- data = data.toUpperCase();\r
-\r
- if ( (data.indexOf("# STOCKHOLM") > -1))\r
- {\r
- reply = "STH";\r
-\r
- break;\r
- }\r
-\r
- if ((data.indexOf("#") == 0) || (data.length() < 1))\r
- {\r
- continue;\r
- }\r
-\r
- if (data.indexOf("PILEUP") > -1)\r
- {\r
- reply = "PileUp";\r
-\r
- break;\r
- }\r
-\r
- if ((data.indexOf("//") == 0) ||\r
- ((data.indexOf("!!") > -1) &&\r
- (data.indexOf("!!") < data.indexOf(\r
- "_MULTIPLE_ALIGNMENT "))))\r
- {\r
- reply = "MSF";\r
-\r
- break;\r
- }\r
- else if (data.indexOf("CLUSTAL") > -1)\r
- {\r
- reply = "CLUSTAL";\r
-\r
- break;\r
- }\r
- else if ((data.indexOf(">P1;") > -1) ||\r
- (data.indexOf(">DL;") > -1))\r
- {\r
- reply = "PIR";\r
-\r
- break;\r
- }\r
- else if (data.indexOf(">") > -1)\r
- {\r
- // could be BLC file, read next line to confirm\r
- data = reader.readLine();\r
-\r
- if (data.indexOf(">") > -1)\r
- {\r
- reply = "BLC";\r
- }\r
- else\r
- {\r
- //Is this a single line BLC file?\r
- reader.readLine();\r
- String data2 = reader.readLine();\r
- if ( data2 != null\r
- && data.indexOf("*")>-1\r
- && data.indexOf("*")==data2.indexOf("*"))\r
- {\r
- reply = "BLC";\r
- }\r
- else\r
- {\r
- reply = "FASTA";\r
- }\r
- }\r
-\r
- break;\r
- }\r
- else if (data.indexOf("HEADER") == 0 ||\r
- data.indexOf("ATOM") == 0)\r
- {\r
- reply = "PDB";\r
- break;\r
- }\r
- else if (data.indexOf(":") < data.indexOf(",")) // && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))\r
- {\r
- // file looks like a concise JNet file\r
- reply = "JnetFile";\r
- break;\r
- }\r