{
Cache.log.warn("ignoring additional "
+ (ae[aa].getValueCount() - 1)
- + "values in annotation element.");
+ + " values in annotation element.");
}
val = ae[aa].getValue(0);
}
Cache.log.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
}
- dataset = (DataSet) getjv2vObj(jal.getDataset());
+ dataset = (DataSet) ((Alignment) getjv2vObj(viewport.getSequenceSetId())).getV_parent(); // jal.getDataset());
+ if (dataset==null)
+ {
+ dataset = (DataSet) getjv2vObj(jal.getDataset());
+ Cache.log.error("Can't find the correct dataset for the alignment in this view. Creating new one.");
+
+ }
// Store any sequence mappings.
if (av.getAlignment().getCodonFrames() != null
&& av.getAlignment().getCodonFrames().length > 0)
.getCodonFrames();
for (int cf = 0; cf < cframes.length; cf++)
{
- if (cframes[cf].getdnaSeqs().length > 0)
+ if (cframes[cf].getdnaSeqs()!=null && cframes[cf].getdnaSeqs().length > 0)
{
jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs();
jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings();