Package org.cipres.treebase.domain.matrix

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

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      String queryBuf = "INSERT INTO PHYLOCHAR(TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION, LOWERLIMIT, UPPERLIMIT) VALUES('N', default, 0, ?, ?, ?) returning phylochar_id";
     
      PreparedStatement ps = pCon.prepareStatement(queryBuf);
      for (MatrixColumnJDBC columnJDBC : columns) {

        ContinuousChar phyloChar = (ContinuousChar) columnJDBC.getPhyloChar();
        ps.setString(1, phyloChar.getDescription()); // phylochar description

        if (phyloChar.getLowerLimit() != null) {
          ps.setDouble(2, phyloChar.getLowerLimit());
        } else {
          ps.setNull(2, Types.DOUBLE);
        }

        if (phyloChar.getUpperLimit() != null) {
          ps.setDouble(3, phyloChar.getUpperLimit());
        } else {
          ps.setNull(3, Types.DOUBLE);
        }

        ResultSet rs = ps.executeQuery();
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    for (int i = 0; i < numChars; i++) {

      //MatrixColumn aColumn = new MatrixColumn();
      MatrixColumnJDBC aColumnJDBC = new MatrixColumnJDBC();
     
      ContinuousChar tbChar = new ContinuousChar();

      String charName = continuousData.getCharacterName(i);
      tbChar.setDescription(charName);

      //aColumn.setCharacter(tbChar);
      aColumnJDBC.setPhyloChar(tbChar);
     
      //Note: Set for itemDefs per column. Disabled for now.
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    List<ContinuousMatrixElementJDBC> elements = new ArrayList<ContinuousMatrixElementJDBC>();
   
    int colIndex = 0;
    for ( org.nexml.model.Character xmlCharacter : xmlMatrix.getCharacters() ) {
      String charName = xmlCharacter.getLabel();
      ContinuousChar tbChar = new ContinuousChar();
      tbChar.setDescription(charName);
      MatrixColumnJDBC aColumnJDBC = new MatrixColumnJDBC();
      aColumnJDBC.setPhyloChar(tbChar);     
      columnJDBCs.add(aColumnJDBC);
      int rowIndex = 0;
      for ( OTU xmlOTU : xmlMatrix.getOTUs().getAllOTUs() ) {
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Related Classes of org.cipres.treebase.domain.matrix.ContinuousChar

  • org.cipres.treebase.dao.jdbc.ContinuousMatrixJDBC
  • org.cipres.treebase.domain.nexus.mesquite.MesquiteContinuousMatrixConverter
  • org.cipres.treebase.domain.nexus.nexml.NexmlMatrixReader
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