import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GroupSet;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
if (!isValidReference(id))
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"(AFClient) Ignoring invalid alphafold query: '" + id + "'");
stopQuery();
return null;
}
ContactMatrixI matrix = new PAEContactMatrix(sequence,
(Map<String, Object>) paeDict);
- ((PAEContactMatrix) matrix).makeGroups(5f, true);
AlignmentAnnotation cmannot = sequence.addContactList(matrix);
if (label != null)
}
SequenceI seq = sm.getSequence();
- Console.debug("##### SEQUENCE FOUND=" + seq.getName());
ContactMatrixI matrix = new PAEContactMatrix(seq,
(Map<String, Object>) pae_obj);
- ((PAEContactMatrix) matrix).makeGroups(5f, true);
- AlignmentAnnotation cmannot = seq.addContactList(matrix);
+ AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
/* this already happens in Sequence.addContactList()
seq.addAlignmentAnnotation(cmannot);
*/