Examples of DiscreteMatrixElement

org.cipres.treebase.domain.matrix.DiscreteMatrixElement
DiscreteMatrixElement.java Created on Mar 27, 2006 @author Jin Ruan

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


          for (int i = 0; i < states.length; i++) {
            int aState = states[i];
            String stateName = categoricalData.getStateName(colIndex, aState);


            DiscreteMatrixElement anElement = createElement(
              columnChar,
              stateName,
              i,
              matrix);
            anElement.setColumn(matrixColumn);
            elements.add(anElement);


            anElement.appendValue(compoundValues);


            if (i < states.length - 1) {
              compoundValues.append(' ');
            }
          }

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


          for (int i = 0; i < states.length; i++) {
            int aState = states[i];
            String stateName = categoricalData.getStateName(colIndex, aState);


            DiscreteMatrixElement anElement = createElement(
              columnChar,
              stateName,
              i,
              matrix);
            anElement.setColumn(matrixColumn);
            elements.add(anElement);


            anElement.appendValue(compoundValues);


            if (i < states.length - 1) {
              compoundValues.append(' ');
            }
          }

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

    int pStateIndex,
    CharacterMatrix pMatrix) {


    DiscreteCharState tbState = null;


    DiscreteMatrixElement element = new DiscreteMatrixElement();
    element.setGap(false);


    if (pStateName != null) {
      // first check the symbol match either "-" gap
      // or "?" missing, set tbState = null;
      if (pStateName.compareToIgnoreCase("" + pMatrix.getGapSymbol()) == 0) {
        element.setGap(true);
      } else if (pStateName.compareToIgnoreCase("" + pMatrix.getMissingSymbol()) != 0) {
        tbState = pColumnChar.getStateByDescription(pStateName);


      }
    }
    element.setCharState(tbState);


    return element;
  }

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


    // create one row with 2 elements:
    MatrixRow r1 = new MatrixRow();
    r1.setTaxonLabel(taxonLabel);


    DiscreteMatrixElement e1 = new DiscreteMatrixElement();
    e1.setColumn(c1);
    e1.setCharState(aState);
    r1.addElement(e1);


    DiscreteMatrixElement e2 = new DiscreteMatrixElement();
    e2.setColumn(c2);
    e2.setCharState(aState);
    r1.addElement(e2);


    // add two segments, each with one element:
    RowSegment seg1 = new RowSegment();


    seg1.setStartIndex(0);
    seg1.setEndIndex(0);
    r1.addSegment(seg1);


    RowSegment seg2 = new RowSegment();


    seg2.setStartIndex(1);
    seg2.setEndIndex(1);
    r1.addSegment(seg2);


    matrix.addRow(r1);


    // TODO: add a second row.
  
    //getMatrixHome().store(taxonLabel);
    getMatrixHome().store(c1);
    getMatrixHome().store(c2);
    getMatrixHome().store(e1);
    getMatrixHome().store(e2);
    getMatrixHome().store(matrix);
    
    // 2. verify
    Long matrixID = matrix.getId();
    Long c1ID = c1.getId();
    Long c2ID = c2.getId();
    Long r1ID = r1.getId();
    Long seg1ID = seg1.getId();
    Long seg2ID = seg2.getId();
    Long e1ID = e1.getId();
    Long e2ID = e2.getId();
    Long taxonID = taxonLabel.getId();


      logger.info("matrix created: " + matrix.getTitle() + "id = " + matrixID + " symbols=" + matrix.getSymbols() + " gap =" + matrix.getGapSymbol());
    logger.info("taxonLabel created: " + taxonLabel.getTaxonLabel() + "id = " + taxonID);
    logger.info("2 columns created: id = " + c1ID + ", " + c2ID);
    logger.info("2 rows created: id = " + r1.getId() + ", ");
    logger.info("2 segments created: id = " + seg1.getId() + ", " + seg2.getId());
    logger.info("2 elements created: id = " + e1.getId() + ", " + e2.getId());


    // force commit immediately, important:
    //setComplete();
    //endTransaction();

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