X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCrossRefAction.java;h=c15cf2d9b7963ed42d9969307380de4b98d9f5cf;hb=71a3cc0202bd8b731f01e5706372e9bae047d592;hp=2ada4d2d7a2a70167bc11a2afb1272de54ab546d;hpb=0b573ed90b14079f7326281f50c0c9cffdace586;p=jalview.git

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 2ada4d2..c15cf2d 100644
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -25,6 +25,7 @@ import jalview.analysis.CrossRef;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsModelI;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -114,7 +115,8 @@ public class CrossRefAction implements Runnable
 
       if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
       {
-        // override default featureColourScheme so products have Ensembl variant colours
+        // override default featureColourScheme so products have Ensembl variant
+        // colours
         featureColourScheme = new SequenceFetcher()
                 .getFeatureColourScheme(DBRefSource.ENSEMBL);
       }
@@ -205,7 +207,8 @@ public class CrossRefAction implements Runnable
        * and for JAL-3330 also to original alignFrame view(s)
        * this currently trashes any original settings.
        */
-      for (AlignmentViewPanel origpanel: alignFrame.getAlignPanels()) {
+      for (AlignmentViewPanel origpanel : alignFrame.getAlignPanels())
+      {
         origpanel.getAlignViewport()
                 .mergeFeaturesStyle(featureColourScheme);
       }
@@ -229,7 +232,7 @@ public class CrossRefAction implements Runnable
       new OOMWarning("whilst fetching crossreferences", e);
     } catch (Throwable e)
     {
-      Cache.log.error("Error when finding crossreferences", e);
+      Console.error("Error when finding crossreferences", e);
     } finally
     {
       alignFrame.setProgressBar(MessageManager.formatMessage(
@@ -292,9 +295,9 @@ public class CrossRefAction implements Runnable
     {
       return;
     }
-    
+
     Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
-    
+
     /*
      * first look for direct dbrefs from sequence to Ensembl
      */
@@ -450,8 +453,7 @@ public class CrossRefAction implements Runnable
       copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
               xrefs.getSequencesArray(), dataset);
     }
-    copyAlignment
-            .setGapCharacter(alignFrame.viewport.getGapCharacter());
+    copyAlignment.setGapCharacter(alignFrame.viewport.getGapCharacter());
 
     StructureSelectionManager ssm = StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance);
@@ -464,8 +466,7 @@ public class CrossRefAction implements Runnable
 
     if (copyAlignment.getHeight() <= 0)
     {
-      System.err.println(
-              "No Sequences generated for xRef type " + source);
+      System.err.println("No Sequences generated for xRef type " + source);
       return null;
     }