import jalview.api.FeatureColourI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.GeneLociI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
@Override
public int compare(DBRefEntry ref1, DBRefEntry ref2)
{
- if (ref1.isChromosome())
+ if (ref1 instanceof GeneLociI)
{
return -1;
}
- if (ref2.isChromosome())
+ if (ref2 instanceof GeneLociI)
{
return 1;
}
FeatureColourI fc = fr.getFeatureColours().get(feature.getType());
if (fc != null && fc.isColourByAttribute())
{
- String attName = fc.getAttributeName();
+ String[] attName = fc.getAttributeName();
String attVal = feature.getValueAsString(attName);
if (attVal != null)
{
- sb.append("; ").append(attName).append("=").append(attVal);
+ sb.append("; ").append(String.join(":", attName)).append("=")
+ .append(attVal);
}
}
}
*/
Collection<List<String>> createLinksFrom(SequenceI seq, String link)
{
- Map<String, List<String>> urlSets = new LinkedHashMap<String, List<String>>();
+ Map<String, List<String>> urlSets = new LinkedHashMap<>();
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{