git://source.jalview.org / jalview.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
JAL-2629 revert to showing Profile parameter even if only 1 choice
[jalview.git] / src / jalview / hmmer / HMMERParamStore.java
diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index d12475a..fbab7a9 100644 (file)
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -1,6 +1,7 @@
 package jalview.hmmer;
 
 import jalview.bin.Cache;
+import jalview.datamodel.SequenceI;
 import jalview.gui.Preferences;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
@@ -8,6 +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;
@@ -15,6 +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;
@@ -95,15 +98,16 @@ public final class HMMERParamStore implements ParamDatastoreI
    */
   private void getHMMSearchParams(List<ArgumentI> args)
   {
-    args.add(new IntegerParameter(
-            MessageManager.getString("label.number_of_results"),
-            MessageManager.getString("label.number_of_results_desc"), true,
-            100, 0, 100000));
+    /*
+     * 'Options'
+     */
+    addChoiceOfHmm(args);
+
     String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
     if (names != null && !names.isEmpty())
     {
-      Collection<String> databases = new ArrayList<>();
-      databases.add(MessageManager.getString("label.this_alignment"));
+      List<String> databases = new ArrayList<>();
+      databases.add(MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY));
       Scanner nameScanner = new Scanner(names);
 
       if (nameScanner.hasNext())
@@ -123,45 +127,56 @@ public final class HMMERParamStore implements ParamDatastoreI
         }
       }
       nameScanner.close();
-      args.add(new Option(MessageManager.getString("label.database"),
+      args.add(new StringParameter(
+              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));
     }
     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));
-    args.add(new LogarithmicParameter(
-            MessageManager.getString("label.seq_e_value"),
-            MessageManager.getString("label.seq_e_value_desc"), false, -3d,
-            -37.92977945, 1d, 10d));
+
     /*
-    args.add(new DoubleParameter(
-            MessageManager.getString("label.seq_score"),
-            MessageManager.getString("label.seq_score_desc"), false,
-            0d, 0d, 10000d));
-       */
+     * '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.dom_e_value"),
-            MessageManager.getString("label.dom_e_value_desc"), false, -3d,
-            -37.92977945, 1d, 10d));
-    /*
-    args.add(new DoubleParameter(
-            MessageManager.getString("label.dom_score"),
-            MessageManager.getString("label.dom_score_desc"), false, 0d,
-            0d,
-            10000d));
-            */
+            MessageManager.getString(HMMSearch.SEQ_EVALUE_KEY),
+            MessageManager.getString("label.seq_e_value_desc"), false, 1D,
+            1E-38, 10D));
+    args.add(new LogarithmicParameter(
+            MessageManager.getString(HMMSearch.DOM_EVALUE_KEY),
+            MessageManager.getString("label.dom_e_value_desc"), false, 1D,
+            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));
   }
 
   /**
@@ -172,6 +187,8 @@ public final class HMMERParamStore implements ParamDatastoreI
    */
   private void getHMMAlignParams(List<ArgumentI> args)
   {
+    addChoiceOfHmm(args);
+
     boolean def = Cache.getDefault(Preferences.HMMALIGN_TRIM_TERMINI,
             false);
     args.add(new BooleanOption(
@@ -181,6 +198,30 @@ public final class HMMERParamStore implements ParamDatastoreI
   }
 
   /**
+   * Adds an argument representing the choice of HMM sequences (profiles)
+   * against which to perform align or search, provided at least one is found
+   * 
+   * @param args
+   */
+  protected void addChoiceOfHmm(List<ArgumentI> args)
+  {
+    List<SequenceI> hmms = viewport.getAlignment().getHmmSequences();
+    if (!hmms.isEmpty())
+    {
+      List<String> options = new ArrayList<>();
+      for (SequenceI hmmSeq : hmms)
+      {
+        options.add(hmmSeq.getName());
+      }
+      String defseq = options.get(0);
+      ArgumentI arg = new StringParameter(
+              MessageManager.getString("label.use_hmm"), null, true, defseq,
+              defseq, options);
+      args.add(arg);
+    }
+  }
+
+  /**
    * Answers default parameters for hmmbuild, taking into account any configured
    * as user preferences
    * 
@@ -188,9 +229,19 @@ public final class HMMERParamStore implements ParamDatastoreI
    */
   private void getHMMBuildParams(List<ArgumentI> args)
   {
-    args.add(new StringParameter(MessageManager.getString("label.hmm_name"),
-            MessageManager.getString("label.hmm_name_desc"), true, ""));
-    // todo only enable Use Reference Annotation if RF is present
+    /*
+     * name to give the computed alignment HMM consensus sequence
+     * (Jalview constructs group HMM consensus sequence names)
+     */
+    String defValue = "Alignment_HMM";
+    StringParameter nameParam = new StringParameter(MessageManager.getString("label.hmm_name"),
+            MessageManager.getString("label.hmm_name_desc"), true, defValue,
+            defValue);
+    args.add(nameParam);
+
+    /*
+     * only enable Use Reference Annotation if RF is present
+     */
     if (viewport.hasReferenceAnnotation())
     {
       args.add(new BooleanOption(
@@ -199,16 +250,22 @@ public final class HMMERParamStore implements ParamDatastoreI
               true, true, null));
     }
 
-    Collection<String> options = new ArrayList<>();
-    options.add(MessageManager.getString("label.alignment"));
-    options.add(MessageManager.getString("label.groups_and_alignment"));
-    options.add(MessageManager.getString("label.groups"));
-    options.add(MessageManager.getString("label.selected_group"));
-
-    args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
-            MessageManager.getString("label.hmmbuild_for_desc"), true,
-            MessageManager.getString("label.alignment"),
-            MessageManager.getString("label.alignment"), options, null));
+    /*
+     * choice of whether to compute HMM for alignment and/or group(s)
+     * - only if there are any groups
+     */
+    if (!viewport.getAlignment().getGroups().isEmpty())
+    {
+      Collection<String> options = new ArrayList<>();
+      options.add(MessageManager.getString("label.alignment"));
+      options.add(MessageManager.getString("label.groups_and_alignment"));
+      options.add(MessageManager.getString("label.groups"));
+      options.add(MessageManager.getString("label.selected_group"));
+      args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
+              MessageManager.getString("label.hmmbuild_for_desc"), true,
+              MessageManager.getString("label.alignment"),
+              MessageManager.getString("label.alignment"), options, null));
+    }
   }
 
   @Override