Package org.cipres.treebase.domain.matrix

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

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  }

  private void checkAnalyzed(Collection<Matrix> mylist, Study study) { 
    Iterator<Matrix> matrixIterator = mylist.iterator();
    while ( matrixIterator.hasNext() ) {
      Matrix matrix = matrixIterator.next();
      if ( matrix.isPublished() ) {
        matrix.setAnalyzed(true);
      }
      else {
        if ( study != null ) {
          Iterator<Matrix> analyzedMatrixIterator = study.getMatrices().iterator();
          ANALYZED: while ( analyzedMatrixIterator.hasNext() ) {
            Matrix analyzedMatrix = analyzedMatrixIterator.next();
            if ( analyzedMatrix.getId() == matrix.getId() ) {
              matrix.setAnalyzed(true);
              break ANALYZED;
            }
          }
        }
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    StringBuilder oversizerowsbldr = new StringBuilder("");
    Iterator<Matrix> matrices = mylist.iterator();

    int i = 0;
    while (matrices.hasNext()) {
      Matrix amat = matrices.next();
      if (amat.getTitle().trim().length() > permittedlength) {
        check = false;
        oversizerowsbldr.append(String.valueOf(i + 1));
        oversizerowsbldr.append(",");
      }
      i++;
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    }

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

    Matrix amatrix = (Matrix) command;

    String username = request.getRemoteUser();

    Long submissionId = getSubmissionHome().findByMatrix(amatrix).getId();
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  protected Object formBackingObject(HttpServletRequest request) {

    if (request.getParameter("matrixid") != null) {

      Long matrixID = Long.parseLong(request.getParameter("matrixid"));
      Matrix pMatrix = getMatrixService().findByID(matrixID);
      return pMatrix;

    } else {
      return null;
    }
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    Map<String,String> referenceMap = new HashMap<String,String>();
    referenceMap.put("deleteelementtype", "Delete this particular matrix");

    Long matrixID = Long.parseLong(request.getParameter("matrixid"));
    Matrix pMatrix = getMatrixService().findByID(matrixID);

    if (pMatrix.getStudy() != null) { // It means this tree is tied to analysis step
      referenceMap.put("generalmessage", "This matrix is tied to an Analysis Step.");
    }

    referenceMap.put("deleteid", "Matrix ID : " + matrixID);
    referenceMap.put("objectname", "Matrix Title : " + pMatrix.getTitle());

    return referenceMap;
  }
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      String idString = request.getParameter("ids");
      String[] ids = idString.split(" +");     
      if ( dataType.equals("Matrices") ) {
        for ( int i = 0; i < ids.length; i++ ) {
          if ( ! TreebaseUtil.isEmpty(ids[i]) ) {
            Matrix matrix = getMatrixService().findByID(Long.parseLong(ids[i]));
            AnalyzedMatrix analyzedMatrix = new AnalyzedMatrix();
            analyzedMatrix.setInput(input);
            analyzedMatrix.setMatrix(matrix);
            analysisStep.addAnalyzedData(analyzedMatrix);
            getAnalysisStepService().update(analysisStep);         
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Related Classes of org.cipres.treebase.domain.matrix.Matrix

  • org.cipres.treebase.auxdata.AddMetaDataAction
  • org.cipres.treebase.auxdata.CommitStudy
  • org.cipres.treebase.dao.matrix.MatrixDAO
  • org.cipres.treebase.dao.matrix.MatrixDAOTest
  • org.cipres.treebase.dao.study.AnalyzedDataDAOTest
  • org.cipres.treebase.dao.study.SubmissionDAOTest
  • org.cipres.treebase.domain.nexus.nexml.NexmlConverter
  • org.cipres.treebase.domain.nexus.nexml.NexmlMatrixReader
  • org.cipres.treebase.domain.search.MatrixSearchResults
  • org.cipres.treebase.domain.search.TreeSearchResults
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