Examples of IVennDataModel

bnGUI.venn.db.IVennDataModel
@author muelleraEncapsulates group/element data.

Examples of bnGUI.venn.db.IVennDataModel

    return venn.numOfCategories();
  }
    
    public AbstractGOCategoryProperties getGoProperties( int row )
    {
        IVennDataModel model = venn.getDataModel();
        if( model == null )
            return null;        
        return (AbstractGOCategoryProperties) model.getGroupProperties(row);
    }

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Examples of bnGUI.venn.db.IVennDataModel

  {
        // NumberFormat format = NumberFormat.getInstance();
        
        DecimalFormat format = new DecimalFormat("#0.0000");
        
        IVennDataModel model = venn.getDataModel();
        if( model == null || model.getNumGroups() == 0 )
            return null;
    
    if( rowIndex < 0 || rowIndex>= model.getNumGroups() )
      return null;
        
        AbstractGOCategoryProperties prop = (AbstractGOCategoryProperties)model.getGroupProperties(rowIndex);
        
    switch( columnIndex )
        {
            case 0:
                return new Integer(1+rowIndex);
        
      case 1: // activated
        return new Boolean( venn.getActivated(rowIndex) );


            case 2: // ID
                if( prop != null )
                    return new Long(prop.getID());
                else
                    return null;
                
      case 3: // category name
        return model.getGroupName(rowIndex);
                          
      case 4: // number of elements (genes) = nChanged
                int n = model.getGroupElements(rowIndex).cardinality();
                if( prop != null )
                    Assert.assertEquals(n,prop.getNChange());
                if (params.logNumElements) {
                  n = AbstractGOCategoryProperties.log(n);
                }

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Examples of bnGUI.venn.db.IVennDataModel

        }
        VennArrangementsOptimizer vennArrsOptim = new VennArrangementsOptimizer();
        vennArrsOptim.setParameters(params);
        VennPanel venn = new VennPanel(vennArrsOptim);
        venn.setParameters(params);
        final IVennDataModel model = loadFiles.getSourceDataModel();


        if (filter == null && (loadFiles.getSourceType() == LoadFiles.SourceType.GO
            || loadFiles.getSourceType() == LoadFiles.SourceType.HTGO)) {
          filter = new GODistanceFilter( goTree );


            // set filterBy to default
          if (model != null) {
            assert model instanceof GeneOntologyReaderModel || model instanceof HTGeneOntologyReaderModel;


            final GODistanceFilter distanceFilter = (GODistanceFilter) filter;
            if (model.getNumGroups() > 0) {
              distanceFilter.getParameters().filterBy =
                ((AbstractGOCategoryProperties) model.getGroupProperties(0)).getFilterBy();
            }
          }


        }

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Examples of bnGUI.venn.db.IVennDataModel

        VennDataSplitter splitter = new VennDataSplitter();
        assertNotNull(splitter);
        
        splitter.setDataModel( model );
        
        IVennDataModel models[] = splitter.getModels();
        
        System.out.println("number of models = "+models.length);
        for(int i=0;i<models.length;++i)
        {
            System.out.println("MODEL "+i);

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Examples of bnGUI.venn.db.IVennDataModel

        repaint();
      return;
    }
        
        // Create one VennDiagramView for each sub-problem
        IVennDataModel models[] = dataSplitter.getModels();
        
        
        // TODO: encapsulate the whole generation process in a factory method
        // Compute scaling factor depending on the maximum cardinality
        int maxCard = 0;

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Examples of bnGUI.venn.db.IVennDataModel

    {
      return;
    }
        
        // Create one VennDiagramView for each sub-problem
        IVennDataModel models[] = unfilteredDataSplitter.getModels();
        
        
        // TODO: encapsulate the whole generation process in a factory method
        // Compute scaling factor depending on the maximum cardinality
        int maxCard = 0;

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Examples of bnGUI.venn.db.IVennDataModel

        for( int i=0; i<errFunc.length; ++i )
        {
            os.write("SUB-PROBLEM "+i+"\n");
            
            // output group names
            IVennDataModel data = views[i].getArrangement().getDataModel();
            
            for( int j=0; j<data.getNumGroups(); ++j )
            {
                os.write("GROUP["+j+"] ");
                os.write(data.getGroupName(j));
                os.write("\n");
            }
            
            double[] opt = optim[i].getOptimum();
            Assert.assertNotNull( opt );

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