From 1e5e507fe9402197a0e925ca71550bae0ab14c72 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 4 Nov 2005 10:54:58 +0000
Subject: [PATCH] Use visible id for sorting

---
 src/jalview/analysis/AlignmentSorter.java |    4 ++--
 src/jalview/appletgui/AlignFrame.java     |    2 +-
 src/jalview/gui/AlignFrame.java           |   12 +++++++++---
 3 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 20101dc..bed083e 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -124,7 +124,7 @@ public class AlignmentSorter
      *
      * @param align The alignment object to sort
      */
-    public static void sortByID(AlignmentI align)
+    public static void sortByID(AlignmentI align, boolean dbprefix)
     {
         int nSeq = align.getHeight();
 
@@ -133,7 +133,7 @@ public class AlignmentSorter
 
         for (int i = 0; i < nSeq; i++)
         {
-            ids[i] = align.getSequenceAt(i).getName();
+            ids[i] = align.getSequenceAt(i).getDisplayId(dbprefix, false);
             seqs[i] = align.getSequenceAt(i);
         }
 
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6e2d32b..7c3ab49 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1210,7 +1210,7 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
                                    HistoryItem.SORT));
-    AlignmentSorter.sortByID(viewport.getAlignment());
+    AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
     alignPanel.repaint();
   }
 
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 89aadac..8737c59 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -161,6 +161,12 @@ public class AlignFrame
 
   }
 
+  public AlignViewport getViewport()
+  {
+    return viewport;
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1872,7 +1878,7 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
                                    HistoryItem.SORT));
-    AlignmentSorter.sortByID(viewport.getAlignment());
+    AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
     alignPanel.repaint();
   }
 
@@ -2464,8 +2470,8 @@ public class AlignFrame
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
-      vs.store(chooser.getSelectedFile().getAbsolutePath()
-          );
+      //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
+      vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
     }
   }
 
-- 
1.7.10.2