- openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+ openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
+ new SequenceI[][]
+ { seq });
jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
- public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+ public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
+ SequenceI[][] seqs)