+
+ if (command.indexOf("getFamName") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ System.out.println(analyser.getFamilyName(inputScanner.nextInt()));
+
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ continue;
+ }
+ if (command.indexOf("sortIntoClans") > -1)
+ {
+ inputScanner.next();
+ analyser.sortIntoClans(inputScanner.next());
+ continue;
+
+ }
+ if (command.indexOf("setFamilies") > -1)
+ {
+ inputScanner.next();
+ analyser.setFamilies(inputScanner.next());
+ continue;
+
+ }
+
+ if (command.indexOf("setHMMs") > -1)
+ {
+ inputScanner.next();
+ analyser.setHmms(inputScanner.next());
+ continue;
+
+ }
+
+ if (command.indexOf("alignWithinClans") > -1)
+ {
+ inputScanner.next();
+ String export = inputScanner.next();
+ String clans = inputScanner.next();
+ analyser.alignWithinClan(export, clans);
+ continue;
+
+ }
+
+ System.out.println("Unrecognised command");