-
- if ((data.indexOf("<") > -1)) // possible Markup Language data i.e HTML,
- // RNAML, XML
- {
- boolean identified = false;
- do
- {
- if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
- {
- reply = HtmlFile.FILE_DESC;
- identified = true;
- break;
- }
-
- if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>"))
- {
- reply = "RNAML";
- identified = true;
- break;
- }
- } while ((data = source.nextLine()) != null);
-
- if (identified)
- {
- break;
- }
- }
-
-
- if (data.indexOf("{\"") > -1)
- {
- reply = JSONFile.FILE_DESC;
- break;
- }
- if ((data.length() < 1) || (data.indexOf("#") == 0))
- {
- lineswereskipped = true;
- continue;
- }
-
- if (data.indexOf("PILEUP") > -1)
- {
- reply = "PileUp";
-
- break;
- }
-
- if ((data.indexOf("//") == 0)
- || ((data.indexOf("!!") > -1) && (data.indexOf("!!") < data
- .indexOf("_MULTIPLE_ALIGNMENT "))))
- {
- reply = "MSF";
-
- break;
- }
- else if (data.indexOf("CLUSTAL") > -1)
- {
- reply = "CLUSTAL";
-
- break;
- }
-
- else if (data.indexOf(">") > -1)