JAL-2358 ensure mappings removed on close Chimera; pull up method;

case-insensitive pdbId check

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index e2e54aa..a30f6d3 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -64,9 +64,7 @@ import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
-import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
 import javax.swing.SwingUtilities;
@@ -338,30 +336,6 @@ public class AppJmol extends StructureViewerBase
     openNewJmol(ap, pe, seqs);
   }
 
-  /**
-   * Returns a list of any Jmol viewers. The list is restricted to those linked
-   * to the given alignment panel if it is not null.
-   */
-  @Override
-  protected List<StructureViewerBase> getViewersFor(AlignmentPanel apanel)
-  {
-    List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
-    JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
-    for (JInternalFrame frame : frames)
-    {
-      if (frame instanceof AppJmol)
-      {
-        if (apanel == null
-                || ((StructureViewerBase) frame).isLinkedWith(apanel))
-        {
-          result.add((StructureViewerBase) frame);
-        }
-      }
-    }
-    return result;
-  }
-
   void initJmol(String command)
   {
     jmb.setFinishedInit(false);

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index b82eef3..7cf3bfc 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -66,7 +66,6 @@ import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
 import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
-import javax.swing.JOptionPane;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 import javax.swing.event.MenuEvent;
@@ -341,28 +340,6 @@ public class ChimeraViewFrame extends StructureViewerBase
     setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
   }
 
-  /**
-   * Returns a list of any Chimera viewers in the desktop. The list is
-   * restricted to those linked to the given alignment panel if it is not null.
-   */
-  @Override
-  protected List<StructureViewerBase> getViewersFor(AlignmentPanel ap)
-  {
-    List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
-    JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
-    for (JInternalFrame frame : frames)
-    {
-      if (frame instanceof ChimeraViewFrame)
-      {
-        if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap))
-        {
-          result.add((StructureViewerBase) frame);
-        }
-      }
-    }
-    return result;
-  }
 
   /**
    * Launch Chimera. If we have a chimera session file name, send Chimera the
@@ -427,35 +404,47 @@ public class ChimeraViewFrame extends StructureViewerBase
    * 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 closeChimera
+   * @param forceCloseChimera
    *          if true, close any linked Chimera process; if false, prompt first
    */
   @Override
-  public void closeViewer(boolean closeChimera)
+  public void closeViewer(boolean forceCloseChimera)
   {
-    if (jmb != null && jmb.isChimeraRunning())
+    if (jmb != null)
     {
-      if (!closeChimera)
+      if (jmb.isChimeraRunning())
       {
-        String prompt = MessageManager.formatMessage(
-                "label.confirm_close_chimera",
-                new Object[] { jmb.getViewerTitle("Chimera", false) });
-        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
+         * force close, or prompt to close, Chimera
          */
-        if (confirm == JvOptionPane.CANCEL_OPTION
-                || confirm == JvOptionPane.CLOSED_OPTION)
+        if (!forceCloseChimera)
         {
-          return;
+          String prompt = MessageManager.formatMessage(
+                  "label.confirm_close_chimera",
+                  new Object[] { jmb.getViewerTitle("Chimera", false) });
+          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;
+          }
+          forceCloseChimera = confirm == JvOptionPane.YES_OPTION;
         }
-        closeChimera = confirm == JvOptionPane.YES_OPTION;
       }
-      jmb.closeViewer(closeChimera);
+
+      /*
+       * close the viewer plus any side-effects e.g. remove mappings
+       * note we do this also if closing Chimera triggered this method
+       */
+      jmb.closeViewer(forceCloseChimera);
     }
+
     setAlignmentPanel(null);
     _aps.clear();
     _alignwith.clear();

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 91d7130..19291ac 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -26,6 +26,7 @@ import jalview.gui.StructureViewer.ViewerType;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.DataSourceType;
 import jalview.jbgui.GStructureViewer;
+import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 
@@ -39,8 +40,8 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 
 /**
  * Base class with common functionality for JMol, Chimera or other structure
@@ -352,8 +353,29 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   protected abstract boolean hasPdbId(String pdbId);
 
-  protected abstract List<StructureViewerBase> getViewersFor(
-          AlignmentPanel alp);
+  /**
+   * Returns a list of any structure viewers of the same type. The list is
+   * restricted to those linked to the given alignment panel if it is not null.
+   */
+  protected List<StructureViewerBase> getViewersFor(AlignmentPanel alp){
+
+    List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
+    JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+    for (JInternalFrame frame : frames)
+    {
+      if (this.getClass().isAssignableFrom(frame.getClass()))
+      {
+        if (alp == null
+                || ((StructureViewerBase) frame).isLinkedWith(alp))
+        {
+          result.add((StructureViewerBase) frame);
+        }
+      }
+    }
+    return result;
+  
+  }
 
   /**
    * Check for any existing views involving this alignment and give user the
@@ -473,8 +495,8 @@ public abstract class StructureViewerBase extends GStructureViewer
           final AlignmentPanel apanel, String pdbId)
   {
     boolean finished = false;
-    String alreadyMapped = apanel.getStructureSelectionManager()
-            .alreadyMappedToFile(pdbId);
+    StructureSelectionManager ssm = apanel.getStructureSelectionManager();
+    String alreadyMapped = ssm.alreadyMappedToFile(pdbId);
 
     if (alreadyMapped != null)
     {

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 65fd5e7..2fd1966 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -299,7 +299,7 @@ public class StructureSelectionManager
   {
     for (StructureMapping sm : mappings)
     {
-      if (sm.getPdbId().equals(pdbid))
+      if (sm.getPdbId().equalsIgnoreCase(pdbid))
       {
         return sm.pdbfile;
       }