X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencemapping.java;h=ee0c2b6f757a6be1b32cabba7f1d8b60cd8f814c;hb=d99d6a98cd0a7009e94ca4166f48741af75cde1e;hp=8223123912c2810677e58b06a642069dace4abe3;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 8223123..ee0c2b6 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -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