import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
-import jalview.bin.Instance;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.ext.ensembl.EnsemblInfo;
import jalview.ext.ensembl.EnsemblMap;
import jalview.io.gff.SequenceOntologyI;
-import jalview.structure.StructureSelectionManager;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.MappingUtils;
/*
* get display scheme (if any) to apply to features
*/
- FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
+ FeatureSettingsModelI featureColourScheme = SequenceFetcher
+ .getInstance()
.getFeatureColourScheme(source);
AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
*/
AlignFrame newFrame = new AlignFrame(xrefsAlignment,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- if (Cache.getDefault("HIDE_INTRONS", true))
+ if (Cache.getDefault(Preferences.HIDE_INTRONS, true))
{
newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
}
copyAlignment
.setGapCharacter(alignFrame.viewport.getGapCharacter());
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Instance.getDesktop());
-
/*
* register any new mappings for sequence mouseover etc
* (will not duplicate any previously registered mappings)
*/
- ssm.registerMappings(dataset.getCodonFrames());
+ Desktop.getInstance().getStructureSelectionManager()
+ .registerMappings(dataset.getCodonFrames());
if (copyAlignment.getHeight() <= 0)
{