X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=118aab8fd31dd1b4f6899dad81a80c904166a831;hb=df27351beb93456a00c6c2ae80ce999749f3b596;hp=2a3da7bb7f81d1b3d9e55e8abd392044858ee7af;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 2a3da7b..118aab8 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;
 
@@ -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)
@@ -188,7 +189,10 @@ 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();