\r
if (abracket > -1)\r
{\r
- if (line.indexOf(" ") > -1) //\r
- {\r
- ///Colur it be this format?\r
- //>54402046 0 1 137 137:\r
- // or this??\r
- // 1 >L1H14 30539 343\r
- try\r
- {\r
- ids.addElement(line.substring(abracket + 1,\r
- line.indexOf(" ", abracket + 1)));\r
-\r
- // remove p Value\r
- line = line.substring(abracket + 1);\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
-\r
- int value = Integer.parseInt(line.substring(0,\r
- line.indexOf(" ")));\r
- starts.addElement(value + "");\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- value = Integer.parseInt(line.substring(0,\r
- line.indexOf(" ")));\r
- ends.addElement(value + "");\r
- }\r
- catch (Exception ex)\r
- {\r
- System.err.println("Error during blockfile read.");\r
- ex.printStackTrace();\r
- starts.addElement("0");\r
- ends.addElement("0");\r
- }\r
- }\r
- else\r
- {\r
- if (line.indexOf("/") > -1)\r
- {\r
- ids.addElement(line.substring(abracket + 1,\r
- line.indexOf("/")));\r
- line = line.substring(line.indexOf("/") + 1);\r
- starts.addElement(line.substring(0,\r
- line.indexOf("-")));\r
- ends.addElement(line.substring(line.indexOf("-") +\r
- 1));\r
- }\r
- else\r
- {\r
- ids.addElement(line.substring(abracket + 1));\r
- starts.addElement("1");\r
- ends.addElement("-1");\r
- }\r
- }\r
+ if (line.indexOf(" ") > -1) //\r
+ {\r
+ line = line.substring(abracket + 1,\r
+ line.indexOf(" ", abracket + 1));\r
+ }\r
+ else\r
+ line = line.substring(abracket+1);\r
+\r
+\r
+ Sequence seq = parseId(line);\r
+ ids.addElement(seq.getName());\r
+ starts.addElement(seq.getStart() + "");\r
+ ends.addElement(seq.getEnd() + "");\r
}\r
}\r
while (!idsFound);\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static String print(SequenceI[] s)\r
+ public String print(SequenceI[] s)\r
{\r
StringBuffer out = new StringBuffer();\r
-\r
+ /**\r
+ * A general parser for ids. Will look for dbrefs in\r
+ * Uniprot format source|id\r
+ * And also Jalview /start-end\r
+ *\r
+ * @String id Id to be parsed\r
+ */\r
int i = 0;\r
int max = -1;\r
\r
while ((i < s.length) && (s[i] != null))\r
{\r
- out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd() + "\n");\r
+ out.append(">" + printId(s[i]) +"\n");\r
\r
if (s[i].getSequence().length() > max)\r
{\r