JAL-2714 HMMSearch cutoff by E-Value, Score or None

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

diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index 6f1f51f..b609f69 100644 (file)
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -9,6 +9,7 @@ import jalview.ws.params.ArgumentI;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.DoubleParameter;
 import jalview.ws.params.simple.IntegerParameter;
 import jalview.ws.params.simple.LogarithmicParameter;
 import jalview.ws.params.simple.Option;
@@ -16,6 +17,7 @@ import jalview.ws.params.simple.StringParameter;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
 import java.util.Scanner;
@@ -96,17 +98,16 @@ public final class HMMERParamStore implements ParamDatastoreI
    */
   private void getHMMSearchParams(List<ArgumentI> args)
   {
+    /*
+     * 'Options'
+     */
     addChoiceOfHmm(args);
 
-    args.add(new IntegerParameter(
-            MessageManager.getString("label.number_of_results"),
-            MessageManager.getString("label.number_of_results_desc"), true,
-            100, 0, 100000));
     String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
     if (names != null && !names.isEmpty())
     {
       List<String> databases = new ArrayList<>();
-      databases.add(MessageManager.getString("label.this_alignment"));
+      databases.add(MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY));
       Scanner nameScanner = new Scanner(names);
 
       if (nameScanner.hasNext())
@@ -126,45 +127,55 @@ public final class HMMERParamStore implements ParamDatastoreI
         }
       }
       nameScanner.close();
-      args.add(new Option(MessageManager.getString("label.database"),
+      args.add(new Option(MessageManager.getString(HMMSearch.DATABASE_KEY),
               MessageManager.getString("label.database_for_hmmsearch"),
-              true, MessageManager.getString("label.this_alignment"),
-              MessageManager.getString("label.this_alignment"), databases,
-              null));
+              true, MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY),
+              MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY),
+              databases, null));
     }
     args.add(new BooleanOption(
-            MessageManager.getString("label.auto_align_seqs"),
+            MessageManager.getString(HMMSearch.AUTO_ALIGN_SEQS_KEY),
             MessageManager.getString("label.auto_align_seqs_desc"), false,
             false, true, null));
     args.add(new BooleanOption(
-            MessageManager.getString("label.use_accessions"),
+            MessageManager.getString(HMMSearch.USE_ACCESSIONS_KEY),
             MessageManager.getString("label.use_accessions_desc"), false,
             false, true, null));
     args.add(new BooleanOption(
-            MessageManager.getString("label.trim_termini"),
+            MessageManager.getString(HMMSearch.TRIM_TERMINI_KEY),
             MessageManager.getString("label.trim_termini_desc"), false,
             false, true, null));
+
+    /*
+     * 'Parameters'
+     */
+    args.add(new IntegerParameter(
+            MessageManager.getString(HMMSearch.NUMBER_OF_RESULTS_KEY),
+            MessageManager.getString("label.number_of_results_desc"), true,
+            100, 0, 100000));
+    args.add(new StringParameter(
+            MessageManager.getString(HMMSearch.REPORTING_CUTOFF_KEY), null,
+            true, HMMSearch.CUTOFF_NONE, HMMSearch.CUTOFF_NONE,
+            Arrays.asList(HMMSearch.CUTOFF_NONE, HMMSearch.CUTOFF_EVALUE,
+                    HMMSearch.CUTOFF_SCORE)));
     args.add(new LogarithmicParameter(
-            MessageManager.getString("label.seq_e_value"),
+            MessageManager.getString(HMMSearch.SEQ_EVALUE_KEY),
             MessageManager.getString("label.seq_e_value_desc"), false, 1D,
-            1E-38, 10D, 10D));
-    /*
-    args.add(new DoubleParameter(
-            MessageManager.getString("label.seq_score"),
-            MessageManager.getString("label.seq_score_desc"), false,
-            0d, 0d, 10000d));
-       */
+            1E-38, 10D));
     args.add(new LogarithmicParameter(
-            MessageManager.getString("label.dom_e_value"),
+            MessageManager.getString(HMMSearch.DOM_EVALUE_KEY),
             MessageManager.getString("label.dom_e_value_desc"), false, 1D,
-            1E-38, 10D, 10D));
-    /*
-    args.add(new DoubleParameter(
-            MessageManager.getString("label.dom_score"),
-            MessageManager.getString("label.dom_score_desc"), false, 0d,
-            0d,
-            10000d));
-            */
+            1E-38, 10D));
+    args.add(
+            new DoubleParameter(
+                    MessageManager.getString(HMMSearch.SEQ_SCORE_KEY),
+                    MessageManager.getString("label.seq_score_desc"), false,
+                    0d, 0d, 1000d));
+    args.add(
+            new DoubleParameter(
+                    MessageManager.getString(HMMSearch.DOM_SCORE_KEY),
+                    MessageManager.getString("label.dom_score_desc"), false,
+                    0d, 0d, 1000d));
   }
 
   /**