X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=857eabc6cc5bb62b084ac6758db5664d04fb5698;hb=6486a5333807ca300db4a28a6bf9899f5dddf5a6;hp=2a3da7bb7f81d1b3d9e55e8abd392044858ee7af;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 2a3da7b..857eabc 100755
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
@@ -89,8 +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"
@@ -108,13 +107,13 @@ public class AnnotationExporter extends JPanel
         {
           text = new FeaturesFile().printGFFFormat(ap.av.alignment
                   .getDataset().getSequencesArray(),
-                  getDisplayedFeatureCols());//ap.av.featuresDisplayed//);
+                  getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
         }
         else
         {
           text = new FeaturesFile().printJalviewFormat(ap.av.alignment
                   .getDataset().getSequencesArray(),
-                  getDisplayedFeatureCols()); // ap.av.featuresDisplayed);
+                  getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
         }
       }
       else
@@ -154,12 +153,14 @@ public class AnnotationExporter extends JPanel
       if (GFFFormat.isSelected())
       {
         text = new FeaturesFile().printGFFFormat(ap.av.alignment
-                .getDataset().getSequencesArray(), getDisplayedFeatureCols());
+                .getDataset().getSequencesArray(),
+                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
       }
       else
       {
         text = new FeaturesFile().printJalviewFormat(ap.av.alignment
-                .getDataset().getSequencesArray(), getDisplayedFeatureCols());
+                .getDataset().getSequencesArray(),
+                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
       }
     }
     else if (!features)
@@ -176,10 +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);
   }
@@ -188,7 +197,10 @@ public class AnnotationExporter extends JPanel
   {
     Hashtable fcols = new Hashtable();
     Enumeration en = ap.av.featuresDisplayed.keys();
-    FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider higher level method ?
+    FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
+                                                                     // higher
+                                                                     // level
+                                                                     // method ?
     while (en.hasMoreElements())
     {
       Object col = en.nextElement();