Jalview 2.6 source licence

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

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index a058c87..de6aaa0 100755 (executable)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,20 +1,19 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
  * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
  * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
  * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE.  See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  */\r
 package jalview.gui;\r
 \r
@@ -89,8 +88,8 @@ public class AnnotationExporter extends JPanel
 \r
   public void toFile_actionPerformed(ActionEvent e)\r
   {\r
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache\r
-            .getProperty("LAST_DIRECTORY"));\r
+    JalviewFileChooser chooser = new JalviewFileChooser(\r
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
 \r
     chooser.setFileView(new JalviewFileView());\r
     chooser.setDialogTitle(features ? "Save Features to File"\r
@@ -108,13 +107,13 @@ public class AnnotationExporter extends JPanel
         {\r
           text = new FeaturesFile().printGFFFormat(ap.av.alignment\r
                   .getDataset().getSequencesArray(),\r
-                  getDisplayedFeatureCols());//ap.av.featuresDisplayed//);\r
+                  getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);\r
         }\r
         else\r
         {\r
           text = new FeaturesFile().printJalviewFormat(ap.av.alignment\r
                   .getDataset().getSequencesArray(),\r
-                  getDisplayedFeatureCols()); // ap.av.featuresDisplayed);\r
+                  getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);\r
         }\r
       }\r
       else\r
@@ -154,12 +153,14 @@ public class AnnotationExporter extends JPanel
       if (GFFFormat.isSelected())\r
       {\r
         text = new FeaturesFile().printGFFFormat(ap.av.alignment\r
-                .getDataset().getSequencesArray(), getDisplayedFeatureCols());\r
+                .getDataset().getSequencesArray(),\r
+                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());\r
       }\r
       else\r
       {\r
         text = new FeaturesFile().printJalviewFormat(ap.av.alignment\r
-                .getDataset().getSequencesArray(), getDisplayedFeatureCols());\r
+                .getDataset().getSequencesArray(),\r
+                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());\r
       }\r
     }\r
     else if (!features)\r
@@ -176,10 +177,18 @@ public class AnnotationExporter extends JPanel
     }\r
 \r
     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
-    cap.setText(text);\r
-    Desktop.addInternalFrame(cap, (features ? "Features for - "\r
-            : "Annotations for - ")\r
-            + ap.alignFrame.getTitle(), 600, 500);\r
+    try\r
+    {\r
+      cap.setText(text);\r
+      Desktop.addInternalFrame(cap, (features ? "Features for - "\r
+              : "Annotations for - ") + ap.alignFrame.getTitle(), 600, 500);\r
+    } catch (OutOfMemoryError oom)\r
+    {\r
+      new OOMWarning("generating "\r
+              + (features ? "Features for - " : "Annotations for - ")\r
+              + ap.alignFrame.getTitle(), oom);\r
+      cap.dispose();\r
+    }\r
 \r
     close_actionPerformed(null);\r
   }\r
@@ -187,8 +196,15 @@ public class AnnotationExporter extends JPanel
   private Hashtable getDisplayedFeatureCols()\r
   {\r
     Hashtable fcols = new Hashtable();\r
+    if (ap.av.featuresDisplayed==null)\r
+    {\r
+      return fcols;\r
+    }\r
     Enumeration en = ap.av.featuresDisplayed.keys();\r
-    FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider higher level method ?\r
+    FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider\r
+                                                                     // higher\r
+                                                                     // level\r
+                                                                     // method ?\r
     while (en.hasMoreElements())\r
     {\r
       Object col = en.nextElement();\r