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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 f95d738..df9ab55 100644 (file)
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -124,6 +124,10 @@ public final class HMMERParamStore implements ParamDatastoreI
             MessageManager.getString(HMMSearch.TRIM_TERMINI_KEY),
             MessageManager.getString("label.trim_termini_desc"), false,
             false, true, null));
+    args.add(new BooleanOption(
+            MessageManager.getString(HMMSearch.RETURN_N_NEW_SEQ),
+            MessageManager.getString("label.check_for_new_sequences_desc"),
+            false, false, false, null));
 
     /*
      * 'Parameters'
@@ -135,11 +139,6 @@ public final class HMMERParamStore implements ParamDatastoreI
     String thisAlignment = MessageManager
             .getString(HMMSearch.THIS_ALIGNMENT_KEY);
     String database = MessageManager.getString("label.database");
-    args.add(new RadioChoiceParameter(
-            MessageManager.getString("action.search"), null,
-            Arrays.asList(thisAlignment,
-                    database),
-            thisAlignment));
     args.add(new FileParameter(database, "", false, "", ""));
     args.add(new IntegerParameter(
             MessageManager.getString(HMMSearch.NUMBER_OF_RESULTS_KEY),
@@ -147,27 +146,61 @@ public final class HMMERParamStore implements ParamDatastoreI
             100, 0, 100000));
     args.add(new RadioChoiceParameter(
             MessageManager.getString(HMMSearch.REPORTING_CUTOFF_KEY), null,
-            Arrays.asList(HMMSearch.CUTOFF_NONE, HMMSearch.CUTOFF_EVALUE,
-                    HMMSearch.CUTOFF_SCORE),
-            HMMSearch.CUTOFF_EVALUE));
+            Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
+                    MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
+            MessageManager.getString(HMMSearch.CUTOFF_EVALUE)));
     args.add(new LogarithmicParameter(
-            MessageManager.getString(HMMSearch.SEQ_EVALUE_KEY),
-            MessageManager.getString("label.seq_e_value_desc"), false, 1D,
-            1E-38, 10D));
+            MessageManager.getString(HMMSearch.REPORTING_SEQ_EVALUE_KEY),
+            MessageManager.getString("label.reporting_seq_e_value_desc"),
+            false, 1D,
+            1E-100, 10D));
     args.add(new LogarithmicParameter(
-            MessageManager.getString(HMMSearch.DOM_EVALUE_KEY),
-            MessageManager.getString("label.dom_e_value_desc"), false, 1D,
-            1E-38, 10D));
+            MessageManager.getString(HMMSearch.REPORTING_DOM_EVALUE_KEY),
+            MessageManager.getString("label.reporting_dom_e_value_desc"),
+            false, 1D,
+            1E-100, 10D));
     args.add(
             new DoubleParameter(
-                    MessageManager.getString(HMMSearch.SEQ_SCORE_KEY),
-                    MessageManager.getString("label.seq_score_desc"), false,
+                    MessageManager
+                            .getString(HMMSearch.REPORTING_SEQ_SCORE_KEY),
+                    MessageManager.getString(
+                            "label.reporting_seq_score_desc"),
+                    false,
                     0d, 0d, 1000d));
     args.add(
             new DoubleParameter(
-                    MessageManager.getString(HMMSearch.DOM_SCORE_KEY),
-                    MessageManager.getString("label.dom_score_desc"), false,
+                    MessageManager
+                            .getString(HMMSearch.REPORTING_DOM_SCORE_KEY),
+                    MessageManager.getString(
+                            "label.reporting_dom_score_desc"),
+                    false,
                     0d, 0d, 1000d));
+    args.add(new RadioChoiceParameter(
+            MessageManager.getString(HMMSearch.INCLUSION_THRESHOLD_KEY),
+            null,
+            Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
+                    MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
+            MessageManager.getString(HMMSearch.CUTOFF_EVALUE)));
+    args.add(new LogarithmicParameter(
+            MessageManager.getString(HMMSearch.INCLUSION_SEQ_EVALUE_KEY),
+            MessageManager.getString("label.inclusion_seq_e_value_desc"),
+            false, 1D,
+            1E-100, 10D));
+    args.add(new LogarithmicParameter(
+            MessageManager.getString(HMMSearch.INCLUSION_DOM_EVALUE_KEY),
+            MessageManager.getString("label.inclusion_dom_e_value_desc"),
+            false, 1D,
+            1E-100, 10D));
+    args.add(new DoubleParameter(
+            MessageManager.getString(HMMSearch.INCLUSION_SEQ_SCORE_KEY),
+            MessageManager.getString("label.inclusion_seq_score_desc"),
+            false, 0d, 0d,
+            1000d));
+    args.add(new DoubleParameter(
+            MessageManager.getString(HMMSearch.INCLUSION_DOM_SCORE_KEY),
+            MessageManager.getString("label.inclusion_dom_score_desc"),
+            false, 0d, 0d,
+            1000d));
   }
 
   /**
@@ -186,34 +219,61 @@ public final class HMMERParamStore implements ParamDatastoreI
 
     // addChoiceOfDatabase(args);
 
-    String thisAlignment = MessageManager
-            .getString(JackHMMER.THIS_ALIGNMENT_KEY);
     String database = MessageManager.getString("label.database");
-    args.add(new RadioChoiceParameter(
-            MessageManager.getString("action.search"), null,
-            Arrays.asList(thisAlignment, database), thisAlignment));
     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(JackHMMER.CUTOFF_NONE, JackHMMER.CUTOFF_EVALUE,
-                    JackHMMER.CUTOFF_SCORE),
-            JackHMMER.CUTOFF_EVALUE));
+            Arrays.asList(MessageManager.getString(JackHMMER.CUTOFF_NONE),
+                    MessageManager.getString(JackHMMER.CUTOFF_EVALUE),
+                    MessageManager.getString(JackHMMER.CUTOFF_SCORE)),
+            MessageManager.getString(JackHMMER.CUTOFF_EVALUE)));
     args.add(new LogarithmicParameter(
-            MessageManager.getString(JackHMMER.SEQ_EVALUE_KEY),
-            MessageManager.getString("label.seq_e_value_desc"), false, 1D,
+            MessageManager.getString(JackHMMER.REPORTING_SEQ_EVALUE_KEY),
+            MessageManager.getString("label.reporting_seq_e_value_desc"),
+            false, 1D,
             1E-38, 10D));
     args.add(new LogarithmicParameter(
-            MessageManager.getString(JackHMMER.DOM_EVALUE_KEY),
-            MessageManager.getString("label.dom_e_value_desc"), false, 1D,
+            MessageManager.getString(JackHMMER.REPORTING_DOM_EVALUE_KEY),
+            MessageManager.getString(
+                    "label.reporting_dom_e_value_desc"),
+            false, 1D,
             1E-38, 10D));
     args.add(new DoubleParameter(
-            MessageManager.getString(JackHMMER.SEQ_SCORE_KEY),
-            MessageManager.getString("label.seq_score_desc"), false, 0d, 0d,
+            MessageManager.getString(JackHMMER.REPORTING_SEQ_SCORE_KEY),
+            MessageManager.getString("label.reporting_seq_score_desc"),
+            false, 0d, 0d,
             1000d));
     args.add(new DoubleParameter(
-            MessageManager.getString(JackHMMER.DOM_SCORE_KEY),
-            MessageManager.getString("label.dom_score_desc"), false, 0d, 0d,
+            MessageManager.getString(JackHMMER.REPORTING_DOM_SCORE_KEY),
+            MessageManager.getString("label.reporting_dom_score_desc"),
+            false, 0d, 0d,
             1000d));
+    args.add(new RadioChoiceParameter(
+            MessageManager.getString(HMMSearch.INCLUSION_THRESHOLD_KEY),
+            null,
+            Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
+                    MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
+            MessageManager.getString(HmmerCommand.CUTOFF_EVALUE)));
+    args.add(new LogarithmicParameter(
+            MessageManager.getString(HMMSearch.INCLUSION_SEQ_EVALUE_KEY),
+            MessageManager.getString("label.inclusion_seq_e_value_desc"),
+            false, 1D, 1E-100, 10D));
+    args.add(new LogarithmicParameter(
+            MessageManager.getString(HMMSearch.INCLUSION_DOM_EVALUE_KEY),
+            MessageManager.getString("label.inclusion_dom_e_value_desc"),
+            false, 1D, 1E-100, 10D));
+    args.add(new DoubleParameter(
+            MessageManager.getString(HMMSearch.INCLUSION_SEQ_SCORE_KEY),
+            MessageManager.getString("label.inclusion_seq_score_desc"),
+            false, 0d, 0d, 1000d));
+    args.add(new DoubleParameter(
+            MessageManager.getString(HMMSearch.INCLUSION_DOM_SCORE_KEY),
+            MessageManager.getString("label.inclusion_dom_score_desc"),
+            false, 0d, 0d, 1000d));
   }
 
   /**