init Jmol with 'SmarterJmolAdapter'

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index e274b84..6312cb1 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -187,7 +187,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
     jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
             getBounds().width, getBounds().height);
-    jmb.allocateViewer(renderPanel, "", null, null, "");
+    jmb.allocateViewer(renderPanel, true, "", null, null, "");
     jmb.newJmolPopup(true, "Jmol", true);
     jmb.evalStateCommand(command);
     jmb.setFinishedInit(true);
@@ -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);
   }
 
   /**