{
progressBar = ap.alignFrame;
- openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+ openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
+ new SequenceI[][]
+ { seq });
}
- private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+ private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
+ PDBEntry[] pdbentrys,
SequenceI[][] seqs)
{
progressBar = ap.alignFrame;
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
- alignAddedStructures = true;
- useAlignmentPanelForSuperposition(ap);
+ alignAddedStructures = alignAdded;
+ useAlignmentPanelForSuperposition(ap);
jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
}
/**
- * create a new Jmol containing several structures superimposed using the
- * given alignPanel.
+ * create a new Jmol containing several structures optionally superimposed
+ * using the given alignPanel.
*
* @param ap
+ * @param alignAdded
+ * - true to superimpose
* @param pe
* @param seqs
*/
- public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+ public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
+ SequenceI[][] seqs)
{
- openNewJmol(ap, pe, seqs);
+ openNewJmol(ap, alignAdded, pe, seqs);
}
jmb.updateColours(ap);
}
// do superposition if asked to
- if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+ if (alignAddedStructures)
{
alignAddedStructures();
}
}
}
});
- alignAddedStructures = false;
+
}
/**