+ public void highlightStructureRegionsFor(StructureListener sl,
+ SequenceI[] seqs, int... columns)
+ {
+ List<SequenceI> to_highlight = new ArrayList<SequenceI>();
+ for (SequenceI seq : seqs)
+ {
+ if (sl.isListeningFor(seq))
+ {
+ to_highlight.add(seq);
+ }
+ }
+ if (to_highlight.size() == 0)
+ {
+ return;
+ }
+ List<AtomSpec> atoms = new ArrayList<>();
+ for (SequenceI seq : to_highlight)
+ {
+ int atomNo;
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
+ || (sm.sequence.getDatasetSequence() != null && sm.sequence
+ .getDatasetSequence() == seq.getDatasetSequence()))
+ {
+
+ for (int i = 0; i < columns.length; i += 2)
+ {
+ ContiguousI positions = seq.findPositions(columns[i] + 1,
+ columns[i + 1] + 1);
+ if (positions == null)
+ {
+ continue;
+ }
+ for (int index = positions.getBegin(); index <= positions
+ .getEnd(); index++)
+ {
+
+ atomNo = sm.getAtomNum(index);
+
+ if (atomNo > 0)
+ {
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain,
+ sm.getPDBResNum(index), atomNo));
+ }
+ }
+ }
+ }
+ }
+ if (atoms.size() > 0)
+ {
+ sl.highlightAtoms(atoms);
+ }
+ }
+ }
+