/*\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 (Development Version 2.4.1)\r
+ * Copyright (C) 2009 AM Waterhouse, J Procter, 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
{\r
text = new FeaturesFile().printGFFFormat(ap.av.alignment\r
.getDataset().getSequencesArray(),\r
- 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
- ap.av.featuresDisplayed);\r
+ getDisplayedFeatureCols(), true,ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);\r
}\r
}\r
else\r
if (GFFFormat.isSelected())\r
{\r
text = new FeaturesFile().printGFFFormat(ap.av.alignment\r
- .getDataset().getSequencesArray(), ap.av.featuresDisplayed);\r
+ .getDataset().getSequencesArray(), getDisplayedFeatureCols(),true,ap.av.isShowNpFeats());\r
}\r
else\r
{\r
text = new FeaturesFile().printJalviewFormat(ap.av.alignment\r
- .getDataset().getSequencesArray(), ap.av.featuresDisplayed);\r
+ .getDataset().getSequencesArray(), getDisplayedFeatureCols(),true,ap.av.isShowNpFeats());\r
}\r
}\r
else if (!features)\r
close_actionPerformed(null);\r
}\r
\r
+ private Hashtable getDisplayedFeatureCols()\r
+ {\r
+ Hashtable fcols = new Hashtable();\r
+ Enumeration en = ap.av.featuresDisplayed.keys();\r
+ FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider higher level method ?\r
+ while (en.hasMoreElements())\r
+ {\r
+ Object col = en.nextElement();\r
+ fcols.put(col, fr.featureColours.get(col));\r
+ }\r
+ return fcols;\r
+ }\r
+\r
public void close_actionPerformed(ActionEvent e)\r
{\r
try\r