X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=289d340260858586e695f5bfd6d036b6f13bcc0e;hb=7856e91f60adc5c2d4943bad84a5a83e1412f00c;hp=1afa15e7673a9a992a60d268311aef9e7d533b84;hpb=4ee3a368d2de9eaa050137f7d45cfac0c432ef53;p=jalview.git

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 1afa15e..289d340 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -57,7 +57,6 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.AtomSpec;
 import jalview.structure.AtomSpecModel;
-import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
 import jalview.structure.StructureCommandsI;
 import jalview.structure.StructureListener;
@@ -981,8 +980,8 @@ public abstract class AAStructureBindingModel
 
     // TODO: JAL-628 colour chains distinctly across all visible models
 
-    executeCommand(commandGenerator.colourByChain(), false,
-            COLOURING_STRUCTURES);
+    executeCommand(false, COLOURING_STRUCTURES,
+            commandGenerator.colourByChain());
   }
 
   /**
@@ -1040,34 +1039,69 @@ public abstract class AAStructureBindingModel
   public void setBackgroundColour(Color col)
   {
     StructureCommandI cmd = commandGenerator.setBackgroundColour(col);
-    executeCommand(cmd, false, null);
+    executeCommand(false, null, cmd);
   }
 
   /**
-   * Sends one command to the structure viewer. If {@code getReply} is true, the
-   * command is sent synchronously, otherwise in a deferred thread.
-   * <p>
-   * If a progress message is supplied, this is displayed before command
-   * execution, and removed afterwards.
+   * Execute one structure viewer command. If {@code getReply} is true, may
+   * optionally return one or more reply messages, else returns null.
    * 
    * @param cmd
    * @param getReply
+   */
+  protected abstract List<String> executeCommand(StructureCommandI cmd,
+          boolean getReply);
+
+  /**
+   * Executes one or more structure viewer commands
+   * 
+   * @param commands
+   * @param getReply
    * @param msg
-   * @return
    */
-  private List<String> executeCommand(StructureCommandI cmd,
+  protected List<String> executeCommands(List<StructureCommandI> commands,
           boolean getReply, String msg)
   {
-    final JalviewStructureDisplayI theViewer = getViewer();
+    return executeCommand(getReply, msg,
+            commands.toArray(new StructureCommandI[commands.size()]));
+  }
+
+  /**
+   * Executes one or more structure viewer commands, optionally returning the
+   * reply, and optionally showing a status message while the command is being
+   * executed.
+   * <p>
+   * If a reply is wanted, the execution is done synchronously (waits),
+   * otherwise it is done in a separate thread (doesn't wait).
+   * 
+   * @param getReply
+   * @param msg
+   * @param cmds
+   * @return
+   */
+  protected List<String> executeCommand(boolean getReply, String msg,
+          StructureCommandI... cmds)
+  {
+    JalviewStructureDisplayI theViewer = getViewer();
     final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
+
     if (getReply)
     {
       /*
-       * synchronous (same thread) execution so reply can be returned
+       * execute and wait for reply
        */
+      List<String> response = new ArrayList<>();
       try
       {
-        return executeCommand(cmd, true);
+        for (StructureCommandI cmd : cmds)
+        {
+          List<String> replies = executeCommand(cmd, true);
+          if (replies != null)
+          {
+            response.addAll(replies);
+          }
+        }
+        return response;
       } finally
       {
         if (msg != null)
@@ -1076,62 +1110,39 @@ public abstract class AAStructureBindingModel
         }
       }
     }
-    else
+
+    /*
+     * fire and forget
+     */
+    String threadName = msg == null ? "StructureCommand" : msg;
+    new Thread(new Runnable()
     {
-      /*
-       * asynchronous (new thread) execution if no reply needed
-       */
-      SwingUtilities.invokeLater(new Runnable()
+      @Override
+      public void run()
       {
-        @Override
-        public void run()
+        try
         {
-          try
+          for (StructureCommandI cmd : cmds)
           {
             executeCommand(cmd, false);
-          } finally
+          }
+        } finally
+        {
+          if (msg != null)
           {
-            if (msg != null)
+            SwingUtilities.invokeLater(new Runnable()
             {
-              theViewer.stopProgressBar(null, handle);
-            }
+              @Override
+              public void run()
+              {
+                theViewer.stopProgressBar(null, handle);
+              }
+            });
           }
         }
-      });
-      return null;
-    }
-  }
-
-  /**
-   * Execute one structure viewer command. If {@code getReply} is true, may
-   * optionally return one or more reply messages, else returns null.
-   * 
-   * @param cmd
-   * @param getReply
-   */
-  protected abstract List<String> executeCommand(StructureCommandI cmd,
-          boolean getReply);
-
-  /**
-   * Executes one or more structure viewer commands
-   * 
-   * @param commands
-   * @param getReply
-   * @param msg
-   */
-  protected List<String> executeCommands(List<StructureCommandI> commands,
-          boolean getReply, String msg)
-  {
-    List<String> response = getReply ? new ArrayList<>() : null;
-    for (StructureCommandI cmd : commands)
-    {
-      List<String> replies = executeCommand(cmd, getReply, msg);
-      if (replies != null)
-      {
-        response.addAll(replies);
       }
-    }
-    return response;
+    }, threadName).start();
+    return null;
   }
 
   /**
@@ -1157,7 +1168,7 @@ public abstract class AAStructureBindingModel
    */
   public void focusView()
   {
-    executeCommand(commandGenerator.focusView(), false, null);
+    executeCommand(false, null, commandGenerator.focusView());
   }
 
   /**
@@ -1276,40 +1287,6 @@ public abstract class AAStructureBindingModel
   protected abstract ViewerType getViewerType();
 
   /**
-   * Send a structure viewer command asynchronously in a new thread. If the
-   * progress message is not null, display this message while the command is
-   * executing.
-   * 
-   * @param command
-   * @param progressMsg
-   */
-  protected void sendAsynchronousCommand(StructureCommandI command,
-          String progressMsg)
-  {
-    final JalviewStructureDisplayI theViewer = getViewer();
-    final long handle = progressMsg == null ? 0
-            : theViewer.startProgressBar(progressMsg);
-    SwingUtilities.invokeLater(new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        try
-        {
-          executeCommand(command, false, null);
-        } finally
-        {
-          if (progressMsg != null)
-          {
-            theViewer.stopProgressBar(null, handle);
-          }
-        }
-      }
-    });
-
-  }
-
-  /**
    * Builds a data structure which records mapped structure residues for each
    * colour. From this we can easily generate the viewer commands for colour by
    * sequence. Constructs and returns a map of {@code Color} to