JAL-2629 can now choose number of jackhmmer iterations

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

diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index 1aff332..df9ab55 100644 (file)
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -221,6 +221,10 @@ public final class HMMERParamStore implements ParamDatastoreI
 
     String database = MessageManager.getString("label.database");
     args.add(new FileParameter(database, "", false, "", ""));
+    args.add(new IntegerParameter(
+            MessageManager.getString(HMMSearch.NUMBER_OF_ITERATIONS),
+            MessageManager.getString("label.number_of_iterations_desc"),
+            true, 5, 1, 20));
     args.add(new RadioChoiceParameter(
             MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
             Arrays.asList(MessageManager.getString(JackHMMER.CUTOFF_NONE),
@@ -235,17 +239,17 @@ public final class HMMERParamStore implements ParamDatastoreI
     args.add(new LogarithmicParameter(
             MessageManager.getString(JackHMMER.REPORTING_DOM_EVALUE_KEY),
             MessageManager.getString(
-                    "label.reporting_seq_dom_e_value_desc"),
+                    "label.reporting_dom_e_value_desc"),
             false, 1D,
             1E-38, 10D));
     args.add(new DoubleParameter(
             MessageManager.getString(JackHMMER.REPORTING_SEQ_SCORE_KEY),
-            MessageManager.getString("label.reporting_seq_seq_score_desc"),
+            MessageManager.getString("label.reporting_seq_score_desc"),
             false, 0d, 0d,
             1000d));
     args.add(new DoubleParameter(
             MessageManager.getString(JackHMMER.REPORTING_DOM_SCORE_KEY),
-            MessageManager.getString("label.reporting_seq_dom_score_desc"),
+            MessageManager.getString("label.reporting_dom_score_desc"),
             false, 0d, 0d,
             1000d));
     args.add(new RadioChoiceParameter(