Package mesquite.lib

Examples of mesquite.lib.SpecsSetVector


    // mesquite.molec.lib.GenCodeModelSet

    if (allSets != null) {
      Iterator<SpecsSetVector> specsSetIter = allSets.iterator();
      while (specsSetIter.hasNext()) {
        SpecsSetVector aSetVector = specsSetIter.next();

        Class setType = aSetVector.getType();
        if (LOGGER.isDebugEnabled()) {
          LOGGER.debug("SpecsSetVector class=" + setType + " size=" + aSetVector.size()); //$NON-NLS-1$
        }

        if (CharWeightSet.class == setType) {
          convertCharWeightSet(pMesqMatrix, aSetVector, m);
          // } else if (CodonPositionsSet.class == aSetVector.getClass()) {
          // convertCodonPositionsSet(pMesqMatrix, aSetVector, m);
          // } else if (CodonPositionsSet.class == aSetVector.getClass()) {
          // convertCodonPositionsSet(pMesqMatrix, aSetVector, m);
        } else if (ParsimonyModelSet.class == setType) {
          // FIXME: convertParsimonyModelSet(pMesqMatrix, aSetVector, m);
        } else if (CharSelectionSet.class == setType) {
          convertCharSet(pMesqMatrix, aSetVector, m);
        } else if (TaxaInclusionSet.class == setType) {
          convertTaxaInclusionSet(pMesqMatrix, aSetVector, m);
        } else if (CharInclusionSet.class == setType) {
          convertCharInclusionSet(pMesqMatrix, aSetVector, m);
        } else if (TaxaPartition.class == setType) {
          convertTaxaPartition(pMesqMatrix, aSetVector, m);
        } else if (CharacterPartition.class == setType) {
          convertCharacterPartition(pMesqMatrix, aSetVector, m);
        } else if (CodonPositionsSet.class == setType) {
          convertCodonPositionsSet(pMesqMatrix, aSetVector, m);
        } else {
          LOGGER
            .info("Unhandled matrix associated set. Class=" + setType + " size=" + aSetVector.size()); //$NON-NLS-1$
        }
      }
    }
    return matrixJDBC;
  }
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