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Merge branch 'patch/JAL-3692enaEndpointFlatfile' into releases/Release_2_11_1_Branch
[jalview.git]
/
src
/
jalview
/
gui
/
CrossRefAction.java
diff --git
a/src/jalview/gui/CrossRefAction.java
b/src/jalview/gui/CrossRefAction.java
index
673bcc0
..
92947e2
100644
(file)
--- a/
src/jalview/gui/CrossRefAction.java
+++ b/
src/jalview/gui/CrossRefAction.java
@@
-39,6
+39,7
@@
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
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;
import jalview.ws.SequenceFetcher;
import java.util.ArrayList;
@@
-111,6
+112,13
@@
public class CrossRefAction implements Runnable
FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
.getFeatureColourScheme(source);
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)
AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
xrefs);
if (!dna)
@@
-170,17
+178,17
@@
public class CrossRefAction implements Runnable
.isShowSequenceFeatures();
newFrame.setShowSeqFeatures(showSequenceFeatures);
copyThis.setShowSeqFeatures(showSequenceFeatures);
.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
*/
.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);
.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);
.getFeatureRenderer();
fr2.transferSettings(myFeatureStyling);
fr2.findAllFeatures(true);