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;
if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
{
- // override default featureColourScheme so products have Ensembl variant colours
+ // override default featureColourScheme so products have Ensembl variant
+ // colours
featureColourScheme = new SequenceFetcher()
.getFeatureColourScheme(DBRefSource.ENSEMBL);
}
* and for JAL-3330 also to original alignFrame view(s)
* this currently trashes any original settings.
*/
- for (AlignmentViewPanel origpanel: alignFrame.getAlignPanels()) {
+ for (AlignmentViewPanel origpanel : alignFrame.getAlignPanels())
+ {
origpanel.getAlignViewport()
.mergeFeaturesStyle(featureColourScheme);
}
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(
{
return;
}
-
+
Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
-
+
/*
* first look for direct dbrefs from sequence to Ensembl
*/
copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
xrefs.getSequencesArray(), dataset);
}
- copyAlignment
- .setGapCharacter(alignFrame.viewport.getGapCharacter());
+ copyAlignment.setGapCharacter(alignFrame.viewport.getGapCharacter());
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
/*
* register any new mappings for sequence mouseover etc
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;
}