JAL-3551 copy Jalview features to Pymol 'p' (with pull refactoring)

[jalview.git] / src / jalview / gui / PymolBindingModel.java

diff --git a/src/jalview/gui/PymolBindingModel.java b/src/jalview/gui/PymolBindingModel.java
index 6787c8a..21ba95c 100644 (file)
--- a/src/jalview/gui/PymolBindingModel.java
+++ b/src/jalview/gui/PymolBindingModel.java
@@ -12,12 +12,21 @@ import jalview.ext.pymol.PymolCommands;
 import jalview.ext.pymol.PymolManager;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.structure.AtomSpec;
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 
 public class PymolBindingModel extends AAStructureBindingModel
 {
+  /*
+   * format for labels shown on structures when mousing over sequence;
+   * see https://pymolwiki.org/index.php/Label#examples
+   * left not final so customisable e.g. with a Groovy script
+   */
+  private static String LABEL_FORMAT = "\"%s %s\" % (resn,resi)";
+
   private PymolManager pymolManager;
 
   private Thread pymolMonitor;
@@ -32,6 +41,8 @@ public class PymolBindingModel extends AAStructureBindingModel
    */
   Map<String, String> pymolObjects = new HashMap<>();
 
+  private String lastLabelSpec;
+
   /**
    * Constructor
    * 
@@ -59,13 +70,43 @@ public class PymolBindingModel extends AAStructureBindingModel
   @Override
   public void highlightAtoms(List<AtomSpec> atoms)
   {
+    /*
+     * https://pymolwiki.org/index.php/Label#examples
+     */
+    StringBuilder sb = new StringBuilder();
+    for (AtomSpec atom : atoms)
+    {
+      // todo promote to StructureCommandsI.showLabel()
+      // todo handle CA|P correctly
+      String modelId = getModelIdForFile(atom.getPdbFile());
+      sb.append(String.format(" %s//%s/%d/CA", modelId,
+              atom.getChain(),
+              atom.getPdbResNum()));
+    }
+    String labelSpec = sb.toString();
+    if (labelSpec.equals(lastLabelSpec))
+    {
+      return;
+    }
+    StructureCommandI command = new StructureCommand("label", labelSpec, LABEL_FORMAT);
+    executeCommand(command, false);
+
+    /*
+     * and remove the label(s) previously shown
+     */
+    if (lastLabelSpec != null)
+    {
+      command = new StructureCommand("label", lastLabelSpec, "");
+      executeCommand(command, false);
+    }
+
+    lastLabelSpec = labelSpec;
   }
 
   @Override
-  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
   {
-    // pull up?
-    return new SequenceRenderer(alignment.getAlignViewport());
+    return new SequenceRenderer(avp.getAlignViewport());
   }
 
   @Override
@@ -88,14 +129,16 @@ public class PymolBindingModel extends AAStructureBindingModel
     return ViewerType.PYMOL;
   }
 
-  public boolean isPymolRunning()
+  @Override
+  public boolean isViewerRunning()
   {
     return pymolManager.isPymolLaunched();
   }
 
+  @Override
   public void closeViewer(boolean closePymol)
   {
-    getSsm().removeStructureViewerListener(this, this.getStructureFiles());
+    super.closeViewer(closePymol);
     if (closePymol)
     {
       pymolManager.exitPymol();
@@ -106,7 +149,6 @@ public class PymolBindingModel extends AAStructureBindingModel
     {
       pymolMonitor.interrupt();
     }
-    releaseUIResources();
   }
 
   public boolean openSession(String pymolSessionFile)
@@ -180,4 +222,28 @@ public class PymolBindingModel extends AAStructureBindingModel
     return ".pse";
   }
 
+  @Override
+  public String getHelpURL()
+  {
+    return "https://pymolwiki.org/";
+  }
+
+  /**
+   * Constructs and sends commands to set atom properties for visible Jalview
+   * features on residues mapped to structure
+   * 
+   * @param avp
+   * @return
+   */
+  public int sendFeaturesToViewer(AlignmentViewPanel avp)
+  {
+    // todo pull up this and JalviewChimeraBinding variant
+    Map<String, Map<Object, AtomSpecModel>> featureValues = buildFeaturesMap(
+            avp);
+    List<StructureCommandI> commands = getCommandGenerator()
+            .setAttributes(featureValues);
+    executeCommands(commands, false, null);
+    return commands.size();
+  }
+
 }