import jalview.schemes.FeatureColour;
import jalview.schemes.FeatureSettingsAdapter;
import jalview.util.MapList;
+import jalview.util.Platform;
import java.awt.Color;
import java.io.UnsupportedEncodingException;
@Override
public AlignmentI getSequenceRecords(String query) throws Exception
{
+
+
+
+ Platform.timeCheck("EG " + query, Platform.TIME_MARK);
+
/*
* convert to a non-duplicated list of gene identifiers
*/
List<String> geneIds = getGeneIds(query);
+
+ Platform.timeCheck("EG genIds " + geneIds.size(), Platform.TIME_MARK);
+
AlignmentI al = null;
for (String geneId : geneIds)
{
/*
* fetch the gene sequence(s) with features and xrefs
*/
+
+ Platform.timeCheck("EG fetch " + geneId, Platform.TIME_MARK);
+
+
AlignmentI geneAlignment = super.getSequenceRecords(geneId);
if (geneAlignment == null)
{
// ensure id has 'correct' case for the Ensembl identifier
geneId = geneAlignment.getSequenceAt(0).getName();
+
+ Platform.timeCheck("EG loci " + geneId, Platform.TIME_MARK);
+
+
findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
+ Platform.timeCheck("EG transcript " + geneId, Platform.TIME_MARK);
+
getTranscripts(geneAlignment, geneId);
}
if (al == null)
al.append(geneAlignment);
}
}
+
+ Platform.timeCheck("EG done", Platform.TIME_MARK);
+
return al;
}