JAL-1333 more superposition debugging and deadlock avoidance

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index 95ea0d7..c0b3a39 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -21,13 +21,13 @@ import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads;
 public class ChimeraManager
 {
 
-  static private Process chimera;
+  private Process chimera;
 
-  static private ListenerThreads chimeraListenerThreads;
+  private ListenerThreads chimeraListenerThreads;
 
-  static private Map<Integer, ChimeraModel> currentModelsMap;
+  private Map<Integer, ChimeraModel> currentModelsMap;
 
-  private static Logger logger = LoggerFactory
+  private Logger logger = LoggerFactory
           .getLogger(ext.edu.ucsf.rbvi.strucviz2.ChimeraManager.class);
 
   private StructureManager structureManager;
@@ -38,7 +38,7 @@ public class ChimeraManager
     chimera = null;
     chimeraListenerThreads = null;
     currentModelsMap = new HashMap<Integer, ChimeraModel>();
-    
+
   }
 
   public List<ChimeraModel> getChimeraModels(String modelName)
@@ -627,7 +627,9 @@ public class ChimeraManager
     }
     return values;
   }
-  private volatile boolean busy=false;
+
+  private volatile boolean busy = false;
+
   /**
    * Send a command to Chimera.
    * 
@@ -647,11 +649,15 @@ public class ChimeraManager
     }
     while (busy)
     {
-      try {
+      try
+      {
         Thread.sleep(25);
-      } catch (InterruptedException q) {};
+      } catch (InterruptedException q)
+      {
+      }
+      ;
     }
-    busy=true;
+    busy = true;
     chimeraListenerThreads.clearResponse(command);
     String text = command.concat("\n");
     // System.out.println("send command to chimera: " + text);
@@ -667,16 +673,16 @@ public class ChimeraManager
       logger.warn("Unable to execute command: " + text);
       logger.warn("Exiting...");
       clearOnChimeraExit();
-      busy=false;
+      busy = false;
       return null;
     }
     if (!reply)
     {
-      busy=false;
+      busy = false;
       return null;
     }
     List<String> rsp = chimeraListenerThreads.getResponse(command);
-    busy=false;
+    busy = false;
     return rsp;
   }
 
@@ -685,4 +691,9 @@ public class ChimeraManager
     return structureManager;
   }
 
+  public boolean isBusy()
+  {
+    return busy;
+  }
+
 }

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 5fc3a6f..fcf89af 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -326,7 +326,7 @@ public abstract class JalviewChimeraBinding extends
     if (cmd.length() > 0)
       cmd.setLength(cmd.length() - 4);
     evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmd + ";focus "
-            + cmd);
+            + cmd,false);
   }
 
   public void closeViewer()
@@ -353,14 +353,14 @@ public abstract class JalviewChimeraBinding extends
     // TODO: colour by chain should colour each chain distinctly across all
     // visible models
     // TODO: http://issues.jalview.org/browse/JAL-628
-    evalStateCommand("select *;color chain");
+    evalStateCommand("select *;color chain",false);
   }
 
   public void colourByCharge()
   {
     colourBySequence = false;
     evalStateCommand("colour *;color white;select ASP,GLU;color red;"
-            + "select LYS,ARG;color blue;select CYS;color yellow");
+            + "select LYS,ARG;color blue;select CYS;color yellow", false);
   }
 
   /**
@@ -408,7 +408,7 @@ public abstract class JalviewChimeraBinding extends
           int[] _refStructure, ColumnSelection[] _hiddenCols)
   {
     assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
-
+    StringBuffer allComs = new StringBuffer(); // whole shebang for superposition
     String[] files = getPdbFile();
     // check to see if we are still waiting for Jmol files
     long starttime = System.currentTimeMillis();
@@ -483,6 +483,7 @@ public abstract class JalviewChimeraBinding extends
       // reference structure - all others are superposed in it
       String[] targetC = new String[files.length];
       String[] chainNames = new String[files.length];
+      String[] atomS = new String[files.length];
       for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
       {
         StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@ -550,6 +551,7 @@ public abstract class JalviewChimeraBinding extends
               }
               chainNames[pdbfnum] = mapping[m].getPdbId()
                       + targetC[pdbfnum];
+              atomS[pdbfnum] = asp.getRNA()!=null ? "P" : "CA";
               // move on to next pdb file
               s = sequence[pdbfnum].length;
               break;
@@ -590,8 +592,7 @@ public abstract class JalviewChimeraBinding extends
                 {
                   molsel.append((run ? "" : ":") + lpos);
                   molsel.append(chainCd);
-                  // molsel.append("} {");
-                  // molsel.append(",");
+                  molsel.append(",");
                 }
               }
               else
@@ -620,12 +621,11 @@ public abstract class JalviewChimeraBinding extends
           {
             selcom[pdbfnum] = molsel.toString();
             selectioncom.append("#" + pdbfnum);
-            selectioncom.append(selcom[pdbfnum].substring(1,
-                    selcom[pdbfnum].length() - 1));
+            selectioncom.append(selcom[pdbfnum]);
             selectioncom.append(" ");
             if (pdbfnum < files.length - 1)
             {
-              selectioncom.append("|");
+              selectioncom.append("| ");
             }
           }
           else
@@ -641,24 +641,29 @@ public abstract class JalviewChimeraBinding extends
         {
           continue;
         }
-        command.append("match ");
+        if (command.length()>0)
+        {
+          command.append(";");
+        }
+        command.append("match");
 
         // form the matched pair strings
         for (int s = 0; s < 2; s++)
         {
+          command.append(" #"+(s == 0 ? pdbfnum : refStructure)+".1");
+          // note - need to select on first model, otherwise it all goes wrong!
           command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
+          command.append("@"+atomS[(s == 0 ? pdbfnum : refStructure)]); // match on backbone alpha/polyphosphate
         }
       }
       if (selectioncom.length() > 0)
       {
         System.out.println("Select regions:\n" + selectioncom.toString());
-        evalStateCommand("~display *; trace *; ribbons "
-                + selectioncom.toString() + "");
-        // selcom.append("; ribbons; ");
         System.out
                 .println("Superimpose command(s):\n" + command.toString());
-
-        evalStateCommand(command.toString());
+        allComs.append("~display all; chain @CA|P; ribbon "
+                + selectioncom.toString() + ";"+command.toString());
+        // selcom.append("; ribbons; ");
       }
     }
     if (selectioncom.length() > 0)
@@ -668,10 +673,12 @@ public abstract class JalviewChimeraBinding extends
         selectioncom.setLength(selectioncom.length() - 1);
       }
       System.out.println("Select regions:\n" + selectioncom.toString());
-      evalStateCommand("~display *; trace *; ribbons "
+      allComs.append("; ~display all; chain @CA|P; ribbon "
               + selectioncom.toString() + "");
       // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
+      evalStateCommand(allComs.toString(),false);
     }
+    
   }
 
   private void checkLaunched()
@@ -686,7 +693,7 @@ public abstract class JalviewChimeraBinding extends
     }
   }
 
-  public void evalStateCommand(final String command)
+  public void evalStateCommand(final String command, boolean resp)
   {
     viewerCommandHistory(false);
     checkLaunched();
@@ -697,7 +704,7 @@ public abstract class JalviewChimeraBinding extends
 //        @Override
 //        public void run()
 //        {
-          lastReply = viewer.sendChimeraCommand(command, true);
+          lastReply = viewer.sendChimeraCommand(command, resp);
           if (debug)
           {
             log("Response from command ('" + command + "') was:\n"
@@ -748,10 +755,23 @@ public abstract class JalviewChimeraBinding extends
                     alignment))
       for (String cbyseq : cpdbbyseq.commands)
       {
-        evalStateCommand(cbyseq);
+        waitForChimera();
+        evalStateCommand(cbyseq, false);
+        waitForChimera();
       }
   }
 
+  private void waitForChimera()
+  {
+    while (viewer.isBusy())
+    {
+      try {
+        Thread.sleep(15);
+      } catch (InterruptedException q)
+      {}
+    }
+  }
+
   public boolean isColourBySequence()
   {
     return colourBySequence;
@@ -899,7 +919,7 @@ public abstract class JalviewChimeraBinding extends
       int mdlNum = cms.get(0).getModelNumber();
 
       viewerCommandHistory(false);
-      viewer.stopListening();
+      // viewer.stopListening();
       if (resetLastRes.length() > 0)
       {
         eval.setLength(0);
@@ -926,7 +946,7 @@ public abstract class JalviewChimeraBinding extends
       
       viewer.sendChimeraCommand(eval.toString(), false);
       viewerCommandHistory(true);
-      viewer.startListening();
+      // viewer.startListening();
     }
   }
 
@@ -1198,7 +1218,7 @@ public abstract class JalviewChimeraBinding extends
               + col.getGreen() + "," + col.getBlue() + "];");
     }
 
-    evalStateCommand(command.toString());
+    evalStateCommand(command.toString(),false);
     viewerCommandHistory(true);
   }
 

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 815957f..10082eb 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -586,7 +586,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
     {
       command = "";
     }
-    jmb.evalStateCommand(command);
+    jmb.evalStateCommand(command, false);
     jmb.setFinishedInit(true);
   }
 
@@ -845,13 +845,13 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
       // do superposition if asked to
       if (alignAddedStructures)
       {
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        new Thread(new Runnable()
         {
           public void run()
           {
             alignStructs_withAllAlignPanels();
           }
-        });
+        }).start();
         alignAddedStructures = false;
       }
       addingStructures = false;