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

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 718f4a5..118aab8 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 (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\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
@@ -108,13 +107,13 @@ public class AnnotationExporter extends JPanel
         {\r
           text = new FeaturesFile().printGFFFormat(ap.av.alignment\r
                   .getDataset().getSequencesArray(),\r
-                  getDisplayedFeatureCols(), true,ap.av.isShowNpFeats());//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(), true,ap.av.isShowNpFeats()); // 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(),true,ap.av.isShowNpFeats());\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(),true,ap.av.isShowNpFeats());\r
+                .getDataset().getSequencesArray(),\r
+                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());\r
       }\r
     }\r
     else if (!features)\r
@@ -188,7 +189,10 @@ public class AnnotationExporter extends JPanel
   {\r
     Hashtable fcols = new Hashtable();\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