Use visible id for sorting

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 89aadac..8737c59 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -161,6 +161,12 @@ public class AlignFrame
 \r
   }\r
 \r
+  public AlignViewport getViewport()\r
+  {\r
+    return viewport;\r
+  }\r
+\r
+\r
   /**\r
    * DOCUMENT ME!\r
    *\r
@@ -1872,7 +1878,7 @@ public class AlignFrame
   {\r
     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
                                    HistoryItem.SORT));\r
-    AlignmentSorter.sortByID(viewport.getAlignment());\r
+    AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);\r
     alignPanel.repaint();\r
   }\r
 \r
@@ -2464,8 +2470,8 @@ public class AlignFrame
     if (value == JalviewFileChooser.APPROVE_OPTION)\r
     {\r
       jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);\r
-      vs.store(chooser.getSelectedFile().getAbsolutePath()\r
-          );\r
+      //vs.store(chooser.getSelectedFile().getAbsolutePath()   );\r
+      vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);\r
     }\r
   }\r
 \r