src/jalview/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   private FeatureRenderer fr = null;
  14
  15   public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
  16           StructureSelectionManager ssm, PDBEntry[] pdbentry,
  17           SequenceI[][] sequenceIs, String[][] chains, String protocol)
  18   {
  19     super(ssm, pdbentry, sequenceIs, chains, protocol);
  20     cvf = chimeraViewFrame;
  21   }
  22
  23   @Override
  24   public FeatureRenderer getFeatureRenderer(
  25           AlignmentViewPanel alignment)
  26   {
  27     AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
  28             : (AlignmentPanel) alignment;
  29     if (ap.av.isShowSequenceFeatures())
  30     {
  31       if (fr == null)
  32       {
  33         fr = (jalview.gui.FeatureRenderer) 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
  51   @Override
  52   public void refreshGUI()
  53   {
  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;
  67     // ignore events from panels not used to colour this view
  68     if (!cvf.isUsedforcolourby(ap))
  69     {
  70       return;
  71     }
  72     if (!isLoadingFromArchive())
  73     {
  74       colourBySequence(ap.av.isShowSequenceFeatures(), ap);
  75     }
  76   }
  77
  78   @Override
  79   public void releaseReferences(Object svl)
  80   {
  81   }
  82
  83   @Override
  84   protected void releaseUIResources()
  85   {
  86   }
  87
  88   @Override
  89   public void refreshPdbEntries()
  90   {
  91   }
  92
  93   /**
  94    * Send an asynchronous command to Chimera, in a new thread, optionally with
  95    * an 'in progress' message in a progress bar somewhere
  96    */
  97   protected void sendAsynchronousCommand(final String command,
  98           final String progressMsg)
  99   {
 100     Thread thread = new Thread(new Runnable()
 101     {
 102
 103       @Override
 104       public void run()
 105       {
 106     long stm = cvf.startProgressBar(progressMsg);
 107     try
 108     {
 109       sendChimeraCommand(command, false);
 110     } finally
 111     {
 112       cvf.stopProgressBar(null, stm);
 113     }
 114       }
 115     });
 116   thread.start();
 117
 118   }
 119 }