gui/JalviewChimeraBindingModel.java

   1 package jalview.gui;
   2
   3 import jalview.api.AlignmentViewPanel;
   4 import jalview.datamodel.PDBEntry;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
   7 import jalview.structure.StructureSelectionManager;
   8
   9 public class JalviewChimeraBindingModel extends JalviewChimeraBinding
  10 {
  11   private ChimeraViewFrame cvf;
  12
  13   public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
  14           StructureSelectionManager ssm, PDBEntry[] pdbentry,
  15           SequenceI[][] sequenceIs, String[][] chains, String protocol)
  16   {
  17     super(ssm, pdbentry, sequenceIs, chains, protocol);
  18     cvf = chimeraViewFrame;
  19   }
  20
  21   FeatureRenderer fr = null;
  22
  23   @Override
  24   public jalview.api.FeatureRenderer getFeatureRenderer(
  25           AlignmentViewPanel alignment)
  26   {
  27     AlignmentPanel ap = (alignment == null) ? cvf.ap
  28             : (AlignmentPanel) alignment;
  29     if (ap.av.showSequenceFeatures)
  30     {
  31       if (fr == null)
  32       {
  33         fr = ap.cloneFeatureRenderer();
  34       }
  35       else
  36       {
  37         ap.updateFeatureRenderer(fr);
  38       }
  39     }
  40
  41     return fr;
  42   }
  43
  44   @Override
  45   public jalview.api.SequenceRenderer getSequenceRenderer(
  46           AlignmentViewPanel alignment)
  47   {
  48     return new SequenceRenderer(((AlignmentPanel) alignment).av);
  49   }
  50   @Override
  51   public void refreshGUI()
  52   {
  53     // appJmolWindow.repaint();
  54     javax.swing.SwingUtilities.invokeLater(new Runnable()
  55     {
  56       public void run()
  57       {
  58         cvf.updateTitleAndMenus();
  59         cvf.revalidate();
  60       }
  61     });
  62   }
  63
  64   public void updateColours(Object source)
  65   {
  66     AlignmentPanel ap = (AlignmentPanel) source, topap;
  67     // ignore events from panels not used to colour this view
  68     if (!cvf.isUsedforcolourby(ap))
  69       return;
  70     if (!isLoadingFromArchive())
  71     {
  72       colourBySequence(ap.av.getShowSequenceFeatures(), ap);
  73     }
  74   }
  75   @Override
  76   public void releaseReferences(Object svl)
  77   {
  78     // TODO Auto-generated method stub
  79
  80   }
  81
  82   @Override
  83   protected void releaseUIResources()
  84   {
  85     // TODO Auto-generated method stub
  86
  87   }
  88
  89   @Override
  90   public void refreshPdbEntries()
  91   {
  92     // TODO Auto-generated method stub
  93
  94   }
  95
  96   @Override
  97   public void showUrl(String url, String target)
  98   {
  99     // TODO Auto-generated method stub
 100
 101   }
 102 }