JAL-2994 utility method to match a list of folder/file patterns

[jalview.git] / src / jalview / util / ProbabilityAnalyserKickstarter.java

diff --git a/src/jalview/util/ProbabilityAnalyserKickstarter.java b/src/jalview/util/ProbabilityAnalyserKickstarter.java
index 999dc1f..59c0a9f 100644 (file)
--- a/src/jalview/util/ProbabilityAnalyserKickstarter.java
+++ b/src/jalview/util/ProbabilityAnalyserKickstarter.java
@@ -116,6 +116,7 @@ public class ProbabilityAnalyserKickstarter
         {
           System.out.println("Command failed");
         }
+        continue;
       }
       if ((command.indexOf("runToEnd") > -1))
       {
@@ -123,14 +124,17 @@ public class ProbabilityAnalyserKickstarter
         {
 
           inputScanner.next();
+          int minCount = inputScanner.nextInt();
+          int maxCount = inputScanner.nextInt();
           boolean keepRaw = inputScanner.nextBoolean();
-          analyser.runToEnd(keepRaw);
+          boolean forClans = inputScanner.nextBoolean();
+          analyser.runToEnd(minCount, maxCount, keepRaw, forClans);
           System.out.println("Task completed");
-          continue;
         } catch (Exception e)
         {
           System.out.println("Command failed");
         }
+        continue;
       }
       // terminates program. Syntax is terminate.
       if (command.indexOf("terminate") > -1)
@@ -155,7 +159,9 @@ public class ProbabilityAnalyserKickstarter
         } catch (Exception e)
         {
           System.out.println("Command failed");
+
         }
+        continue;
       }
 
       if (command.indexOf("getFamName") > -1)
@@ -164,12 +170,12 @@ public class ProbabilityAnalyserKickstarter
         {
         inputScanner.next();
         System.out.println(analyser.getFamilyName(inputScanner.nextInt()));
-          inputScanner.close();
-          continue;
+
         } catch (Exception e)
         {
           System.out.println("Command failed");
         }
+        continue;
       }
       if (command.indexOf("sortIntoClans") > -1)
       {
@@ -193,11 +199,18 @@ public class ProbabilityAnalyserKickstarter
         continue;
 
       }
-      if (command.indexOf("hmmbuild") > -1)
+
+      if (command.indexOf("alignWithinClans") > -1)
       {
-        analyser.hmmBuild();
+        inputScanner.next();
+        String export = inputScanner.next();
+        String clans = inputScanner.next();
+        analyser.alignWithinClan(export, clans);
         continue;
+
       }
+
+      System.out.println("Unrecognised command");
     }