X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FCrossRefAction.java;h=3f3c2985083a43c9ca09227f3cfcb98abe25d605;hb=47806656477f02076cac0467c7374e231a59ab7e;hp=21a0a84cb97cbe1f559e3602fe71b4b2f9ef2a3f;hpb=353109c11d706b29ae5bc9606f0e12223aa45a98;p=jalview.git

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 21a0a84..3f3c298 100644
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -34,7 +34,6 @@ 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;
@@ -108,7 +107,8 @@ public class CrossRefAction implements Runnable
       /*
        * get display scheme (if any) to apply to features
        */
-      FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
+      FeatureSettingsModelI featureColourScheme = SequenceFetcher
+              .getInstance()
               .getFeatureColourScheme(source);
 
       AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
@@ -176,10 +176,14 @@ public class CrossRefAction implements Runnable
       /*
        * copy feature rendering settings to split frame
        */
-      newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
-              .transferSettings(myFeatureStyling);
-      copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
-              .transferSettings(myFeatureStyling);
+      FeatureRenderer fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
+              .getFeatureRenderer();
+      fr1.transferSettings(myFeatureStyling);
+      fr1.findAllFeatures(true);
+      FeatureRenderer fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
+              .getFeatureRenderer();
+      fr2.transferSettings(myFeatureStyling);
+      fr2.findAllFeatures(true);
 
       /*
        * apply 'database source' feature configuration
@@ -272,15 +276,15 @@ public class CrossRefAction implements Runnable
       return;
     }
     
-    Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
+    Set<String> ensemblDivisions = EnsemblInfo.getDivisions();
     
     /*
      * first look for direct dbrefs from sequence to Ensembl
      */
     String[] divisionsArray = ensemblDivisions
             .toArray(new String[ensemblDivisions.size()]);
-    DBRefEntry[] seqRefs = seq.getDBRefs();
-    DBRefEntry[] directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
+    List<DBRefEntry> seqRefs = seq.getDBRefs();
+    List<DBRefEntry> directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
             divisionsArray);
     if (directEnsemblRefs != null)
     {
@@ -300,8 +304,8 @@ public class CrossRefAction implements Runnable
     {
       if (dbref.getMap() != null && dbref.getMap().getTo() != null)
       {
-        DBRefEntry[] dbrefs = dbref.getMap().getTo().getDBRefs();
-        DBRefEntry[] indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
+        List<DBRefEntry> dbrefs = dbref.getMap().getTo().getDBRefs();
+        List<DBRefEntry> indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
                 divisionsArray);
         if (indirectEnsemblRefs != null)
         {
@@ -336,7 +340,7 @@ public class CrossRefAction implements Runnable
 
     /*
      * hack: ignore cross-references to Ensembl protein ids
-     * (can't fetch chromosomal mapping for these)
+     * (or use map/translation perhaps?)
      * todo: is there an equivalent in EnsemblGenomes?
      */
     if (accession.startsWith("ENSP"))
@@ -432,14 +436,12 @@ 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)
      */
-    ssm.registerMappings(dataset.getCodonFrames());
+    Desktop.getStructureSelectionManager()
+            .registerMappings(dataset.getCodonFrames());
 
     if (copyAlignment.getHeight() <= 0)
     {