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

Package org.cipres.treebase.domain.matrix

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

org.cipres.treebase.domain.matrix.RowSegment
RowSegment.java Created on Mar 21, 2006 @author Jin Ruan

    HttpServletRequest request,
    HttpServletResponse response,
    Object command,
    BindException bindExp) throws Exception {


    RowSegment aRowSegment = (RowSegment) command;
    Long matrixRowId = ControllerUtil.getMatrixRowId(request);
    MatrixRow matrixRow = mMatrixRowService.findByID(matrixRowId);


    if (LOGGER.isDebugEnabled()) {
      LOGGER.debug("++MARTIX ROW ID++ : " + matrixRowId.toString());
    }


    if (request.getParameter(ACTION_DELETE) != null) {
      mRowSegmentService.deleteRowSegment(aRowSegment);
    } else {
      System.out.println("MARTIX ROW ID In Submit Button: " + matrixRowId.toString());
      ExecutionResult executionResult = new ExecutionResult();
      boolean test = aRowSegment.validate(executionResult);
      if (test) {
        if (request.getParameter(ACTION_SUBMIT) != null) {
          matrixRow.addSegment(aRowSegment);
          mMatrixRowService.update(matrixRow);
        } else if (request.getParameter(ACTION_UPDATE) != null) {

View Full Code Here

  protected Object formBackingObject(HttpServletRequest request) throws ServletException {


    Long matrixRowId = ControllerUtil.getMatrixRowId(request);
    MatrixRow matrixRow = getMatrixRowService().findByID(matrixRowId);


    RowSegment rowSegment = null;


    String rowSegmentId = ServletRequestUtils.getStringParameter(request, "id", null);


    if (rowSegmentId == null) {
      rowSegment = new RowSegment();
      rowSegment.setMatrixRow(matrixRow);
      rowSegment.setTaxonLabel(matrixRow.getTaxonLabel());
      
      int endIndex = matrixRow.getSymbolString().length();
      if (endIndex >= 1) {
        rowSegment.setStartIndex(1);
        rowSegment.setEndIndex(endIndex);
      }
      
      return rowSegment;
    }

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    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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    List<MatrixElement> elements = pRow.getElementsReadOnly();
    if (elements.size() <= pEnd) {
      return null;
    }


    RowSegment seg = new RowSegment();


    seg.setStartIndex(pStart);
    seg.setEndIndex(pEnd);
    pRow.addSegment(seg);


    // use cascade persistence to
    update(pRow);
    seg = update(seg);

View Full Code Here

    }


    for (List<String> lineStr : pValues) {
      boolean isCreate = true;
      boolean hasErr = false;
      RowSegment aRowSegment = null;


      if (rowSegmentIdColIndex >= 0) {
        // row seg id column is mapped, need to check whether it has
        // value:
        String rsIDStr = lineStr.get(rowSegmentIdColIndex);
        if (!TreebaseUtil.isEmpty(rsIDStr)) {
          isCreate = false;


          Long rsID = Long.valueOf(rsIDStr);
          RowSegment existingRS = getRowSegmentHome().getPersistedObjectByID(
            RowSegment.class,
            rsID);
          if (existingRS == null) {
            // Error:
            hasErr = true;
            pExecution.addErrorMessage("Error: Row Segment id " + rsID
              + " is not found");
          } else {
            aRowSegment = existingRS;
          }
        }
      }


      if (!hasErr) {
        
        // check and create a new rs:
        if (isCreate) {
          aRowSegment = new RowSegment();
        }


        Map<String, MatrixRow> taxonLabelRowMap = pMatrix.buildTaxonLabelRowMap();
        aRowSegment.update(pMappedFields, lineStr, taxonLabelRowMap, pExecution);

View Full Code Here

      return rowSegmentCommand;
    }


    // setCancelParamKey("?id=" + matrix_row_id.toString());


    RowSegment rowSegment = mRowSegmentService.findByID(Long.parseLong(matrix_row_segment_id));
    rowSegmentCommand.setRowSegment(rowSegment);


    rowSegmentCommand.setMatrixRowDataSelected(rowSegment.getSegmentData());
    
    return rowSegmentCommand;
  }

View Full Code Here

    HttpServletRequest request,
    HttpServletResponse response,
    Object command,
    BindException bindExp) throws Exception {


    RowSegment arowsegment = (RowSegment) command;
    if (arowsegment.getId() == null) {
      return new ModelAndView(getCancelView());
      // Attempt is made to delete an object that does not exist anymore.
    }


    String username = request.getRemoteUser();
    arowsegment = getRowSegmentService().resurrect(arowsegment);


    Matrix amatrix = arowsegment.getMatrixRow().getMatrix();
    Long submissionId = getSubmissionHome().findByMatrix(amatrix).getId();


    TBPermission perm2 = getSubmissionService().getPermission(username, submissionId);


    if (perm2 == TBPermission.WRITE) {
      getRowSegmentService().deleteRowSegment(
        getRowSegmentService().findByID(arowsegment.getId()));
    } else {


      if (LOGGER.isDebugEnabled()) {
        LOGGER.debug("Sorry Authorization Failure, you cannot delete this rowsegment.");
      }

View Full Code Here

   */
  @Override
  protected Object formBackingObject(HttpServletRequest request) {


    String rsmentid = request.getParameter("rowsegmentid");
    RowSegment pRowSegment = null;
    if (rsmentid != null) {
      pRowSegment = getRowSegmentService().findByID(Long.parseLong(rsmentid));
      if (pRowSegment == null) {
        pRowSegment = new RowSegment();
      }
      // Even if rowsegmentid is provided, pRowSegment could still be null because rowsegment
      // with that particular id might have been deleted and user is pressing the back button
      // on the browser.

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    String noidavailable = null;


    String rsId = request.getParameter("rowsegmentid");
    if (rsId != null) {
      Long rsmentID = Long.parseLong(rsId);
      RowSegment pRowSegment = getRowSegmentService().findByID(rsmentID);


      referenceMap.put("deleteid", "RowSegment ID : " + rsmentID);


      if (pRowSegment == null) {
        noidavailable = "Rowsement with id <u>" + rsId + "</u> does not exist.";
      } else {
        referenceMap.put("objectname", "RowSegment Title : " + pRowSegment.getTitle());
      }
    } else {
      noidavailable = "Rowsement with id <u>" + rsId + "<u> does not exist.";
    }
    referenceMap.put("noidavailable", noidavailable);

View Full Code Here

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Related Classes of org.cipres.treebase.domain.matrix.RowSegment

org.cipres.treebase.domain.matrix.RowSegmentService.RowSegmentField

org.cipres.treebase.domain.taxon.SpecimenLabel

org.cipres.treebase.service.matrix.MatrixServiceImplTest

org.cipres.treebase.service.matrix.RowSegmentServiceImpl

org.cipres.treebase.web.controllers.DeleteARowSegmentController

org.cipres.treebase.web.controllers.MatrixRowSegmentFormController

org.cipres.treebase.web.controllers.SingleRowSegmentController

java.lang.reflect.Method

javax.persistence.Column

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