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(AlignmentViewPanel alignment)
  25   {
  26     AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
  27             : (AlignmentPanel) alignment;
  28     if (ap.av.isShowSequenceFeatures())
  29     {
  30       if (fr == null)
  31       {
  32         fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
  33       }
  34       else
  35       {
  36         ap.updateFeatureRenderer(fr);
  37       }
  38     }
  39
  40     return fr;
  41   }
  42
  43   @Override
  44   public jalview.api.SequenceRenderer getSequenceRenderer(
  45           AlignmentViewPanel alignment)
  46   {
  47     return new SequenceRenderer(((AlignmentPanel) alignment).av);
  48   }
  49
  50   @Override
  51   public void refreshGUI()
  52   {
  53     javax.swing.SwingUtilities.invokeLater(new Runnable()
  54     {
  55       public void run()
  56       {
  57         cvf.updateTitleAndMenus();
  58         cvf.revalidate();
  59       }
  60     });
  61   }
  62
  63   public void updateColours(Object source)
  64   {
  65     AlignmentPanel ap = (AlignmentPanel) source;
  66     // ignore events from panels not used to colour this view
  67     if (!cvf.isUsedforcolourby(ap))
  68     {
  69       return;
  70     }
  71     if (!isLoadingFromArchive())
  72     {
  73       colourBySequence(ap.av.isShowSequenceFeatures(), ap);
  74     }
  75   }
  76
  77   @Override
  78   public void releaseReferences(Object svl)
  79   {
  80   }
  81
  82   @Override
  83   protected void releaseUIResources()
  84   {
  85   }
  86
  87   @Override
  88   public void refreshPdbEntries()
  89   {
  90   }
  91
  92   /**
  93    * Send an asynchronous command to Chimera, in a new thread, optionally with
  94    * an 'in progress' message in a progress bar somewhere
  95    */
  96   protected void sendAsynchronousCommand(final String command,
  97           final String progressMsg)
  98   {
  99     Thread thread = new Thread(new Runnable()
 100     {
 101
 102       @Override
 103       public void run()
 104       {
 105         long stm = cvf.startProgressBar(progressMsg);
 106         try
 107         {
 108           sendChimeraCommand(command, false);
 109         } finally
 110         {
 111           cvf.stopProgressBar(null, stm);
 112         }
 113       }
 114     });
 115     thread.start();
 116
 117   }
 118 }