+ if (checkPIR)
+ {
+ String dta = null;
+ if (!starterm)
+ {
+ do
+ {
+ try
+ {
+ dta = source.nextLine();
+ } catch (IOException ex)
+ {
+ }
+ ;
+ if (dta != null && dta.indexOf("*") > -1)
+ {
+ starterm = true;
+ }
+ } while (dta != null && !starterm);
+ }
+ if (starterm)
+ {
+ reply = "PIR";
+ break;
+ }
+ else
+ {
+ reply = "FASTA"; // probably a bad choice!
+ }
+ }
+ // read as a FASTA (probably)
+ break;
+ }
+ 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;