JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

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

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 51ac2ee..b04661e 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;
@@ -39,6 +40,7 @@ import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.ws.SequenceFetcher;
 
 import java.util.ArrayList;
@@ -111,6 +113,13 @@ 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)
@@ -170,32 +179,41 @@ public class CrossRefAction implements Runnable
               .isShowSequenceFeatures();
       newFrame.setShowSeqFeatures(showSequenceFeatures);
       copyThis.setShowSeqFeatures(showSequenceFeatures);
-      FeatureRenderer myFeatureStyling = alignFrame.alignPanel
+      FeatureRendererModel myFeatureStyling = alignFrame.alignPanel
               .getSeqPanel().seqCanvas.getFeatureRenderer();
 
       /*
        * copy feature rendering settings to split frame
        */
-      FeatureRenderer fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
+      FeatureRendererModel fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
               .getFeatureRenderer();
       fr1.transferSettings(myFeatureStyling);
       fr1.findAllFeatures(true);
-      FeatureRenderer fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
+      FeatureRendererModel fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
               .getFeatureRenderer();
       fr2.transferSettings(myFeatureStyling);
       fr2.findAllFeatures(true);
 
       /*
        * 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
@@ -212,7 +230,7 @@ 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(
@@ -283,8 +301,8 @@ public class CrossRefAction implements Runnable
      */
     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)
     {
@@ -304,8 +322,8 @@ 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)
         {