JAL-2629 can now choose number of jackhmmer iterations

[jalview.git] / src / jalview / hmmer / Search.java

diff --git a/src/jalview/hmmer/Search.java b/src/jalview/hmmer/Search.java
index 5c7da7c..ceb79e5 100644 (file)
--- a/src/jalview/hmmer/Search.java
+++ b/src/jalview/hmmer/Search.java
@@ -329,6 +329,15 @@ public abstract class Search extends HmmerCommand
             searchAlignment = false;
           }
         }
+        else if (MessageManager.getString(NUMBER_OF_ITERATIONS)
+                .equals(name))
+        {
+          if (!arg.getValue().isEmpty())
+          {
+            args.add("-N");
+            args.add(arg.getValue());
+          }
+        }
       }
     }