"getSeqsAsArray", new Class[]
{}).invoke(jmf));
cl.getMethod("addAnnotations", new Class[]
- { Alignment.class }).invoke(jmf, al);
+ { AlignmentI.class }).invoke(jmf, al);
for (SequenceI sq : al.getSequences())
{
if (sq.getDatasetSequence() != null)
{
- sq.getDatasetSequence().getPDBId().clear();
+ sq.getDatasetSequence().getAllPDBEntries().clear();
}
else
{
- sq.getPDBId().clear();
+ sq.getAllPDBEntries().clear();
}
}
replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
{
if (sq.getDatasetSequence() != null)
{
- if (sq.getDatasetSequence().getPDBId() != null)
+ if (sq.getDatasetSequence().getAllPDBEntries() != null)
{
- sq.getDatasetSequence().getPDBId().clear();
+ sq.getDatasetSequence().getAllPDBEntries().clear();
}
}
else
{
- if (sq.getPDBId() != null)
+ if (sq.getAllPDBEntries() != null)
{
- sq.getPDBId().clear();
+ sq.getAllPDBEntries().clear();
}
}
}