Package bnGUI.venn.db

Examples of bnGUI.venn.db.AbstractGOCategoryProperties

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            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);
                }
        return new Integer( n );

            case 5: // nTotal
                if( prop != null )
                  if (params.logNumElements) {
                    return new Integer(prop.getNTotalLog());
                  }
                  else {
                    return new Integer(prop.getNTotal());
                  }
                else
                    return null;
               
      case 6: // p-value
        if( prop != null )
          //return new Float(prop.pValue);
//          return format.format(prop.pValue);
          return format.format(prop.getPFDRValue());
        else
          return null;
               
//            case 7: // FDR
//                if( prop != null && prop instanceof GOCategoryProperties3p3fdr)
//                    //return new Float(prop.FDR);
//                    return format.format(((GOCategoryProperties3p3fdr) prop).FDR);
//                else
//                    return null;
                   
            case 8: // minDist
              if( prop != null )
              {
                if( prop.getMeanDist() >= 1 )
                  return new Float( prop.getMeanDist() );
              }
              return null;
    }
    return null;
  }
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                        {
                            col = table.convertColumnIndexToModel(col);
                            if( col == 2 )
                            {
                                CategoryTableData model = (CategoryTableData)table.getModel();
                                AbstractGOCategoryProperties props = model.getGoProperties(row);
                                if( props != null )
                                {
                                    BrowserControl.displayURL( createGoURL( props.getID() ) );
                                }
                            }
                        }
                    }
                }
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    final int numGroups = model.getNumGroups();

    String label = null;
    for (int i = 0; i < numGroups; i++) {
      AbstractGOCategoryProperties prop = (AbstractGOCategoryProperties) model.getGroupProperties(i);
      if (label == null) {
        label = prop.getPFDRLabel();
      } else {
        if (! prop.getPFDRLabel().equals(label)) {
          throw new IllegalStateException();
        }
      }
    }
   
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        }
      }
     
        // make combo box for p/fdr selection
      GODistanceFilter.Parameters filterParameters = filter0.getParameters();
        final AbstractGOCategoryProperties prop = (AbstractGOCategoryProperties) sourceDataModel.getGroupProperties(0);
        if (prop.getClass().equals(GOCategoryProperties1p.class)) {
            makeComboBox(true, false, false, false, false, false, false, false);
        } else if (prop.getClass().equals(GOCategoryProperties1p1fdr.class)) {
            makeComboBox(true, true, false, false, false, false, false, false);
        } else if (prop.getClass().equals(GOCategoryProperties3p.class)) {
            makeComboBox(false, false, true, true, true, false, false, false);
        } else if (prop.getClass().equals(GOCategoryProperties3p3fdr.class)) {
          makeComboBox(false, false, true, true, true, true, true, true);
        } else {
          throw new IllegalArgumentException();
        }
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Related Classes of bnGUI.venn.db.AbstractGOCategoryProperties

  • bnGUI.venn.CategoryTable
  • bnGUI.venn.CategoryTableData
  • bnGUI.venn.gui.FilterPanel
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