X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMERParamStore.java;h=df9ab55fa012e39a57eacd97eb15920484c04eff;hb=857348180124be7ab86d7de1e4d3f780e65b1fdd;hp=f7c33b19a2d46d4b2fcc4f07bb407991d70c3d7d;hpb=5b552cc983ae304b23b696498e869dd6724fd1a5;p=jalview.git

diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index f7c33b1..df9ab55 100644
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -146,28 +146,61 @@ public final class HMMERParamStore implements ParamDatastoreI
             100, 0, 100000));
     args.add(new RadioChoiceParameter(
             MessageManager.getString(HMMSearch.REPORTING_CUTOFF_KEY), null,
-            Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_NONE),
-                    MessageManager.getString(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,
+            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,
+            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));
   }
 
   /**
@@ -188,6 +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),
@@ -195,21 +232,48 @@ public final class HMMERParamStore implements ParamDatastoreI
                     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));
   }
 
   /**