyTreeTest
  • edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTester
  • edu.msu.cme.rdp.classifier.train.validation.movingwindow.WindowTester
  • edu.msu.cme.rdp.classifier.train.validation.NBClassifierTest
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