- 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
- ids.addElement(line.substring(abracket + 1,\r
- line.indexOf(" ", abracket + 1)));\r
-\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
- int value = Integer.parseInt(line.substring(0, line.indexOf(" ")));\r
- starts.addElement(value+"");\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- value = Integer.parseInt(line.substring(0, 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
+ for (int i = 0; i < ids.size(); i++)\r
+ {\r
+ if (seqstrings[i] == null)\r
+ {\r
+ seqstrings[i] = new StringBuffer();\r
+ }\r
+ }\r