- {\r
- \r
- ArrayList<String> str = new ArrayList<String>();\r
- StringBuffer command = new StringBuffer();\r
- \r
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
- {\r
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);\r
- \r
- if (mapping == null || mapping.length < 1)\r
- continue;\r
- \r
- int lastPos = -1;\r
- for (int s = 0; s < sequence[pdbfnum].length; s++)\r
- {\r
- for (int sp, m = 0; m < mapping.length; m++)\r
- {\r
- if (mapping[m].getSequence() == sequence[pdbfnum][s]\r
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)\r
- {\r
- SequenceI asp = alignment.getSequenceAt(sp);\r
- for (int r = 0; r < asp.getLength(); r++)\r
- {\r
- // no mapping to gaps in sequence\r
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))\r
- {\r
- continue;\r
- }\r
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));\r
- \r
- if (pos < 1 || pos == lastPos)\r
- continue;\r
- \r
- lastPos = pos;\r
- \r
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);\r
- \r
- if (fr != null)\r
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);\r
- String newSelcom = (mapping[m].getChain() != " " ? ":"\r
- + mapping[m].getChain() : "")\r
- + "/"\r
- + (pdbfnum + 1)\r
- + ".1"\r
- + ";color["\r
- + col.getRed()\r
- + ","\r
- + col.getGreen()\r
- + ","\r
- + col.getBlue() + "]";\r
+ {
+ ArrayList<String> str = new ArrayList<String>();
+ StringBuffer command = new StringBuffer();
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+
+ if (mapping == null || mapping.length < 1)
+ continue;
+
+ int lastPos = -1;
+ for (int s = 0; s < sequence[pdbfnum].length; s++)
+ {
+ 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 (fr != null)
+ 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() + "]";