+ public abstract void highlightAtoms(List<AtomSpec> atoms);
+
+ protected boolean isNucleotide()
+ {
+ return this.nucleotide;
+ }
+
+ /**
+ * Returns a readable description of all mappings for the wrapped pdbfile to
+ * any mapped sequences
+ *
+ * @param pdbfile
+ * @param seqs
+ * @return
+ */
+ public String printMappings()
+ {
+ if (pdbEntry == null)
+ {
+ return "";
+ }
+ StringBuilder sb = new StringBuilder(128);
+ for (int pdbe = 0; pdbe < getPdbCount(); pdbe++)
+ {
+ String pdbfile = getPdbEntry(pdbe).getFile();
+ List<SequenceI> seqs = Arrays.asList(getSequence()[pdbe]);
+ sb.append(getSsm().printMappings(pdbfile, seqs));
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Returns the mapped structure position for a given aligned column of a given
+ * sequence, or -1 if the column is gapped, beyond the end of the sequence, or
+ * not mapped to structure.
+ *
+ * @param seq
+ * @param alignedPos
+ * @param mapping
+ * @return
+ */
+ protected int getMappedPosition(SequenceI seq, int alignedPos,
+ StructureMapping mapping)
+ {
+ if (alignedPos >= seq.getLength())
+ {
+ return -1;
+ }
+
+ if (Comparison.isGap(seq.getCharAt(alignedPos)))
+ {
+ return -1;
+ }
+ int seqPos = seq.findPosition(alignedPos);
+ int pos = mapping.getPDBResNum(seqPos);
+ return pos;
+ }
+
+ /**
+ * Helper method to identify residues that can participate in a structure
+ * superposition command. For each structure, identify a sequence in the
+ * alignment which is mapped to the structure. Identify non-gapped columns in
+ * the sequence which have a mapping to a residue in the structure. Returns
+ * the index of the first structure that has a mapping to the alignment.
+ *
+ * @param alignment
+ * the sequence alignment which is the basis of structure
+ * superposition
+ * @param matched
+ * a BitSet, where bit j is set to indicate that every structure has
+ * a mapped residue present in column j (so the column can
+ * participate in structure alignment)
+ * @param structures
+ * an array of data beans corresponding to pdb file index
+ * @return
+ */
+ protected int findSuperposableResidues(AlignmentI alignment,
+ BitSet matched, SuperposeData[] structures)
+ {
+ int refStructure = -1;
+ String[] files = getStructureFiles();
+ if (files == null)
+ {
+ return -1;
+ }
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
+ int lastPos = -1;
+
+ /*
+ * 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)
+ {
+ if (refStructure < 0)
+ {
+ refStructure = pdbfnum;
+ }
+ for (int r = 0; r < alignment.getWidth(); r++)
+ {
+ if (!matched.get(r))
+ {
+ continue;
+ }
+ int pos = getMappedPosition(theSequence, r, mapping);
+ if (pos < 1 || pos == lastPos)
+ {
+ matched.clear(r);
+ continue;
+ }
+ lastPos = pos;
+ structures[pdbfnum].pdbResNo[r] = pos;
+ }
+ String chain = mapping.getChain();
+ if (chain != null && chain.trim().length() > 0)
+ {
+ structures[pdbfnum].chain = chain;
+ }
+ structures[pdbfnum].pdbId = mapping.getPdbId();
+ structures[pdbfnum].isRna = theSequence.getRNA() != null;
+
+ /*
+ * move on to next pdb file (ignore sequences for other chains
+ * for the same structure)
+ */
+ s = seqCountForPdbFile;
+ break;
+ }
+ }
+ }
+ }
+ return refStructure;
+ }
+
+ /**
+ * Returns true if the structure viewer has loaded all of the files of
+ * interest (identified by the file mapping having been set up), or false if
+ * any are still not loaded after a timeout interval.
+ *
+ * @param files
+ */
+ protected boolean waitForFileLoad(String[] files)
+ {
+ /*
+ * give up after 10 secs plus 1 sec per file
+ */
+ long starttime = System.currentTimeMillis();
+ long endTime = 10000 + 1000 * files.length + starttime;
+ String notLoaded = null;
+
+ boolean waiting = true;
+ while (waiting && System.currentTimeMillis() < endTime)
+ {
+ waiting = false;
+ for (String file : files)
+ {
+ notLoaded = file;
+ if (file == null)
+ {
+ continue;
+ }
+ try
+ {
+ StructureMapping[] sm = getSsm().getMapping(file);
+ if (sm == null || sm.length == 0)
+ {
+ waiting = true;
+ }
+ } catch (Throwable x)
+ {
+ waiting = true;
+ }
+ }
+ }
+
+ if (waiting)
+ {
+ System.err.println(
+ "Timed out waiting for structure viewer to load file "
+ + notLoaded);
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ public boolean isListeningFor(SequenceI seq)