package jalview.gui;
import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
}
}
if (sfetch == null
- || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
- || lastDasSourceRegistry != (jalview.bin.Cache
- .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
+ || dasRegistry != Cache.getDasSourceRegistry()
+ || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
+ .getDasRegistryURL() + Cache
.getDasSourceRegistry().getLocalSourceString())
.hashCode())
{
.getString("status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
- dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
+ dasRegistry = Cache.getDasSourceRegistry();
dasRegistry.refreshSources();
jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
}
} catch (Exception e)
{
- jalview.bin.Cache.log.info("Error retrieving " + item
+ Cache.log.info(
+ "Error retrieving " + item
+ " from " + proxy.getDbName(), e);
nextfetch.add(item);
}
if (preferredFeatureColours != null)
{
- af.viewport.applyFeaturesStyle(preferredFeatureColours);
+ af.getViewport().applyFeaturesStyle(preferredFeatureColours);
}
+ if (Cache.getDefault("HIDE_INTRONS", true))
+ {
+ af.avc.markColumnsContainingFeatures(true, false, false,
+ SequenceOntologyI.EXON);
+ af.getViewport().hideSelectedColumns();
+ }
+
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+ af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
false));
} catch (Exception ex)
{