- for (int sp, m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
- {
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
- String newSelcom = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/"
- + (pdbfnum + 1)
- + ".1"
- + ";color["
- + col.getRed()
- + ","
- + col.getGreen()
- + ","
- + col.getBlue() + "]";
- if (command.toString().endsWith(newSelcom))
- {
- command = condenseCommand(command.toString(), pos);
- continue;
- }
- // TODO: deal with case when buffer is too large for Jmol to parse
- // - execute command and flush
-
- command.append(";select " + pos);
- command.append(newSelcom);
- }
- break;
- }
- }