X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=9c6231a2e066a9e0d8892f493cb06389082669e7;hb=cd05157564b53f68ca9eb3ade15d0e687b57572d;hp=2a3da7bb7f81d1b3d9e55e8abd392044858ee7af;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 2a3da7b..9c6231a 100755
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,24 +1,24 @@
 /*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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;
 
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 import java.awt.event.*;
@@ -45,7 +45,7 @@ public class AnnotationExporter extends JPanel
 
   AlignmentAnnotation[] annotations;
 
-  Vector sequenceGroups;
+  List<SequenceGroup> sequenceGroups;
 
   Hashtable alignmentProperties;
 
@@ -62,7 +62,7 @@ public class AnnotationExporter extends JPanel
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "", 260, 125);
+    Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width, frame.getPreferredSize().height);
   }
 
   public void exportFeatures(AlignmentPanel ap)
@@ -74,7 +74,7 @@ public class AnnotationExporter extends JPanel
   }
 
   public void exportAnnotations(AlignmentPanel ap,
-          AlignmentAnnotation[] annotations, Vector sequenceGroups,
+          AlignmentAnnotation[] annotations, List<SequenceGroup> list,
           Hashtable alProperties)
   {
     this.ap = ap;
@@ -82,15 +82,15 @@ public class AnnotationExporter extends JPanel
     GFFFormat.setVisible(false);
     CSVFormat.setVisible(true);
     this.annotations = annotations;
-    this.sequenceGroups = sequenceGroups;
+    this.sequenceGroups = list;
     this.alignmentProperties = alProperties;
     frame.setTitle("Export Annotations");
   }
 
   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"
@@ -106,15 +106,15 @@ public class AnnotationExporter extends JPanel
       {
         if (GFFFormat.isSelected())
         {
-          text = new FeaturesFile().printGFFFormat(ap.av.alignment
+          text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
                   .getDataset().getSequencesArray(),
-                  getDisplayedFeatureCols());//ap.av.featuresDisplayed//);
+                  getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
         }
         else
         {
-          text = new FeaturesFile().printJalviewFormat(ap.av.alignment
+          text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
                   .getDataset().getSequencesArray(),
-                  getDisplayedFeatureCols()); // ap.av.featuresDisplayed);
+                  getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
         }
       }
       else
@@ -153,13 +153,15 @@ public class AnnotationExporter extends JPanel
     {
       if (GFFFormat.isSelected())
       {
-        text = new FeaturesFile().printGFFFormat(ap.av.alignment
-                .getDataset().getSequencesArray(), getDisplayedFeatureCols());
+        text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
+                .getDataset().getSequencesArray(),
+                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
       }
       else
       {
-        text = new FeaturesFile().printJalviewFormat(ap.av.alignment
-                .getDataset().getSequencesArray(), getDisplayedFeatureCols());
+        text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
+                .getDataset().getSequencesArray(),
+                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
       }
     }
     else if (!features)
@@ -176,10 +178,18 @@ 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);
   }
@@ -187,8 +197,15 @@ public class AnnotationExporter extends JPanel
   private Hashtable getDisplayedFeatureCols()
   {
     Hashtable fcols = new Hashtable();
+    if (ap.av.featuresDisplayed == null)
+    {
+      return fcols;
+    }
     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();
@@ -209,7 +226,8 @@ public class AnnotationExporter extends JPanel
 
   private void jbInit() throws Exception
   {
-    this.setLayout(flowLayout1);
+    this.setLayout(new BorderLayout());
+    
     toFile.setText("to File");
     toFile.addActionListener(new ActionListener()
     {
@@ -257,8 +275,8 @@ public class AnnotationExporter extends JPanel
     buttonGroup.add(jalviewFormat);
     buttonGroup.add(GFFFormat);
     buttonGroup.add(CSVFormat);
-    this.add(jPanel3, null);
-    this.add(jPanel1, null);
+    this.add(jPanel3, BorderLayout.CENTER);
+    this.add(jPanel1, BorderLayout.SOUTH);
   }
 
   JPanel jPanel1 = new JPanel();