Hidden representatives moved from sequence to viewport

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

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index c80c326..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
@@ -121,7 +121,7 @@ public class AlignmentSorter
             tmp.addElement(seqs[i]);\r
         }\r
 \r
-        algn.clear();\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
@@ -198,7 +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