JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / src / jalview / gui / CrossRefAction.java

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 2ee741b..b5275e8 100644 (file)
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -34,6 +34,7 @@ import jalview.datamodel.SequenceI;
 import jalview.ext.ensembl.EnsemblInfo;
 import jalview.ext.ensembl.EnsemblMap;
 import jalview.io.gff.SequenceOntologyI;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
@@ -107,8 +108,7 @@ public class CrossRefAction implements Runnable
       /*
        * get display scheme (if any) to apply to features
        */
-      FeatureSettingsModelI featureColourScheme = SequenceFetcher
-              .getInstance()
+      FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
               .getFeatureColourScheme(source);
 
       AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
@@ -141,7 +141,7 @@ public class CrossRefAction implements Runnable
        */
       AlignFrame newFrame = new AlignFrame(xrefsAlignment,
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
-      if (Cache.getDefault(Preferences.HIDE_INTRONS, true))
+      if (Cache.getDefault("HIDE_INTRONS", true))
       {
         newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
       }
@@ -276,7 +276,7 @@ public class CrossRefAction implements Runnable
       return;
     }
     
-    Set<String> ensemblDivisions = EnsemblInfo.getDivisions();
+    Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
     
     /*
      * first look for direct dbrefs from sequence to Ensembl
@@ -436,12 +436,14 @@ public class CrossRefAction implements Runnable
     copyAlignment
             .setGapCharacter(alignFrame.viewport.getGapCharacter());
 
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+
     /*
      * register any new mappings for sequence mouseover etc
      * (will not duplicate any previously registered mappings)
      */
-    Desktop.getInstance().getStructureSelectionManager()
-            .registerMappings(dataset.getCodonFrames());
+    ssm.registerMappings(dataset.getCodonFrames());
 
     if (copyAlignment.getHeight() <= 0)
     {