From 8449a33e712dfec13771d4e1b8be20bf625f190b Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 20 Aug 2010 12:32:13 +0000
Subject: [PATCH] refactor jmol api so it doesn't clash with Swing component
 method. * JAL-582

---
 src/jalview/appletgui/AppletJmolBinding.java |    2 +-
 src/jalview/appletgui/ExtJmol.java           |    2 +-
 src/jalview/ext/jmol/JalviewJmolBinding.java |    8 ++++----
 src/jalview/gui/AppJmol.java                 |   11 ++++++++---
 src/jalview/gui/AppJmolBinding.java          |    2 +-
 5 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 89d053b..9299af2 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -68,7 +68,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   }
 
-  public void updateUI()
+  public void refreshGUI()
   {
     appletJmolBinding.updateTitleAndMenus();
   }
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 2c5da17..8e42f2a 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -86,7 +86,7 @@ public class ExtJmol extends JalviewJmolBinding
     ap.alignFrame.showURL(url, target);
   }
 
-  public void updateUI()
+  public void refreshGUI()
   {
     // ignore
   }
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 929411f..44a9993 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -778,7 +778,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
         break;
       case JmolConstants.CALLBACK_SYNC:
       case JmolConstants.CALLBACK_RESIZE:
-        updateUI();
+        refreshGUI();
         break;
       case JmolConstants.CALLBACK_MEASURE:
 
@@ -824,7 +824,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
     if (errorMsg != null)
     {
       fileLoadingError = errorMsg;
-      updateUI();
+      refreshGUI();
       return;
     }
     // the rest of this routine ignores the arguments, and simply interrogates
@@ -970,7 +970,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
       {
         fr.featuresAdded();
       }
-      updateUI();
+      refreshGUI();
     }
   }
 
@@ -1060,7 +1060,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * state change. this could be because structures were loaded, or because an
    * error has occured.
    */
-  public abstract void updateUI();
+  public abstract void refreshGUI();
 
   public void allocateViewer(Component renderPanel, String htmlName,
           URL documentBase, URL codeBase, String commandOptions)
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index e274b84..9e1e35a 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -364,13 +364,18 @@ public class AppJmol extends GStructureViewer implements Runnable,
   public void viewMapping_actionPerformed(ActionEvent actionEvent)
   {
     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
-    jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
-            550, 600);
-    for (int pdbe = 0; pdbe<jmb.pdbentry.length; pdbe++) {
+    try {for (int pdbe = 0; pdbe<jmb.pdbentry.length; pdbe++) {
       cap.appendText(StructureSelectionManager.getStructureSelectionManager()
             .printMapping(jmb.pdbentry[pdbe].getFile()));
       cap.appendText("\n");
+    }} catch (OutOfMemoryError e)
+    {
+      new OOMWarning("composing sequence-structure alignments for display in text box.", e);
+      cap.dispose();
+      return;
     }
+    jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
+            550, 600);
   }
 
   /**
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 9f7090a..39d198d 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -81,7 +81,7 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   }
 
   @Override
-  public void updateUI()
+  public void refreshGUI()
   {
     // appJmolWindow.repaint();
     appJmolWindow.updateTitleAndMenus();
-- 
1.7.10.2