+
+ @Override
+ public void showStructures(AlignViewportI av, boolean refocus)
+ {
+ StringBuilder cmd = new StringBuilder(128);
+ cmd.append("~display; ~ribbon;");
+ String atomSpec = getMappedResidues(av);
+ cmd.append("ribbon ").append(atomSpec);
+ if (!isShowAlignmentOnly())
+ {
+ cmd.append("chain @CA|P; ribbon");
+ }
+ if (refocus)
+ {
+ cmd.append("; focus");
+ }
+ sendChimeraCommand(cmd.toString(), false);
+ }
+
+ /**
+ * Builds a Chimera atomSpec of residues mapped from sequences, of the format
+ * (#model:residues.chain)
+ *
+ * <pre>
+ * #0:2-94.A | #1:1-93.C | #2:1-93.A
+ * </pre>
+ *
+ * Only residues visible in the alignment are included, that is, hidden columns
+ * and sequences are excluded.
+ *
+ * @param av
+ * @return
+ */
+ private String getMappedResidues(AlignViewportI av)
+ {
+ AlignmentI alignment = av.getAlignment();
+ final int width = alignment.getWidth();
+
+ String[] files = getStructureFiles();
+
+ StringBuilder atomSpec = new StringBuilder(256);
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
+
+ /*
+ * Find the first mapped sequence (if any) for this PDB entry which is in
+ * the alignment
+ */
+ final int seqCountForPdbFile = getSequence()[pdbfnum].length;
+ for (int s = 0; s < seqCountForPdbFile; s++)
+ {
+ for (StructureMapping mapping : mappings)
+ {
+ final SequenceI theSequence = getSequence()[pdbfnum][s];
+ if (mapping.getSequence() == theSequence
+ && alignment.findIndex(theSequence) > -1)
+ {
+ String chainCd = mapping.getChain();
+ if (!isShowChain(mapping.getPdbId(), chainCd))
+ {
+ continue;
+ }
+ Iterator<int[]> visible;
+ if (isShowAlignmentOnly())
+ {
+ visible = alignment.getHiddenColumns()
+ .getVisContigsIterator(0, width, true);
+ }
+ else
+ {
+ visible = Collections.singletonList(new int[] { 0, width })
+ .iterator();
+ }
+ while (visible.hasNext())
+ {
+ int[] visibleRegion = visible.next();
+ int seqStartPos = theSequence.findPosition(visibleRegion[0]);
+ int seqEndPos = theSequence.findPosition(visibleRegion[1]);
+ List<int[]> residueRanges = mapping
+ .getPDBResNumRanges(seqStartPos, seqEndPos);
+ if (!residueRanges.isEmpty())
+ {
+ if (atomSpec.length() > 0)
+ {
+ atomSpec.append("| ");
+ }
+ atomSpec.append(getModelSpec(pdbfnum)).append(":");
+ boolean first = true;
+ for (int[] range : residueRanges)
+ {
+ if (!first)
+ {
+ atomSpec.append(",");
+ }
+ first = false;
+ atomSpec.append(range[0]).append("-").append(range[1]);
+ atomSpec.append(".").append(chainCd);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ return atomSpec.toString();
+ }