JAL-4034 Fix #2 show an icon and a button to press to initiate search

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

diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index a2a3184..689106a 100644 (file)
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -1,44 +1,44 @@
+/*
+ * 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 javax.swing.JComponent;
+import javax.swing.SwingUtilities;
+
 import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 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
 {
-  private ChimeraViewFrame cvf;
-
-  private FeatureRenderer fr = null;
-
   public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
           StructureSelectionManager ssm, PDBEntry[] pdbentry,
-          SequenceI[][] sequenceIs, String[][] chains, String protocol)
-  {
-    super(ssm, pdbentry, sequenceIs, chains, protocol);
-    cvf = chimeraViewFrame;
-  }
-
-  @Override
-  public FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment)
+          SequenceI[][] sequenceIs, DataSourceType protocol)
   {
-    AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
-            : (AlignmentPanel) alignment;
-    if (ap.av.showSequenceFeatures)
-    {
-      if (fr == null)
-      {
-        fr = ap.cloneFeatureRenderer();
-      }
-      else
-      {
-        ap.updateFeatureRenderer(fr);
-      }
-    }
-
-    return fr;
+    super(ssm, pdbentry, sequenceIs, protocol);
+    setViewer(chimeraViewFrame);
   }
 
   @Override
@@ -51,42 +51,15 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   @Override
   public void refreshGUI()
   {
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
-        cvf.updateTitleAndMenus();
-        cvf.revalidate();
+        JalviewStructureDisplayI theViewer = getViewer();
+        theViewer.updateTitleAndMenus();
+        ((JComponent) theViewer).revalidate();
       }
     });
   }
-
-  public void updateColours(Object source)
-  {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    // ignore events from panels not used to colour this view
-    if (!cvf.isUsedforcolourby(ap))
-    {
-      return;
-    }
-    if (!isLoadingFromArchive())
-    {
-      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
-    }
-  }
-
-  @Override
-  public void releaseReferences(Object svl)
-  {
-  }
-
-  @Override
-  protected void releaseUIResources()
-  {
-  }
-
-  @Override
-  public void refreshPdbEntries()
-  {
-  }
 }