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);
}
/*
* copy feature rendering settings to split frame
*/
- newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
- .transferSettings(myFeatureStyling);
- copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
- .transferSettings(myFeatureStyling);
+ FeatureRenderer fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer();
+ fr1.transferSettings(myFeatureStyling);
+ fr1.findAllFeatures(true);
+ FeatureRenderer fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer();
+ fr2.transferSettings(myFeatureStyling);
+ fr2.findAllFeatures(true);
/*
* apply 'database source' feature configuration
*/
String[] divisionsArray = ensemblDivisions
.toArray(new String[ensemblDivisions.size()]);
- DBRefEntry[] seqRefs = seq.getDBRefs();
- DBRefEntry[] directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
+ List<DBRefEntry> seqRefs = seq.getDBRefs();
+ List<DBRefEntry> directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
divisionsArray);
if (directEnsemblRefs != null)
{
{
if (dbref.getMap() != null && dbref.getMap().getTo() != null)
{
- DBRefEntry[] dbrefs = dbref.getMap().getTo().getDBRefs();
- DBRefEntry[] indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
+ List<DBRefEntry> dbrefs = dbref.getMap().getTo().getDBRefs();
+ List<DBRefEntry> indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
divisionsArray);
if (indirectEnsemblRefs != null)
{
copyAlignment
.setGapCharacter(alignFrame.viewport.getGapCharacter());
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
-
/*
* register any new mappings for sequence mouseover etc
* (will not duplicate any previously registered mappings)
*/
- ssm.registerMappings(dataset.getCodonFrames());
+ Desktop.getStructureSelectionManager()
+ .registerMappings(dataset.getCodonFrames());
if (copyAlignment.getHeight() <= 0)
{