Examples of mesquite.lib.characters.CodonPositionsSet

    // see mesquite.lists.CharListCodonPos.CharListCodonPos


    for (int i = 0; i < pSetVector.size(); i++) {
      SpecsSet ss = (SpecsSet) pSetVector.elementAt(i);
      if (ss instanceof CodonPositionsSet) {
        CodonPositionsSet cpSet = (CodonPositionsSet) ss;
        CodonPositionSet tbCodonPosSet = createCodonPosSet(pMesqMatrix, cpSet, pMatrix);


        pMatrix.getCodonPosSets().add(tbCodonPosSet);
      }
    }


    CodonPositionsSet defaultCodonPosSet = (CodonPositionsSet) pMesqMatrix
      .getCurrentSpecsSet(CodonPositionsSet.class);
    if (defaultCodonPosSet != null) {
      CodonPositionSet tbCodonPosSet = createCodonPosSet(
        pMesqMatrix,
        defaultCodonPosSet,


    //Based on ManageCodonPositions.nexusStringForSpecsSet
    
    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);


        if (iw == 0) {
          interval = 1;
        } else {
          interval = 3;
        }


        someValues = false;


        int lastWritten = -1;
        ColumnRange range = null;
        for (int ic = 0; ic < pNumChar; ic++) {
          
          //for noncoding ranges, the interval is 3, need add 2: 
          if (continuing > 0 && iw > 0 && ic < pNumChar -2) {
            ic = ic +2;
          }
          
          if (codonPossSet.equals(ic, posIndex)
            || (codonPossSet.getInt(ic) == MesquiteInteger.unassigned && (iw == unassignedPosition))) {
            
            if (continuing == 0) {
              lastWritten = ic;


              range = new ColumnRange();

Examples of mesquite.lib.characters.CodonPositionsSet

Related Classes of mesquite.lib.characters.CodonPositionsSet