- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
- {\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
- if (command.length() > newSelcom.length()
- && command.substring(
- command.length() - newSelcom.length())
- .equals(newSelcom))
- {\r
- command = VarnaCommands.condenseCommand(command, pos);\r
- continue;\r
- }\r
- // TODO: deal with case when buffer is too large for Jmol to parse\r
- // - execute command and flush\r
- \r
- command.append(";");\r
- if (command.length()>51200)\r
- {\r
- // add another chunk\r
- str.add(command.toString());\r
- command.setLength(0);\r
- }\r
- command.append("select " + pos);\r
- command.append(newSelcom);\r
- }\r
- break;\r
- }\r
- }\r
- }\r
- }\r
- {\r
- // add final chunk\r
- str.add(command.toString());\r
- command.setLength(0);\r
- }\r
- return str.toArray(new String[str.size()]);\r
- }\r
-\r
- public static StringBuffer condenseCommand(StringBuffer command, int pos)\r
- {\r
- \r
- // work back to last 'select'\r
- int p=command.length(),q=p;\r
+ SequenceI[][] sequence, SequenceRenderer sr,
+ FeatureColourFinder finder, AlignmentI alignment)
+ {
+ 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.getResidueColour(sequence[pdbfnum][s], r,
+ finder);
+
+ String newSelcom = (mapping[m].getChain() != " "
+ ? ":" + mapping[m].getChain()
+ : "") + "/" + (pdbfnum + 1) + ".1" + ";color["
+ + col.getRed() + "," + col.getGreen() + ","
+ + col.getBlue() + "]";
+ if (command.length() > newSelcom.length() && command
+ .substring(command.length() - newSelcom.length())
+ .equals(newSelcom))
+ {
+ command = VarnaCommands.condenseCommand(command, pos);
+ continue;
+ }
+ // TODO: deal with case when buffer is too large for Jmol to parse
+ // - execute command and flush
+
+ command.append(";");
+ if (command.length() > 51200)
+ {
+ // add another chunk
+ str.add(command.toString());
+ command.setLength(0);
+ }
+ command.append("select " + pos);
+ command.append(newSelcom);
+ }
+ break;
+ }
+ }
+ }
+ }
+ {
+ // add final chunk
+ str.add(command.toString());
+ command.setLength(0);
+ }
+ return str.toArray(new String[str.size()]);
+ }
+
+ public static StringBuffer condenseCommand(StringBuffer command, int pos)
+ {
+
+ // work back to last 'select'
+ int p = command.length(), q = p;