+ if (data.indexOf("{\"") > -1)
+ {
+ reply = FileFormat.Json;
+ break;
+ }
+ int lessThan = data.indexOf("<");
+ if ((lessThan > -1)) // possible Markup Language data i.e HTML,
+ // RNAML, XML
+ {
+ String upper = data.toUpperCase(Locale.ROOT);
+ if (upper.substring(lessThan).startsWith("<HTML"))
+ {
+ reply = FileFormat.Html;
+ break;
+ }
+ if (upper.substring(lessThan).startsWith("<RNAML"))
+ {
+ reply = FileFormat.Rnaml;
+ break;
+ }
+ if (isXml && data.contains(
+ "<NS2:JALVIEWUSERCOLOURS SCHEMENAME=\"SEQUENCE FEATURES\" XMLNS:NS2=\"WWW.JALVIEW.ORG/COLOURS\">"))
+ {
+ reply = FileFormat.FeatureSettings;
+ break;
+ }
+ }
+
+ if ((data.length() < 1) || (data.indexOf("#") == 0))
+ {
+ lineswereskipped = true;
+ continue;
+ }
+
+ if (data.indexOf("PILEUP") > -1)
+ {
+ reply = FileFormat.Pileup;
+
+ break;
+ }
+
+ if ((data.indexOf("//") == 0) || ((data.indexOf("!!") > -1) && (data
+ .indexOf("!!") < data.indexOf("_MULTIPLE_ALIGNMENT "))))
+ {
+ reply = FileFormat.MSF;
+
+ break;
+ }
+ else if (data.indexOf("CLUSTAL") > -1)
+ {
+ reply = FileFormat.Clustal;
+
+ break;
+ }
+