Examples of CodonPositionSet


    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,
        pMatrix);


      pMatrix.setDefaultCodonPosSet(tbCodonPosSet);

Examples of org.cipres.treebase.domain.matrix.CodonPositionSet

    CharacterMatrix pMatrix) {


    // See ManageCodonPositionset.nexusStringForSpecsSet
    // Also see DNAData.getCodonsAsNexusCharSets


    CodonPositionSet tbCodonSet = new CodonPositionSet();
    tbCodonSet.setTitle(pCodonPosSet.getName());


    int numChars = pMesqMatrix.getNumChars();


    // create one collection of columnRange for each columnRangeConvertHelper
    decodeNumSpecsSetForCodonPosSet(tbCodonSet, pCodonPosSet, numChars);

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