- String output = new FormatAdapter().formatSequences(format,\r
- viewport.getAlignment().\r
- getSequences());\r
+\r
+ String[] omitHidden = null;\r
+\r
+ if (viewport.hasHiddenColumns)\r
+ {\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ "The Alignment contains hidden columns."\r
+ + "\nDo you want to save only the visible alignment?",\r
+ "Save / Omit Hidden Columns",\r
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (reply == JOptionPane.YES_OPTION)\r
+ omitHidden = viewport.getViewAsString(false);\r
+ }\r
+\r
+ String output = new FormatAdapter().formatSequences(\r
+ format,\r
+ viewport.alignment.getSequencesArray(),\r
+ omitHidden);\r
+\r