X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencemapping.java;h=21745537f193d8b4c2d6273e2005befa5ac17e53;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=55a4fe729788504b79d1cdb6f8d5ce0fc06663d6;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 55a4fe7..2174553 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -22,6 +22,7 @@ import java.util.Vector;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
 import jalview.io.VamsasAppDatastore;
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.objects.core.AlignmentSequence;
@@ -346,9 +347,9 @@ public class Sequencemapping extends Rangetype
       if (!sense)
       {
         mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense
-        mapping = new jalview.util.MapList(mapping.getToRanges(), mapping
-                .getFromRanges(), mapping.getToRatio(), mapping
-                .getFromRatio());
+        mapping = new jalview.util.MapList(mapping.getToRanges(),
+                mapping.getFromRanges(), mapping.getToRatio(),
+                mapping.getFromRatio());
         afc.addMap(to, from, mapping);
       }
       else
@@ -364,7 +365,7 @@ public class Sequencemapping extends Rangetype
     }
     bindjvvobj(mapping, sequenceMapping);
     jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager().addMappings(
+            .getStructureSelectionManager(Desktop.instance).addMappings(
                     new AlignedCodonFrame[]
                     { afc });
     // Try to link up any conjugate database references in the two sequences