JAL-1115 refactor reordering code operating directly on Sequence collection as Alignm...

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 9e5c4fb..5a199bb 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1457,48 +1457,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {\r
       return;\r
     }\r
-\r
-    if (up)\r
-    {\r
-      for (int i = 1; i < viewport.getAlignment().getHeight(); i++)\r
-      {\r
-        SequenceI seq = viewport.getAlignment().getSequenceAt(i);\r
-        if (!sg.getSequences(null).contains(seq))\r
-        {\r
-          continue;\r
-        }\r
-\r
-        SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);\r
-        if (sg.getSequences(null).contains(temp))\r
-        {\r
-          continue;\r
-        }\r
-\r
-        viewport.getAlignment().getSequences().setElementAt(temp, i);\r
-        viewport.getAlignment().getSequences().setElementAt(seq, i - 1);\r
-      }\r
-    }\r
-    else\r
-    {\r
-      for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)\r
-      {\r
-        SequenceI seq = viewport.getAlignment().getSequenceAt(i);\r
-        if (!sg.getSequences(viewport.getHiddenRepSequences()).contains(seq))\r
-        {\r
-          continue;\r
-        }\r
-\r
-        SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);\r
-        if (sg.getSequences(viewport.getHiddenRepSequences()).contains(temp))\r
-        {\r
-          continue;\r
-        }\r
-\r
-        viewport.getAlignment().getSequences().setElementAt(temp, i);\r
-        viewport.getAlignment().getSequences().setElementAt(seq, i + 1);\r
-      }\r
-    }\r
-\r
+    viewport.getAlignment().moveSelectedSequencesByOne(sg, up ? null : viewport.getHiddenRepSequences(), up);\r
     alignPanel.paintAlignment(true);\r
   }\r
 \r