JAL-2016 push getFeatureColourScheme(source) into SequenceFetcher

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0d6efe4..b48a750 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -32,7 +32,7 @@ import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsControllerI;
-import jalview.api.FeatureSettingsI;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.ScoreModelI;
@@ -100,7 +100,6 @@ import jalview.ws.SequenceFetcher;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
@@ -4733,22 +4732,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           if (xrefs != null)
           {
             /*
-             * figure out colour scheme if any to apply to features
+             * get display scheme (if any) to apply to features
              */
-            ASequenceFetcher sftch = new SequenceFetcher();
-            List<DbSourceProxy> proxies = sftch.getSourceProxy(source);
-            FeatureSettingsI featureColourScheme = null;
-            for (DbSourceProxy proxy : proxies)
-            {
-              FeatureSettingsI preferredColours = proxy
-                      .getFeatureColourScheme();
-              if (preferredColours != null)
-              {
-                featureColourScheme = preferredColours;
-                break;
-              }
-            }
-            Alignment al = makeCrossReferencesAlignment(
+            FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
+                    .getFeatureColourScheme(source);
+
+            AlignmentI al = makeCrossReferencesAlignment(
                     alignment.getDataset(), xrefs);
 
             AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
@@ -4896,31 +4885,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
 
       /**
-       * Makes an alignment containing the given sequences; the sequences are
-       * added to the given alignment dataset, and the dataset is set on (shared
-       * by) the new alignment
+       * Makes an alignment containing the given sequences. If this is of the
+       * same type as the given dataset (nucleotide/protein), then the new
+       * alignment shares the same dataset, and its dataset sequences are added
+       * to it. Otherwise a new dataset sequence is created for the
+       * cross-references.
        * 
        * @param dataset
        * @param seqs
        * @return
        */
-      protected Alignment makeCrossReferencesAlignment(Alignment dataset,
-              Alignment seqs)
+      protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
+              AlignmentI seqs)
       {
+        boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
+
         SequenceI[] sprods = new SequenceI[seqs.getHeight()];
         for (int s = 0; s < sprods.length; s++)
         {
           sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
-          if (dataset.getSequences() == null
-                  || !dataset.getSequences().contains(
-                          sprods[s].getDatasetSequence()))
+          if (sameType)
           {
-            dataset.addSequence(sprods[s].getDatasetSequence());
+            if (dataset.getSequences() == null
+                    || !dataset.getSequences().contains(
+                            sprods[s].getDatasetSequence()))
+            {
+              dataset.addSequence(sprods[s].getDatasetSequence());
+            }
           }
           sprods[s].updatePDBIds();
         }
         Alignment al = new Alignment(sprods);
-        al.setDataset(dataset);
+        if (sameType)
+        {
+          al.setDataset((Alignment) dataset);
+        }
+        else
+        {
+          al.createDatasetAlignment();
+        }
         return al;
       }