X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMERParamStore.java;h=f95d738cf564991a89ff8a035d2d6ec06c4df125;hb=1beac3545a78d4c5c3274dbb53296708d693efe0;hp=c6684812324a8a46cc8fdd9c440e5e2c9f9035c1;hpb=ae08e9be88ca8cafe0f27ca2d9927db487e35db2;p=jalview.git

diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index c668481..f95d738 100644
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -1,20 +1,26 @@
 package jalview.hmmer;
 
 import jalview.bin.Cache;
+import jalview.datamodel.SequenceI;
 import jalview.gui.Preferences;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 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.FileParameter;
 import jalview.ws.params.simple.IntegerParameter;
 import jalview.ws.params.simple.LogarithmicParameter;
 import jalview.ws.params.simple.Option;
+import jalview.ws.params.simple.RadioChoiceParameter;
 import jalview.ws.params.simple.StringParameter;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Collection;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Scanner;
 
@@ -26,28 +32,38 @@ public final class HMMERParamStore implements ParamDatastoreI
 
   private static final String HMMSEARCH = "hmmsearch";
 
-  String name;
+  private static final String JACKHMMER = "jackhmmer";
 
-  List<WsParamSetI> presets = new ArrayList<>();
+  private String name;
 
-  private HMMERParamStore(String nam)
+  private List<WsParamSetI> presets = new ArrayList<>();
+
+  private AlignmentViewport viewport;
+
+  private HMMERParamStore(String nam, AlignmentViewport av)
   {
+    this.viewport = av;
     this.name = nam;
   }
 
-  public static HMMERParamStore forBuild()
+  public static HMMERParamStore forBuild(AlignmentViewport viewport)
+  {
+    return new HMMERParamStore(HMMBUILD, viewport);
+  }
+
+  public static HMMERParamStore forAlign(AlignmentViewport viewport)
   {
-    return new HMMERParamStore(HMMBUILD);
+    return new HMMERParamStore(HMMALIGN, viewport);
   }
 
-  public static HMMERParamStore forAlign()
+  public static HMMERParamStore forSearch(AlignmentViewport viewport)
   {
-    return new HMMERParamStore(HMMALIGN);
+    return new HMMERParamStore(HMMSEARCH, viewport);
   }
 
-  public static HMMERParamStore forSearch()
+  public static HMMERParamStore forJackhmmer(AlignmentViewport viewport)
   {
-    return new HMMERParamStore(HMMSEARCH);
+    return new HMMERParamStore(JACKHMMER, viewport);
   }
 
   @Override
@@ -77,111 +93,291 @@ public final class HMMERParamStore implements ParamDatastoreI
     case HMMBUILD:
       getHMMBuildParams(args);
       break;
+    case JACKHMMER:
+      getJackhmmerParams(args);
     default:
     }
 
     return args;
   }
 
+  /**
+   * Answers default parameters for hmmsearch, taking into account any
+   * configured as user preferences
+   * 
+   * @param args
+   */
   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));
-    String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
-    if (names != null && !names.isEmpty())
-    {
-      Collection<String> databases = new ArrayList<>();
-      databases.add(MessageManager.getString("label.this_alignment"));
-      Scanner nameScanner = new Scanner(names);
-
-      if (nameScanner.hasNext())
-      {
-        while (nameScanner.hasNext())
-        {
-          String next = nameScanner.next();
-          if ("null".equals(next))
-          {
-            Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
-            Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
-          }
-          else
-          {
-            databases.add(next);
-          }
-        }
-      }
-      nameScanner.close();
-      args.add(new Option(MessageManager.getString("label.database"),
-              MessageManager.getString("label.database_for_hmmsearch"),
-              true, MessageManager.getString("label.this_alignment"),
-              MessageManager.getString("label.this_alignment"), databases,
-              null));
-    }
+    /*
+     * 'Options'
+     */
     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));
+            false, false, 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'
+     */
+    addChoiceOfHmm(args);
+
+    // addChoiceOfDatabase(args);
+
+    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),
+            MessageManager.getString("label.number_of_results_desc"), true,
+            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));
     args.add(new LogarithmicParameter(
-            MessageManager.getString("label.dom_e_value_desc"),
-            MessageManager.getString("label.dom_e_value_desc"), false, -3d,
-            -37.92977945, 1d, 10d));
+            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));
+  }
+
+  /**
+   * Answers default parameters for jackhmmer, taking into account any configured
+   * as user preferences
+   * 
+   * @param args
+   */
+  private void getJackhmmerParams(List<ArgumentI> args)
+  {
+
     /*
+     * 'Parameters'
+     */
+    addChoiceOfSequence(args);
+
+    // 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 RadioChoiceParameter(
+            MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
+            Arrays.asList(JackHMMER.CUTOFF_NONE, JackHMMER.CUTOFF_EVALUE,
+                    JackHMMER.CUTOFF_SCORE),
+            JackHMMER.CUTOFF_EVALUE));
+    args.add(new LogarithmicParameter(
+            MessageManager.getString(JackHMMER.SEQ_EVALUE_KEY),
+            MessageManager.getString("label.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,
+            1E-38, 10D));
+    args.add(new DoubleParameter(
+            MessageManager.getString(JackHMMER.SEQ_SCORE_KEY),
+            MessageManager.getString("label.seq_score_desc"), false, 0d, 0d,
+            1000d));
     args.add(new DoubleParameter(
-            MessageManager.getString("label.dom_score"),
-            MessageManager.getString("label.dom_score_desc"), false, 0d,
-            0d,
-            10000d));
-            */
+            MessageManager.getString(JackHMMER.DOM_SCORE_KEY),
+            MessageManager.getString("label.dom_score_desc"), false, 0d, 0d,
+            1000d));
   }
 
+  /**
+   * Constructs a choice parameter for database to search; always includes 'this
+   * alignment', and also includes any databases held under user preferences key
+   * "HMMSEARCH_DBS" as a comma-delimited list
+   * 
+   * @param args
+   */
+  protected void addChoiceOfDatabase(List<ArgumentI> args)
+  {
+    String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+    if (names == null || names.isEmpty())
+    {
+      return;
+    }
+
+    List<String> filePaths = new ArrayList<>();
+    List<String> fileNames = new ArrayList<>();
+
+    String thisAlignment = MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY);
+    filePaths.add(thisAlignment);
+    fileNames.add(thisAlignment);
+
+    Scanner nameScanner = new Scanner(names);
+    nameScanner.useDelimiter(Preferences.COMMA);
+
+    while (nameScanner.hasNext())
+    {
+      String next = nameScanner.next();
+      if ("null".equals(next))
+      {
+        Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+      }
+      else
+      {
+        filePaths.add(next);
+        int pos = next.lastIndexOf(File.separator);
+        String fileName = next.substring(pos + 1);
+        fileNames.add(fileName);
+      }
+    }
+    nameScanner.close();
+    ArgumentI databasesOption = new StringParameter(
+            MessageManager.getString(HMMSearch.DATABASE_KEY),
+            MessageManager.getString("label.database_for_hmmsearch"), true,
+            thisAlignment,
+            thisAlignment,
+            filePaths, fileNames);
+    args.add(databasesOption);
+  }
+
+  /**
+   * Answers default parameters for hmmalign, taking into account any configured
+   * as user preferences
+   * 
+   * @param args
+   */
   private void getHMMAlignParams(List<ArgumentI> args)
   {
+    addChoiceOfHmm(args);
+
+    boolean def = Cache.getDefault(Preferences.HMMALIGN_TRIM_TERMINI,
+            false);
     args.add(new BooleanOption(
             MessageManager.getString("label.trim_termini"),
             MessageManager.getString("label.trim_termini_desc"),
-            false, false, true, null));
+            false, false, def, null));
+  }
+
+  /**
+   * 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, null);
+      args.add(arg);
+    }
+  }
+
+  /**
+   * Adds an argument representing the choice of sequence against which to perform
+   * jackhmmer
+   * 
+   * @param args
+   */
+  protected void addChoiceOfSequence(List<ArgumentI> args)
+  {
+    List<SequenceI> sequences = viewport.getAlignment().getSequences();
+
+    List<String> options = new ArrayList<>();
+
+    for (SequenceI seq : sequences)
+    {
+      options.add(seq.getName());
+    }
+
+    String defseq = options.get(0);
+    ArgumentI arg = new StringParameter(
+            MessageManager.getString("label.use_sequence"), null, true,
+            defseq,
+            defseq, options, null);
+    args.add(arg);
   }
 
+  /**
+   * Answers default parameters for hmmbuild, taking into account any configured
+   * as user preferences
+   * 
+   * @param args
+   */
   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
-    args.add(new BooleanOption(
-            MessageManager.getString("label.use_reference"),
-            MessageManager.getString("label.use_reference_desc"), true,
-            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));
+    /*
+     * 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(
+              MessageManager.getString("label.use_reference"),
+              MessageManager.getString("label.use_reference_desc"), true,
+              true, true, null));
+    }
+
+    /*
+     * choice of whether to compute HMM for alignment and/or group(s)
+     * - only if there are any groups
+     */
+    if (!viewport.getAlignment().getGroups().isEmpty())
+    {
+      List<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