X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPymolBindingModel.java;h=538b101b22015f22a4099e08915eab15924fd132;hb=refs%2Ftags%2FDevelop-2_11_2_0-d20201215;hp=af4afb0d31a281d4a2aa8a906709e345a4eab607;hpb=42f4227ed213d422a87d3b22fc9e85d14ffaf53f;p=jalview.git

diff --git a/src/jalview/gui/PymolBindingModel.java b/src/jalview/gui/PymolBindingModel.java
index af4afb0..538b101 100644
--- a/src/jalview/gui/PymolBindingModel.java
+++ b/src/jalview/gui/PymolBindingModel.java
@@ -1,26 +1,34 @@
 package jalview.gui;
 
+import java.util.ArrayList;
+import java.util.HashMap;
+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;
 import jalview.structures.models.AAStructureBindingModel;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
 public class PymolBindingModel extends AAStructureBindingModel
 {
-  private PymolManager pymolManager;
+  /*
+   * 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 Thread pymolMonitor;
+  private PymolManager pymolManager;
 
   /*
    * full paths to structure files opened in PyMOL
@@ -32,6 +40,8 @@ public class PymolBindingModel extends AAStructureBindingModel
    */
   Map<String, String> pymolObjects = new HashMap<>();
 
+  private String lastLabelSpec;
+
   /**
    * Constructor
    * 
@@ -59,20 +69,50 @@ 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
   protected List<String> executeCommand(StructureCommandI command,
           boolean getReply)
   {
-    System.out.println(command.toString()); // debug
+    // System.out.println(command.toString()); // debug
     return pymolManager.sendCommand(command, getReply);
   }
 
@@ -88,38 +128,17 @@ 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());
-    if (closePymol)
-    {
-      pymolManager.exitPymol();
-    }
-    // if (this.pymolListener != null)
-    // {
-    // pymolListener.shutdown();
-    // pymolListener = null;
-    // }
+    super.closeViewer(closePymol);
     pymolManager = null;
-
-    if (pymolMonitor != null)
-    {
-      pymolMonitor.interrupt();
-    }
-    releaseUIResources();
-  }
-
-  public boolean openSession(String pymolSessionFile)
-  {
-    StructureCommandI cmd = getCommandGenerator()
-            .loadFile(pymolSessionFile);
-    executeCommand(cmd, false);
-    return true;
   }
 
   public boolean launchPymol()
@@ -129,16 +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)
@@ -173,4 +193,40 @@ public class PymolBindingModel extends AAStructureBindingModel
     return file;
   }
 
+  /**
+   * Returns the file extension to use for a saved viewer session file (.pse)
+   * 
+   * @return
+   * @see https://pymolwiki.org/index.php/Save
+   */
+  @Override
+  public String getSessionFileExtension()
+  {
+    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();
+  }
+
 }