JAL-2629 hmm search UI and structural improvements, inclusion thresholds

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

diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index f7c33b1..1aff332 100644 (file)
--- 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));
   }
 
   /**
@@ -195,21 +228,48 @@ 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_seq_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_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_seq_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));
   }
 
   /**