Examples of AnalyzedTree

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

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        mPhyloTreeService.update(phyloTree);
        if (!editFieldCommand.getChecked()) {
          continue; // skip current iteration if not
        }
        // 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");
      for ( int i = 0; i < treeBlockList.size(); i++ ) {
        EditFieldCommand editFieldCommand = treeBlockList.get(i);
        if ( ! editFieldCommand.getChecked() ) {
          continue;  // skip current iteration if not checked
        }       
        TreeBlock treeBlock = mPhyloTreeService.findTreeBlockByID(editFieldCommand.getTreeBlock().getId());
        if ( treeBlock == null ) {
          LOGGER.warn("No treeblock!!!");
        }
        else {
          LOGGER.warn(treeBlock.getTitle());
          Iterator<PhyloTree> treeIterator = treeBlock.getTreeListIterator();
          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();
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Examples of org.cipres.treebase.domain.study.AnalyzedTree

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      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();
        Long tbID = treeBlock.getId();
        if ( ! selectedTreeBlocks.containsKey(tbID) && ! incompleteTreeBlocks.containsKey(tbID) ) {
          int seen = 0;
          for ( AnalyzedData innerData : selectedData ) {
            if ( innerData instanceof AnalyzedTree ) {             
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Examples of org.cipres.treebase.domain.study.AnalyzedTree

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              ContextManager.getStudyService().save(theTreeBlock); // XXX should be some treeblock-specific service
              theSubmission.addPhyloTreeBlock(theTreeBlock);
              ContextManager.getSubmissionService().save(theSubmission);
            }     
           
            AnalyzedTree theTree = new AnalyzedTree();
            theTree.setInput(false);
            String treeID = ioSection.getsval("tree_id");
            PhyloTree treeData = trees.get(treeID);

            treeData.setStudy(theStudy);
            ContextManager.getTaxonLabelService().updateStudyForAllLabels(treeData, theStudy);
            treeData.setTB1TreeID(treeID);
            ContextManager.getPhyloTreeService().save(treeData);
            theTreeBlock.addPhyloTree(treeData);
            theSubmission.addPhyloTreeBlockIfNecessary(theTreeBlock);
            ContextManager.getSubmissionService().save(theSubmission);
            theTree.setTree(treeData);
            theData = theTree;
          } else {
            throw new Error("Unknown IO section '" + ioSection.label + "' in study " + aux.getString(null, "study_id"));
          }
          theData.setAnalysisStep(theAnalysisStep);
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Examples of org.cipres.treebase.domain.study.AnalyzedTree

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    AnalysisStep step1 = new AnalysisStep();
    step1.setName("step1 " + newName);
    s.addAnalysis(a1);
    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.AnalyzedTree

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            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());
            analyzedDataCommand.setDataId(analyzedTree.getTree().getId());
          }

          analyzedDataCommandList.add(analyzedDataCommand);
        } // end for
        // add analyzedData for analysisStepCommand
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Examples of org.cipres.treebase.domain.study.AnalyzedTree

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        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());
        analyzedDataCommand.setDataId(analyzedTree.getTree().getId());
      }
      list.add(analyzedDataCommand);
    }

    // save the analysis step object user has selected
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Examples of org.cipres.treebase.domain.study.AnalyzedTree

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            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());
            analyzedDataCommand.setDataId(analyzedTree.getTree().getId());
          }
          analyzedDataCommandList.add(analyzedDataCommand);
        } // end for
        // add analyzedData for analysisStepCommand
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Examples of org.cipres.treebase.domain.study.AnalyzedTree

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            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());
            analyzedDataCommand.setDataId(analyzedTree.getTree().getId());
          }
          analyzedDataCommandList.add(analyzedDataCommand);
        } // end for
        // add analyzedData for analysisStepCommand
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Examples of org.cipres.treebase.domain.study.AnalyzedTree

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            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());
            analyzedDataCommand.setDataId(analyzedTree.getTree().getId());
          }
          analyzedDataCommandList.add(analyzedDataCommand);
        } // end for
        // add analyzedData for analysisStepCommand
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Examples of org.cipres.treebase.domain.study.AnalyzedTree

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      }
      else if ( dataType.equals("Trees") ) {
        for ( int i = 0; i < ids.length; i++ ) {
          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") ) {
        for ( int i = 0; i < ids.length; i++ ) {
          if ( ! TreebaseUtil.isEmpty(ids[i]) ) {
            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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