List of addAnalyzedData() Examples

Examples of addAnalyzedData()

org.cipres.treebase.domain.study.AnalysisStep.addAnalyzedData()
Append a new analyzed data to the end of the list. Manage bi-directional relationship. Reset the analysis validated flag. Creation date: Feb 22, 2006 12:06:25 PM @param pData AnalyzedData

Examples of org.cipres.treebase.domain.study.AnalysisStep.addAnalyzedData()

        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();
      for (int i = 0; i < treeList.size(); i++) {

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Examples of org.cipres.treebase.domain.study.AnalysisStep.addAnalyzedData()

        }
        // checked
        AnalyzedTree analyzedTree = new AnalyzedTree();
        analyzedTree.setInput(input);
        analyzedTree.setTree(phyloTree);
        analysisStep.addAnalyzedData(analyzedTree);
        mAnalysisStepService.update(analysisStep);
      }
    } else if ( dataType.equals(Constants.TREE_LIST)) {
      List<EditFieldCommand> treeBlockList = data.getTreeBlockList();
      LOGGER.warn("Going to set tree block as analyzed data");

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Examples of org.cipres.treebase.domain.study.AnalysisStep.addAnalyzedData()

          while (treeIterator.hasNext()) {
            PhyloTree phyloTree = treeIterator.next();
            AnalyzedTree analyzedTree = new AnalyzedTree();
            analyzedTree.setInput(input);
            analyzedTree.setTree(phyloTree);
            analysisStep.addAnalyzedData(analyzedTree);
            mAnalysisStepService.update(analysisStep);
          }
          /*
          AnalyzedTreeBlock analyzedTreeBlock = new AnalyzedTreeBlock();
          analyzedTreeBlock.setInput(input);

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Examples of org.cipres.treebase.domain.study.AnalysisStep.addAnalyzedData()

          } else {
            throw new Error("Unknown IO section '" + ioSection.label + "' in study " + aux.getString(null, "study_id"));
          }
          theData.setAnalysisStep(theAnalysisStep);
          ContextManager.getAnalyzedDataService().save(theData);
          theAnalysisStep.addAnalyzedData(theData);
          ContextManager.getAnalysisStepService().save(theAnalysisStep);
        }
      }
      
      // TODO: fix submission taxa list

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Examples of org.cipres.treebase.domain.study.AnalysisStep.addAnalyzedData()

    a1.addAnalysisStep(step1);


    AnalyzedTree treeData = new AnalyzedTree();
    treeData.setTree(tree);
    treeData.setInput(Boolean.FALSE);
    step1.addAnalyzedData(treeData);


    getFixture().store(tree);
    getFixture().store(tree2);
    getFixture().store(block);

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Examples of org.cipres.treebase.domain.study.AnalysisStep.addAnalyzedData()

          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);          
          }
        }      
      }
      else if ( dataType.equals("Trees") ) {

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Examples of org.cipres.treebase.domain.study.AnalysisStep.addAnalyzedData()

          if ( ! TreebaseUtil.isEmpty(ids[i]) ) {
            PhyloTree phyloTree = getPhyloTreeService().findByID(Long.parseLong(ids[i]));  
            AnalyzedTree analyzedTree = new AnalyzedTree();
            analyzedTree.setInput(input);
            analyzedTree.setTree(phyloTree);
            analysisStep.addAnalyzedData(analyzedTree);
            getAnalysisStepService().update(analysisStep);
          }        
        }      
      }
      else if ( dataType.equals("TreeBlocks") ) {

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Examples of org.cipres.treebase.domain.study.AnalysisStep.addAnalyzedData()

            TreeBlock treeBlock = getPhyloTreeService().findTreeBlockByID(Long.parseLong(ids[i]));
            for ( PhyloTree phyloTree : treeBlock.getTreeList() ) {
              AnalyzedTree analyzedTree = new AnalyzedTree();
              analyzedTree.setInput(input);
              analyzedTree.setTree(phyloTree);
              analysisStep.addAnalyzedData(analyzedTree);
              getAnalysisStepService().update(analysisStep);            
            }
          }        
        }      
      }

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