X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPymolBindingModel.java;h=538b101b22015f22a4099e08915eab15924fd132;hb=789a8f2ab91523923a6fa307acb4323b2bd7e756;hp=fc957bb6e4f55520c07706802d29a2c7a7812965;hpb=d85a2741994c169e1b81db8f9166f5214ff1f561;p=jalview.git

diff --git a/src/jalview/gui/PymolBindingModel.java b/src/jalview/gui/PymolBindingModel.java
index fc957bb..538b101 100644
--- a/src/jalview/gui/PymolBindingModel.java
+++ b/src/jalview/gui/PymolBindingModel.java
@@ -6,12 +6,14 @@ import java.util.List;
 import java.util.Map;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 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;
@@ -28,8 +30,6 @@ public class PymolBindingModel extends AAStructureBindingModel
 
   private PymolManager pymolManager;
 
-  private Thread pymolMonitor;
-
   /*
    * full paths to structure files opened in PyMOL
    */
@@ -103,10 +103,9 @@ public class PymolBindingModel extends AAStructureBindingModel
   }
 
   @Override
-  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
   {
-    // pull up?
-    return new SequenceRenderer(alignment.getAlignViewport());
+    return new SequenceRenderer(avp.getAlignViewport());
   }
 
   @Override
@@ -139,24 +138,7 @@ public class PymolBindingModel extends AAStructureBindingModel
   public void closeViewer(boolean closePymol)
   {
     super.closeViewer(closePymol);
-    if (closePymol)
-    {
-      pymolManager.exitPymol();
-    }
     pymolManager = null;
-
-    if (pymolMonitor != null)
-    {
-      pymolMonitor.interrupt();
-    }
-  }
-
-  public boolean openSession(String pymolSessionFile)
-  {
-    StructureCommandI cmd = getCommandGenerator()
-            .loadFile(pymolSessionFile);
-    executeCommand(cmd, false);
-    return true;
   }
 
   public boolean launchPymol()
@@ -166,16 +148,17 @@ public class PymolBindingModel extends AAStructureBindingModel
       return true;
     }
 
-    boolean launched = pymolManager.launchPymol();
-    if (launched)
+    Process pymol = pymolManager.launchPymol();
+    if (pymol != null)
     {
       // start listening for PyMOL selections - how??
+      startExternalViewerMonitor(pymol);
     }
     else
     {
-      System.err.println("Failed to launch PyMOL!");
+      Cache.log.error("Failed to launch PyMOL!");
     }
-    return launched;
+    return pymol != null;
   }
 
   public void openFile(PDBEntry pe)
@@ -222,4 +205,28 @@ 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();
+  }
+
 }