Merge branch 'develop' into features/JAL-2295setChimeraAttributes

[jalview.git] / src / jalview / gui / JalviewChimeraBindingModel.java

diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index a2a3184..c1f15e5 100644 (file)
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -1,9 +1,30 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
 
 public class JalviewChimeraBindingModel extends JalviewChimeraBinding
@@ -12,25 +33,25 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
 
   private FeatureRenderer fr = null;
 
+
   public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
           StructureSelectionManager ssm, PDBEntry[] pdbentry,
-          SequenceI[][] sequenceIs, String[][] chains, String protocol)
+          SequenceI[][] sequenceIs, DataSourceType protocol)
   {
-    super(ssm, pdbentry, sequenceIs, chains, protocol);
+    super(ssm, pdbentry, sequenceIs, protocol);
     cvf = chimeraViewFrame;
   }
 
   @Override
-  public FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment)
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
     AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
             : (AlignmentPanel) alignment;
-    if (ap.av.showSequenceFeatures)
+    if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
       {
-        fr = ap.cloneFeatureRenderer();
+        fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
       }
       else
       {
@@ -53,6 +74,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   {
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         cvf.updateTitleAndMenus();
@@ -61,6 +83,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     });
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
@@ -71,7 +94,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     }
     if (!isLoadingFromArchive())
     {
-      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+      colourBySequence(ap.av.isShowSequenceFeatures(), ap);
     }
   }
 
@@ -89,4 +112,41 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   public void refreshPdbEntries()
   {
   }
+
+  /**
+   * Send an asynchronous command to Chimera, in a new thread, optionally with
+   * an 'in progress' message in a progress bar somewhere
+   */
+  @Override
+  protected void sendAsynchronousCommand(final String command,
+          final String progressMsg)
+  {
+    Thread thread = new Thread(new Runnable()
+    {
+
+      @Override
+      public void run()
+      {
+        long handle = 0;
+        if (progressMsg != null)
+        {
+          handle = cvf.startProgressBar(progressMsg);
+        }
+        try
+        {
+          sendChimeraCommand(command, false);
+        } finally
+        {
+          if (progressMsg != null)
+          {
+            cvf.stopProgressBar(null, handle);
+          }
+        }
+      }
+    });
+    thread.start();
+
+  }
+
+
 }