Examples of AnalyzedMatrix

Examples of org.cipres.treebase.domain.study.AnalyzedMatrix

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    Map<Long, Boolean> selectedTreeBlocks = new HashMap<Long,Boolean>();
    Map<Long, Boolean> incompleteTreeBlocks = new HashMap<Long,Boolean>();

    for (AnalyzedData data : selectedData) {
      if (data instanceof AnalyzedMatrix) {
        AnalyzedMatrix analyzedMatrix = (AnalyzedMatrix) data;
        selectedMatrices.put(analyzedMatrix.getMatrix().getId(), analyzedMatrix
          .isInputData());
      } else if (data instanceof AnalyzedTree) {
        AnalyzedTree analyzedTree = (AnalyzedTree) data;
        selectedTrees.put(analyzedTree.getTree().getId(), analyzedTree.isInputData());
        TreeBlock treeBlock = analyzedTree.getTree().getTreeBlock();
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Examples of org.cipres.treebase.domain.study.AnalyzedMatrix

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        Matrix matrix = mMatrixService.findByID(editFieldCommand.getMatrix().getId());
        matrix.setTitle(editFieldCommand.getMatrix().getTitle());
        mMatrixService.update(matrix);
        if (!editFieldCommand.getChecked()) continue; // skip current iteration if not
        // checked
        AnalyzedMatrix analyzedMatrix = new AnalyzedMatrix();
        analyzedMatrix.setInput(input);
        analyzedMatrix.setMatrix(matrix);
        analysisStep.addAnalyzedData(analyzedMatrix);
        mAnalysisStepService.update(analysisStep);
      }// end for
    } else if (dataType.equals(Constants.TREE_KEY)) {
      List<EditFieldCommand> treeList = data.getTreeList();
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Examples of org.cipres.treebase.domain.study.AnalyzedMatrix

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      { // handle INPUT_MATRIX and OUTPUT_TREE in each ANALYSIS section
        TreeBlock theTreeBlock = null;
        for (ValueSection ioSection : an.getIOSections()) {
          AnalyzedData theData;
          if (ioSection.label.equals("INPUT_MATRIX")) {
            AnalyzedMatrix theMatrix = new AnalyzedMatrix();
            theMatrix.setInput(true);
            String matrixID = ioSection.getsval("matrix_id");
           
            Matrix matrixData = matrices.get(matrixID);
                 
            if (matrixData == null) {
              warn("Matrix " + matrixID + "is used in analysis " + an.getString("analysis_id") + " but is not listed in any MATRIX section for its study");
              return new ValueNone();
            }

            matrixData.setStudy(theStudy);
            ContextManager.getTaxonLabelService().updateStudyForAllLabels(matrixData, theStudy);
            matrixData.setTB1MatrixID(matrixID);
            ContextManager.getMatrixService().save(matrixData);
            theSubmission.addMatrixIfNecessary(matrixData);
            ContextManager.getSubmissionService().save(theSubmission);
            theMatrix.setMatrix(matrixData);
            theData = theMatrix;
          } else if (ioSection.label.equals("OUTPUT_TREE")) {
         
            if (theTreeBlock == null) {
              theTreeBlock = new TreeBlock();
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Examples of org.cipres.treebase.domain.study.AnalyzedMatrix

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          BeanUtils.copyProperties(analyzedDataCommand, analyzedData);
          String inputOutput = (analyzedData.isInputData()) ? ("Input") : ("Output");
          analyzedDataCommand.setInputOutputType(inputOutput);

          if (analyzedData instanceof AnalyzedMatrix) {
            AnalyzedMatrix analyzedMatrix = (AnalyzedMatrix) analyzedData;
            analyzedDataCommand.setDataType(Constants.MATRIX_KEY);
            analyzedDataCommand.setDisplayName(analyzedMatrix.getMatrix().getTitle());
            analyzedDataCommand.setId(analyzedMatrix.getId());
            analyzedDataCommand.setDataId(analyzedMatrix.getMatrix().getId());
          } else if (analyzedData instanceof AnalyzedTree) {
            AnalyzedTree analyzedTree = (AnalyzedTree) analyzedData;
            analyzedDataCommand.setDataType(Constants.TREE_KEY);
            analyzedDataCommand.setDisplayName(analyzedTree.getTree().getLabel());
            analyzedDataCommand.setId(analyzedTree.getId());
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Examples of org.cipres.treebase.domain.study.AnalyzedMatrix

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      analyzedDataCommand = new AnalyzedDataCommand();
      String inputOutput = (data.isInputData()) ? ("Input") : ("Output");
      analyzedDataCommand.setInputOutputType(inputOutput);

      if (data instanceof AnalyzedMatrix) {
        AnalyzedMatrix analyzedMatrix = (AnalyzedMatrix) data;
        analyzedDataCommand.setDataType(Constants.MATRIX_KEY);
        analyzedDataCommand.setDisplayName(analyzedMatrix.getMatrix().getTitle());
        analyzedDataCommand.setId(analyzedMatrix.getId());
        analyzedDataCommand.setDataId(analyzedMatrix.getMatrix().getId());
      } else if (data instanceof AnalyzedTree) {
        AnalyzedTree analyzedTree = (AnalyzedTree) data;
        analyzedDataCommand.setDataType(Constants.TREE_KEY);
        analyzedDataCommand.setDisplayName(analyzedTree.getTree().getLabel());
        analyzedDataCommand.setId(analyzedTree.getId());
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Examples of org.cipres.treebase.domain.study.AnalyzedMatrix

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          AnalyzedDataCommand analyzedDataCommand = new AnalyzedDataCommand();
          BeanUtils.copyProperties(analyzedDataCommand, analyzedData);
          String inputOutput = (analyzedData.isInputData()) ? ("Input") : ("Output");
          analyzedDataCommand.setInputOutputType(inputOutput);
          if (analyzedData instanceof AnalyzedMatrix) {
            AnalyzedMatrix analyzedMatrix = (AnalyzedMatrix) analyzedData;
            analyzedDataCommand.setDataType(Constants.MATRIX_KEY);
            analyzedDataCommand.setDisplayName(analyzedMatrix.getMatrix().getTitle());
            analyzedDataCommand.setId(analyzedMatrix.getId());
            analyzedDataCommand.setDataId(analyzedMatrix.getMatrix().getId());
          } else if (analyzedData instanceof AnalyzedTree) {
            AnalyzedTree analyzedTree = (AnalyzedTree) analyzedData;
            analyzedDataCommand.setDataType(Constants.TREE_KEY);
            analyzedDataCommand.setDisplayName(analyzedTree.getTree().getLabel());
            analyzedDataCommand.setId(analyzedTree.getId());
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Examples of org.cipres.treebase.domain.study.AnalyzedMatrix

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          AnalyzedDataCommand analyzedDataCommand = new AnalyzedDataCommand();
          BeanUtils.copyProperties(analyzedDataCommand, analyzedData);
          String inputOutput = (analyzedData.isInputData()) ? ("Input") : ("Output");
          analyzedDataCommand.setInputOutputType(inputOutput);
          if (analyzedData instanceof AnalyzedMatrix) {
            AnalyzedMatrix analyzedMatrix = (AnalyzedMatrix) analyzedData;
            analyzedDataCommand.setDataType(Constants.MATRIX_KEY);
            analyzedDataCommand.setDisplayName(analyzedMatrix.getMatrix().getTitle());
            analyzedDataCommand.setId(analyzedMatrix.getId());
            analyzedDataCommand.setDataId(analyzedMatrix.getMatrix().getId());
          } else if (analyzedData instanceof AnalyzedTree) {
            AnalyzedTree analyzedTree = (AnalyzedTree) analyzedData;
            analyzedDataCommand.setDataType(Constants.TREE_KEY);
            analyzedDataCommand.setDisplayName(analyzedTree.getTree().getLabel());
            analyzedDataCommand.setId(analyzedTree.getId());
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Examples of org.cipres.treebase.domain.study.AnalyzedMatrix

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          AnalyzedDataCommand analyzedDataCommand = new AnalyzedDataCommand();
          BeanUtils.copyProperties(analyzedDataCommand, analyzedData);
          String inputOutput = (analyzedData.isInputData()) ? ("Input") : ("Output");
          analyzedDataCommand.setInputOutputType(inputOutput);
          if (analyzedData instanceof AnalyzedMatrix) {
            AnalyzedMatrix analyzedMatrix = (AnalyzedMatrix) analyzedData;
            analyzedDataCommand.setDataType(Constants.MATRIX_KEY);
            analyzedDataCommand.setDisplayName(analyzedMatrix.getMatrix().getTitle());
            analyzedDataCommand.setId(analyzedMatrix.getId());
            analyzedDataCommand.setDataId(analyzedMatrix.getMatrix().getId());
          } else if (analyzedData instanceof AnalyzedTree) {
            AnalyzedTree analyzedTree = (AnalyzedTree) analyzedData;
            analyzedDataCommand.setDataType(Constants.TREE_KEY);
            analyzedDataCommand.setDisplayName(analyzedTree.getTree().getLabel());
            analyzedDataCommand.setId(analyzedTree.getId());
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Examples of org.cipres.treebase.domain.study.AnalyzedMatrix

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      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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