X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=e73ce07bcee5dddc98d8a078295d55de919061de;hb=42498abb930c08393b09fc7af2564b7f210ac294;hp=34ad659402361ea2c50394a9356a3117003b6e67;hpb=f831ddf7f52d6c4a1918e87d94877b22bd322648;p=jalview.git

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 34ad659..e73ce07 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -23,7 +23,7 @@ package jalview.gui;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.StructureViewer.ViewerType;
@@ -110,6 +110,8 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   protected boolean allChainsSelected = false;
 
+  protected JMenu viewSelectionMenu;
+
   /**
    * Default constructor
    */
@@ -744,17 +746,17 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void itemStateChanged(ItemEvent e)
       {
-        alignStructs.setEnabled(_alignwith.size() > 0);
+        alignStructs.setEnabled(!_alignwith.isEmpty());
         alignStructs.setToolTipText(MessageManager.formatMessage(
                 "label.align_structures_using_linked_alignment_views",
-                new String[] { String.valueOf(_alignwith.size()) }));
+                _alignwith.size()));
       }
     };
-    JMenu alpanels = new ViewSelectionMenu(
+    viewSelectionMenu = new ViewSelectionMenu(
             MessageManager.getString("label.superpose_with"), this,
             _alignwith, handler);
     handler.itemStateChanged(null);
-    viewerActionMenu.add(alpanels);
+    viewerActionMenu.add(viewSelectionMenu, 0);
     viewerActionMenu.addMenuListener(new MenuListener()
     {
       @Override
@@ -781,16 +783,24 @@ public abstract class StructureViewerBase extends GStructureViewer
   public void setJalviewColourScheme(ColourSchemeI cs) {
     getBinding().setJalviewColourScheme(cs);
   }
+
+  /**
+   * Sends commands to the structure viewer to superimpose structures based on
+   * currently associated alignments. May optionally return an error message for
+   * the operation.
+   */
   @Override
-  protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+  protected String alignStructs_actionPerformed(
+          ActionEvent actionEvent)
   {
-    alignStructs_withAllAlignPanels();
+    return alignStructs_withAllAlignPanels();
   }
-  protected void alignStructs_withAllAlignPanels()
+
+  protected String alignStructs_withAllAlignPanels()
   {
     if (getAlignmentPanel() == null)
     {
-      return;
+      return null;
     }
   
     if (_alignwith.size() == 0)
@@ -798,10 +808,11 @@ public abstract class StructureViewerBase extends GStructureViewer
       _alignwith.add(getAlignmentPanel());
     }
   
+    String reply = null;
     try
     {
       AlignmentI[] als = new Alignment[_alignwith.size()];
-      ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+      HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
       int[] alm = new int[_alignwith.size()];
       int a = 0;
   
@@ -809,9 +820,15 @@ public abstract class StructureViewerBase extends GStructureViewer
       {
         als[a] = ap.av.getAlignment();
         alm[a] = -1;
-        alc[a++] = ap.av.getColumnSelection();
+        alc[a++] = ap.av.getAlignment().getHiddenColumns();
+      }
+      reply = getBinding().superposeStructures(als, alm, alc);
+      if (reply != null)
+      {
+        String text = MessageManager.formatMessage(
+                "error.superposition_failed", reply);
+        statusBar.setText(text);
       }
-      getBinding().superposeStructures(als, alm, alc);
     } catch (Exception e)
     {
       StringBuffer sp = new StringBuffer();
@@ -822,7 +839,9 @@ public abstract class StructureViewerBase extends GStructureViewer
       Cache.log.info("Couldn't align structures with the " + sp.toString()
               + "associated alignment panels.", e);
     }
+    return reply;
   }
+
   @Override
   public void background_actionPerformed(ActionEvent actionEvent)
   {
@@ -900,7 +919,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       {
         // TODO: cope with multiple PDB files in view
         in = new BufferedReader(
-                new FileReader(getBinding().getPdbFile()[0]));
+                new FileReader(getBinding().getStructureFiles()[0]));
         File outFile = chooser.getSelectedFile();
   
         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
@@ -952,6 +971,10 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   protected abstract String getViewerName();
+
+  /**
+   * Configures the title and menu items of the viewer panel.
+   */
   public void updateTitleAndMenus()
   {
     AAStructureBindingModel binding = getBinding();
@@ -963,10 +986,30 @@ public abstract class StructureViewerBase extends GStructureViewer
     setChainMenuItems(binding.getChainNames());
   
     this.setTitle(binding.getViewerTitle(getViewerName(), true));
-    if (binding.getPdbFile().length > 1 && binding.getSequence().length > 1)
+
+    /*
+     * enable 'Superpose with' if more than one mapped structure
+     */
+    viewSelectionMenu.setEnabled(false);
+    if (getBinding().getStructureFiles().length > 1
+            && getBinding().getSequence().length > 1)
     {
-      viewerActionMenu.setVisible(true);
+      viewSelectionMenu.setEnabled(true);
     }
+
+    /*
+     * Show action menu if it has any enabled items
+     */
+    viewerActionMenu.setVisible(false);
+    for (int i = 0; i < viewerActionMenu.getItemCount(); i++)
+    {
+      if (viewerActionMenu.getItem(i).isEnabled())
+      {
+        viewerActionMenu.setVisible(true);
+        break;
+      }
+    }
+
     if (!binding.isLoadingFromArchive())
     {
       seqColour_actionPerformed(null);