Merge branch 'develop' into feature/JAL-3551Pymol

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 0c5c5f0..e180f6b 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -39,7 +39,6 @@ import java.util.Vector;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.JRadioButtonMenuItem;
@@ -51,6 +50,7 @@ import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.DataSourceType;
@@ -677,7 +677,10 @@ public abstract class StructureViewerBase extends GStructureViewer
     });
 
     viewerColour = new JRadioButtonMenuItem();
-    // text is set in overrides of this method
+    viewerColour
+            .setText(MessageManager.getString("label.colour_with_viewer"));
+    viewerColour.setToolTipText(MessageManager
+            .getString("label.let_viewer_manage_structure_colours"));
     viewerColour.setName(ViewerColour.ByViewer.name());
     viewerColour.setSelected(!binding.isColourBySequence());
 
@@ -715,10 +718,18 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void itemStateChanged(ItemEvent e)
       {
-        alignStructs.setEnabled(!_alignwith.isEmpty());
-        alignStructs.setToolTipText(MessageManager.formatMessage(
-                "label.align_structures_using_linked_alignment_views",
-                _alignwith.size()));
+        if (_alignwith.isEmpty())
+        {
+          alignStructs.setEnabled(false);
+          alignStructs.setToolTipText(null);
+        }
+        else
+        {
+          alignStructs.setEnabled(true);
+          alignStructs.setToolTipText(MessageManager.formatMessage(
+                  "label.align_structures_using_linked_alignment_views",
+                  _alignwith.size()));
+        }
       }
     };
     viewSelectionMenu = new ViewSelectionMenu(
@@ -789,16 +800,23 @@ public abstract class StructureViewerBase extends GStructureViewer
     return reply;
   }
 
+  /**
+   * Opens a colour chooser dialog, and applies the chosen colour to the
+   * background of the structure viewer
+   */
   @Override
   public void background_actionPerformed()
   {
-    Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_background_colour"),
-            null);
-    if (col != null)
+    String ttl = MessageManager.getString("label.select_background_colour");
+    ColourChooserListener listener = new ColourChooserListener()
     {
-      getBinding().setBackgroundColour(col);
-    }
+      @Override
+      public void colourSelected(Color c)
+      {
+        getBinding().setBackgroundColour(c);
+      }
+    };
+    JalviewColourChooser.showColourChooser(this, ttl, null, listener);
   }
 
   @Override
@@ -856,6 +874,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   @Override
   public void pdbFile_actionPerformed()
   {
+    // TODO: JAL-3048 not needed for Jalview-JS - save PDB file
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty("LAST_DIRECTORY"));
 
@@ -1151,4 +1170,50 @@ public abstract class StructureViewerBase extends GStructureViewer
     return getBinding() == null ? null : getBinding().saveSession();
   }
 
+  /**
+   * Close down this instance of Jalview's Chimera viewer, giving the user the
+   * option to close the associated Chimera window (process). They may wish to
+   * keep it open until they have had an opportunity to save any work.
+   * 
+   * @param forceClose
+   *          if true, close any linked Chimera process; if false, prompt first
+   */
+  @Override
+  public void closeViewer(boolean forceClose)
+  {
+    AAStructureBindingModel binding = getBinding();
+    if (binding != null && binding.isViewerRunning())
+    {
+      if (!forceClose)
+      {
+        String viewerName = getViewerName();
+        String prompt = MessageManager
+                .formatMessage("label.confirm_close_viewer", new Object[]
+                { binding.getViewerTitle(viewerName, false), viewerName });
+        prompt = JvSwingUtils.wrapTooltip(true, prompt);
+        int confirm = JvOptionPane.showConfirmDialog(this, prompt,
+                MessageManager.getString("label.close_viewer"),
+                JvOptionPane.YES_NO_CANCEL_OPTION);
+        /*
+         * abort closure if user hits escape or Cancel
+         */
+        if (confirm == JvOptionPane.CANCEL_OPTION
+                || confirm == JvOptionPane.CLOSED_OPTION)
+        {
+          return;
+        }
+        forceClose = confirm == JvOptionPane.YES_OPTION;
+      }
+      binding.closeViewer(forceClose);
+    }
+    setAlignmentPanel(null);
+    _aps.clear();
+    _alignwith.clear();
+    _colourwith.clear();
+    // TODO: check for memory leaks where instance isn't finalised because jmb
+    // holds a reference to the window
+    // jmb = null;
+    dispose();
+  }
+
 }