JAL-3551 working proof of concept of Jalview driving PyMOL

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index ae34bd0..3553d68 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -24,7 +24,6 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
@@ -34,10 +33,10 @@ import jalview.gui.StructureViewer.ViewerType;
 import jalview.httpserver.AbstractRequestHandler;
 import jalview.io.DataSourceType;
 import jalview.structure.AtomSpec;
-import jalview.structure.StructureCommandsI.SuperposeData;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
 
 import java.io.File;
 import java.io.FileOutputStream;
@@ -45,7 +44,6 @@ import java.io.IOException;
 import java.io.PrintWriter;
 import java.net.BindException;
 import java.util.ArrayList;
-import java.util.BitSet;
 import java.util.Collections;
 import java.util.Iterator;
 import java.util.LinkedHashMap;
@@ -352,7 +350,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * @param getResponse
    */
   @Override
-  public List<String> executeCommand(final String command,
+  public List<String> executeCommand(final StructureCommandI command,
           boolean getResponse)
   {
     if (chimeraManager == null || command == null)
@@ -362,43 +360,21 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     }
     List<String> reply = null;
     // trim command or it may never find a match in the replyLog!!
+    String cmd = command.getCommand().trim();
     List<String> lastReply = chimeraManager
-            .sendChimeraCommand(command.trim(), getResponse);
+            .sendChimeraCommand(cmd, getResponse);
     if (getResponse)
     {
       reply = lastReply;
       if (debug)
       {
-        log("Response from command ('" + command + "') was:\n" + lastReply);
+        log("Response from command ('" + cmd + "') was:\n" + lastReply);
       }
     }
 
     return reply;
   }
 
-  /**
-   * @param command
-   */
-  protected void executeWhenReady(String command)
-  {
-    waitForChimera();
-    executeCommand(command, false);
-    waitForChimera();
-  }
-
-  private void waitForChimera()
-  {
-    while (chimeraManager != null && chimeraManager.isBusy())
-    {
-      try
-      {
-        Thread.sleep(15);
-      } catch (InterruptedException q)
-      {
-      }
-    }
-  }
-
   @Override
   public synchronized String[] getStructureFiles()
   {
@@ -582,7 +558,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
        * Chimera:  https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html
        * ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
        */
-      String command = getCommandGenerator().saveSession(filepath);
+      String command = getCommandGenerator().saveSession(filepath)
+              .getCommand();
       List<String> reply = chimeraManager.sendChimeraCommand(command, true);
       if (reply.contains("Session written"))
       {
@@ -611,7 +588,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      * Chimera:  https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html
      * ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html
      */
-    executeCommand("open " + filepath, true);
+    executeCommand(getCommandGenerator().loadFile(filepath), true);
     // todo: test for failure - how?
     return true;
   }
@@ -660,20 +637,20 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       return 0;
     }
 
-    String[] commands = getCommandGenerator()
+    List<StructureCommandI> commands = getCommandGenerator()
             .setAttributesForFeatures(getSsm(), files, getSequence(), avp);
-    if (commands.length > 10)
+    if (commands.size() > 10)
     {
       sendCommandsByFile(commands);
     }
     else
     {
-      for (String command : commands)
+      for (StructureCommandI command : commands)
       {
         sendAsynchronousCommand(command, null);
       }
     }
-    return commands.length;
+    return commands.size();
   }
 
   /**
@@ -683,21 +660,22 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * 
    * @param commands
    */
-  protected void sendCommandsByFile(String[] commands)
+  protected void sendCommandsByFile(List<StructureCommandI> commands)
   {
     try
     {
       File tmp = File.createTempFile("chim", getCommandFileExtension());
       tmp.deleteOnExit();
       PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
-      for (String command : commands)
+      for (StructureCommandI command : commands)
       {
-        out.println(command);
+        out.println(command.getCommand());
       }
       out.flush();
       out.close();
       String path = tmp.getAbsolutePath();
-      String command = getCommandGenerator().openCommandFile(path);
+      StructureCommandI command = getCommandGenerator()
+              .openCommandFile(path);
       sendAsynchronousCommand(command, null);
     } catch (IOException e)
     {
@@ -737,7 +715,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     // fails for 'average.bfactor' (which is bad):
 
     String cmd = "list residues attr '" + attName + "'";
-    List<String> residues = executeCommand(cmd, true);
+    List<String> residues = executeCommand(new StructureCommand(cmd), true);
 
     boolean featureAdded = createFeaturesForAttributes(attName, residues);
     if (featureAdded)
@@ -852,14 +830,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   @Override
-  public int getModelNoForFile(String pdbFile)
+  public String getModelIdForFile(String pdbFile)
   {
     List<ChimeraModel> foundModels = chimeraMaps.get(pdbFile);
     if (foundModels != null && !foundModels.isEmpty())
     {
-      return foundModels.get(0).getModelNumber();
+      return String.valueOf(foundModels.get(0).getModelNumber());
     }
-    return -1;
+    return "";
   }
 
   /**