annotation might have been deleted

[jalview.git] / src / jalview / analysis / AlignmentSorter.java

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index e63b6e5..778142c 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -52,8 +52,8 @@ public class AlignmentSorter
 \r
         for (int i = 0; i < nSeq; i++)\r
         {\r
-            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),\r
-                                       s.getSequence());\r
+            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),\r
+                                       s.getSequenceAsString());\r
             seqs[i] = align.getSequenceAt(i);\r
         }\r
 \r
@@ -113,13 +113,24 @@ public class AlignmentSorter
     {\r
         // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
         Vector algn = align.getSequences();\r
+        Vector tmp = new Vector();\r
 \r
-        int index = 0;\r
         for (int i = 0; i < seqs.length; i++)\r
         {\r
           if(algn.contains(seqs[i]))\r
-            algn.setElementAt(seqs[i], index++);\r
+            tmp.addElement(seqs[i]);\r
+        }\r
+\r
+        algn.removeAllElements();\r
+        //User may have hidden seqs, then clicked undo or redo\r
+        for (int i = 0; i < tmp.size(); i++)\r
+        {\r
+          algn.addElement(tmp.elementAt(i));\r
         }\r
+\r
+\r
+\r
+\r
     }\r
 \r
     /**\r
@@ -187,7 +198,7 @@ public class AlignmentSorter
             {\r
                 SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);\r
 \r
-                if (sg.getSize(false) > sg2.getSize(false))\r
+                if (sg.getSize() > sg2.getSize())\r
                 {\r
                     groups.insertElementAt(sg, j);\r
 \r