Package mesquite.lib

Examples of mesquite.lib.SpecsSet

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    ParsimonyModelSet defaultModelSet = (ParsimonyModelSet) pMesqMatrix
      .getCurrentSpecsSet(ParsimonyModelSet.class);
    boolean foundDefault = false;
    for (int i = 0; i < pSetVector.size(); i++) {
      SpecsSet ss = (SpecsSet) pSetVector.elementAt(i);
      if (ss instanceof ParsimonyModelSet) {
        ParsimonyModelSet pmSet = (ParsimonyModelSet) ss;

        TypeSet typeSet = createTypeSet(pMesqMatrix, pmSet, pMatrix);
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    CharacterData pMesqMatrix,
    SpecsSetVector pSetVector,
    CharacterMatrix pMatrix) {

    for (int i = 0; i < pSetVector.size(); i++) {
      SpecsSet ss = (SpecsSet) pSetVector.elementAt(i);
      if (ss instanceof CharSelectionSet) {
        CharSelectionSet charSet = (CharSelectionSet) ss;
        UserDefinedCharSet tbCharSet = createCharSet(pMesqMatrix, charSet, pMatrix);

        pMatrix.getCharSets().add(tbCharSet);
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    CharacterData pMesqMatrix,
    SpecsSetVector pSetVector,
    CharacterMatrix pMatrix) {

    for (int i = 0; i < pSetVector.size(); i++) {
      SpecsSet ss = (SpecsSet) pSetVector.elementAt(i);
      if (ss instanceof CharacterPartition) {
        CharacterPartition partition = (CharacterPartition) ss;
        // org.cipres.treebase.domain.matrix.CharWeightSet tbWeightSet = create(
        // pMesqMatrix,
        // wtSet,
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    CharacterMatrix pMatrix) {

    // 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);
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    CharacterData pMesqMatrix,
    SpecsSetVector pSetVector,
    CharacterMatrix pMatrix) {

    for (int i = 0; i < pSetVector.size(); i++) {
      SpecsSet ss = (SpecsSet) pSetVector.elementAt(i);
      if (ss instanceof CharWeightSet) {
        CharWeightSet wtSet = (CharWeightSet) ss;
        org.cipres.treebase.domain.matrix.CharWeightSet tbWeightSet = createWeightSet(
          pMesqMatrix,
          wtSet,
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Related Classes of mesquite.lib.SpecsSet

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