From 1b85d0acd9a09b646ac2dd6f1ea6db5db6f3731d Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 18 Aug 2010 16:50:34 +0000
Subject: [PATCH] JAL-612 - catch hidden OOM related to filling in cut and
 paste text boxes

---
 src/MCview/PDBViewer.java               |   10 ++++++++--
 src/jalview/gui/AlignFrame.java         |   11 +++++++++--
 src/jalview/gui/AnnotationExporter.java |   20 ++++++++++++++------
 src/jalview/gui/TreePanel.java          |   11 +++++++++--
 4 files changed, 40 insertions(+), 12 deletions(-)

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 50a501d..35e2308 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -564,8 +564,14 @@ public class PDBViewer extends JInternalFrame implements Runnable
   public void mapping_actionPerformed(ActionEvent e)
   {
     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
-    Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
-    cap.setText(pdbcanvas.mappingDetails.toString());
+    try {
+      cap.setText(pdbcanvas.mappingDetails.toString());
+      Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("Opening sequence to structure mapping report",oom);
+      cap.dispose();
+    }
   }
 
   public void allchains_itemStateChanged(ItemEvent e)
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3ac30ae..b0d30a2 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1005,11 +1005,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
+
+    try {
+      cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+            viewport.alignment, omitHidden, viewport.colSel));
     Desktop.addInternalFrame(cap, "Alignment output - "
             + e.getActionCommand(), 600, 500);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("Outputting alignment as "+e.getActionCommand(),oom);
+      cap.dispose();
+    }
 
-    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
-            viewport.alignment, omitHidden, viewport.colSel));
   }
 
   /**
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 118aab8..857eabc 100755
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -88,8 +88,8 @@ public class AnnotationExporter extends JPanel
 
   public void toFile_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(features ? "Save Features to File"
@@ -177,10 +177,18 @@ public class AnnotationExporter extends JPanel
     }
 
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    cap.setText(text);
-    Desktop.addInternalFrame(cap, (features ? "Features for - "
-            : "Annotations for - ")
-            + ap.alignFrame.getTitle(), 600, 500);
+    try
+    {
+      cap.setText(text);
+      Desktop.addInternalFrame(cap, (features ? "Features for - "
+              : "Annotations for - ") + ap.alignFrame.getTitle(), 600, 500);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("generating "
+              + (features ? "Features for - " : "Annotations for - ")
+              + ap.alignFrame.getTitle(), oom);
+      cap.dispose();
+    }
 
     close_actionPerformed(null);
   }
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 45fc0df..cc63ee4 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -364,12 +364,19 @@ public class TreePanel extends GTreePanel
       buffer.append("PID");
     }
 
-    Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 
     jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
             .getTopNode());
-    cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
+    try {
+      cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
             tree.isHasRootDistance()));
+      Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("generating newick tree file",oom);
+      cap.dispose();
+    }
+
   }
 
   /**
-- 
1.7.10.2