import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
+import jalview.api.FeatureSettingsI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.ScoreModelI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+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;
@Override
public void fetchSequence_actionPerformed(ActionEvent e)
{
- new SequenceFetcher(this);
+ new jalview.gui.SequenceFetcher(this);
}
@Override
* alternative protein products for my protein's gene
*/
List<SequenceI> addedPeers = new ArrayList<SequenceI>();
- AlignmentI alignment = AlignFrame.this.getViewport().getAlignment();
+ AlignmentI alignment = AlignFrame.this.getViewport()
+ .getAlignment();
Alignment xrefs = CrossRef.findXrefSequences(sel, dna, source,
alignment, addedPeers);
if (xrefs != null)
{
+ /*
+ * figure out colour 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(
alignment.getDataset(), xrefs);
copyThis.setShowSeqFeatures(showSequenceFeatures);
FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
.getFeatureRenderer();
+
/*
* copy feature rendering settings to split frame
*/
copyThis.alignPanel.getSeqPanel().seqCanvas
.getFeatureRenderer().transferSettings(
myFeatureStyling);
+
+ /*
+ * apply 'database source' feature configuration
+ * if any was found
+ */
+ newFrame.getViewport()
+ .applyFeaturesStyle(featureColourScheme);
+ copyThis.getViewport()
+ .applyFeaturesStyle(featureColourScheme);
+
SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
dna ? newFrame : copyThis);
newFrame.setVisible(true);
* @param prods
* @return
*/
- protected Alignment makeCrossReferencesAlignment(
-Alignment dataset,
+ protected Alignment makeCrossReferencesAlignment(Alignment dataset,
Alignment prods)
{
SequenceI[] sprods = new SequenceI[prods.getHeight()];
alignPanel.paintAlignment(true);
}
}
- else
- {
- new FileLoader().LoadFile(viewport, file, protocol, format);
- }
+ else
+ {
+ new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
}
}
if (isAnnotation)
@Override
public void run()
{
- boolean isNuclueotide = alignPanel.alignFrame
- .getViewport().getAlignment()
- .isNucleotide();
+ boolean isNuclueotide = alignPanel.alignFrame.getViewport()
+ .getAlignment().isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(),
- alignPanel.alignFrame, null,
- alignPanel.alignFrame.featureSettings,
- isNuclueotide)
+ .getSequenceSelection(), alignPanel.alignFrame, null,
+ alignPanel.alignFrame.featureSettings, isNuclueotide)
.fetchDBRefs(false);
}
}).start();
@Override
public void run()
{
- final jalview.ws.SequenceFetcher sf = SequenceFetcher
+ final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
.getSequenceFetcherSingleton(me);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
.getSequenceSelection(),
alignPanel.alignFrame, dassource,
alignPanel.alignFrame.featureSettings,
- isNuclueotide)
- .fetchDBRefs(false);
+ isNuclueotide).fetchDBRefs(false);
}
}).start();
}
.getSequenceSelection(),
alignPanel.alignFrame, dassource,
alignPanel.alignFrame.featureSettings,
- isNuclueotide)
- .fetchDBRefs(false);
+ isNuclueotide).fetchDBRefs(false);
}
}).start();
}
.getSequenceSelection(),
alignPanel.alignFrame, dassrc,
alignPanel.alignFrame.featureSettings,
- isNuclueotide)
- .fetchDBRefs(false);
+ isNuclueotide).fetchDBRefs(false);
}
}).start();
}