/*
* 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)
{
/*
* hack: ignore cross-references to Ensembl protein ids
- * (can't fetch chromosomal mapping for these)
+ * (or use map/translation perhaps?)
* todo: is there an equivalent in EnsemblGenomes?
*/
if (accession.startsWith("ENSP"))