JAL-4034 Fix #2 show an icon and a button to press to initiate search

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

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index ac0e82a..c15cf2d 100644 (file)
--- 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;
@@ -112,6 +113,14 @@ public class CrossRefAction implements Runnable
       FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
               .getFeatureColourScheme(source);
 
+      if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
+      {
+        // override default featureColourScheme so products have Ensembl variant
+        // colours
+        featureColourScheme = new SequenceFetcher()
+                .getFeatureColourScheme(DBRefSource.ENSEMBL);
+      }
+
       AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
               xrefs);
       if (!dna)
@@ -188,15 +197,25 @@ public class CrossRefAction implements Runnable
 
       /*
        * apply 'database source' feature configuration
-       * if any was found
+       * if any - first to the new splitframe view about to be displayed
        */
-      // TODO is this the feature colouring for the original
-      // alignment or the fetched xrefs? either could be Ensembl
+
       newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
       copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
 
+      /*
+       * and for JAL-3330 also to original alignFrame view(s)
+       * this currently trashes any original settings.
+       */
+      for (AlignmentViewPanel origpanel : alignFrame.getAlignPanels())
+      {
+        origpanel.getAlignViewport()
+                .mergeFeaturesStyle(featureColourScheme);
+      }
+
       SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
               dna ? newFrame : copyThis);
+
       newFrame.setVisible(true);
       copyThis.setVisible(true);
       String linkedTitle = MessageManager
@@ -213,7 +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(
@@ -276,16 +295,16 @@ public class CrossRefAction implements Runnable
     {
       return;
     }
-    
+
     Set<String> ensemblDivisions = new 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)
     {
@@ -305,8 +324,8 @@ 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)
         {
@@ -434,8 +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);
@@ -448,8 +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;
     }