Package mesquite.lib

Examples of mesquite.lib.MesquiteNumber

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    Set<CharWeight> tbWeights = new HashSet<CharWeight>();

    // create one char weight for each columnRangeConvertHelper
    Collection<ColumnRangeConvertHelper> colRangeHelpers = decodeNumSpecsSet(pWtSet, numChars);
    for (ColumnRangeConvertHelper helper : colRangeHelpers) {
      MesquiteNumber mesNum = helper.getNumber();

      CharWeight charWeight = null;
      if (mesNum.getValueClass() == MesquiteNumber.INT) {
        charWeight = new IntegerCharWeight(mesNum.getIntValue());
      } else {
        charWeight = new RealCharWeight(mesNum.getDoubleValue());
      }

      charWeight.setWeightColumns(helper.getColRanges());

      tbWeights.add(charWeight);
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      // an array to keep track of distinct numbers are already converted
      NumberArray usedNumbers = new NumberArray(pNumChar);
      usedNumbers.deassignArray();

      for (int iw = 0; iw < pNumChar; iw++) {
        MesquiteNumber aNumber = new MesquiteNumber();
        MesquiteNumber secondNumber = new MesquiteNumber();

        pNumSpecsSet.placeValue(iw, aNumber);

        // bypass this char if the number is already converted
        if (usedNumbers.findValue(aNumber) < 0) {
          int continuing = 1;

          ColumnRangeConvertHelper aHelper = new ColumnRangeConvertHelper();
          aHelper.setNumber(aNumber);

          int startIndex = CharacterStates.toExternal(iw);
          ColumnRange range = new ColumnRange();
          range.setStartColIndex(startIndex - 1);

          for (int ic = iw + 1; ic < pNumChar; ic = ic + 1) {
            pNumSpecsSet.placeValue(ic, secondNumber);
            if (secondNumber.equals(aNumber)) {
              if (continuing == 0) {
                // discontinue
                range = new ColumnRange();
                range.setStartColIndex(ic);
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    if (pNumSpecsSet != null) {

      CodonPositionsSet codonPossSet = (CodonPositionsSet) pNumSpecsSet;
      int unassignedPosition = 4;
      MesquiteNumber posIndex = new MesquiteNumber();

      boolean someValues = false;

      int interval = 1;

      for (int iw = 0; iw < 5; iw++) {
        posIndex.setValue(iw);
        int continuing = 0;

        ColumnRangeConvertHelper aHelper = new ColumnRangeConvertHelper();
        aHelper.setNumber(posIndex);
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Related Classes of mesquite.lib.MesquiteNumber

  • org.cipres.treebase.domain.nexus.mesquite.MesquiteMatrixConverter
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