JAL-2629 update spikes/mungo to latest

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 30299e9..d4c9656 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -1,5 +1,6 @@
 package jalview.hmmer;
 
+import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -11,15 +12,18 @@ import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StockholmFile;
+import jalview.util.FileUtils;
 import jalview.util.MessageManager;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.Option;
 
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.Scanner;
 
@@ -27,6 +31,8 @@ import javax.swing.JOptionPane;
 
 public class HMMSearch extends HmmerCommand
 {
+  private static final String PARAMNAME_NO_OF_RESULTS = MessageManager.getString("label.number_of_results");
+
   static final String HMMSEARCH = "hmmsearch";
 
   boolean realign = false;
@@ -56,32 +62,34 @@ public class HMMSearch extends HmmerCommand
   @Override
   public void run()
   {
-    HiddenMarkovModel hmm = af.getSelectedHMM();
+    HiddenMarkovModel hmm = getHmmProfile();
     if (hmm == null)
     {
-      JOptionPane.showMessageDialog(af,
-              MessageManager.getString("warn.no_selected_hmm"));
+      // shouldn't happen if we got this far
+      Cache.log.error("Error: no hmm for hmmsearch");
       return;
     }
 
-    SequenceI hmmSeq = af.getSelectedHMMSequence();
+    SequenceI hmmSeq = hmm.getConsensusSequence();// af.getSelectedHMMSequence();
     long msgId = System.currentTimeMillis();
     af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
             msgId);
 
     try
     {
-      File hmmFile = createTempFile("hmm", ".hmm");
-      File hitsAlignmentFile = createTempFile("hitAlignment", ".sto");
-      File searchOutputFile = createTempFile("searchOutput", ".sto");
+      File hmmFile = FileUtils.createTempFile("hmm", ".hmm");
+      File hitsAlignmentFile = FileUtils.createTempFile("hitAlignment",
+              ".sto");
+      File searchOutputFile = FileUtils.createTempFile("searchOutput",
+              ".sto");
 
       exportHmm(hmm, hmmFile.getAbsoluteFile());
 
       boolean ran = runCommand(searchOutputFile, hitsAlignmentFile, hmmFile);
       if (!ran)
       {
-        JvOptionPane.showInternalMessageDialog(af,
-                MessageManager.getString("warn.hmmsearch_failed"));
+        JvOptionPane.showInternalMessageDialog(af, MessageManager
+                .formatMessage("warn.command_failed", "hmmsearch"));
         return;
       }
 
@@ -122,9 +130,9 @@ public class HMMSearch extends HmmerCommand
     List<String> args = new ArrayList<>();
     args.add(command);
     args.add("-o");
-    args.add(searchOutputFile.getAbsolutePath());
+    args.add(getFilePath(searchOutputFile));
     args.add("-A");
-    args.add(hitsAlignmentFile.getAbsolutePath());
+    args.add(getFilePath(hitsAlignmentFile));
 
     boolean dbFound = false;
     String dbPath = "";
@@ -152,7 +160,7 @@ public class HMMSearch extends HmmerCommand
         }
         else if (MessageManager.getString("label.seq_e_value").equals(name))
         {
-          args.add("--incE");
+          args.add("-E");
           args.add(arg.getValue());
         }
         else if (MessageManager.getString("label.seq_score").equals(name))
@@ -160,10 +168,10 @@ public class HMMSearch extends HmmerCommand
           args.add("-incT");
           args.add(arg.getValue());
         }
-        else if (MessageManager.getString("label.dom_e_value_desc")
+        else if (MessageManager.getString("label.dom_e_value")
                 .equals(name))
         {
-          args.add("--incdomE");
+          args.add("--domE");
           args.add(arg.getValue());
         }
         else if (MessageManager.getString("label.dom_score").equals(name))
@@ -194,15 +202,16 @@ public class HMMSearch extends HmmerCommand
     {
       /*
        * no external database specified for search, so
-       * export current alignment as 'database' to search
+       * export current alignment as 'database' to search,
+       * excluding any HMM consensus sequences it contains
        */
-      databaseFile = createTempFile("database", ".sto");
+      databaseFile = FileUtils.createTempFile("database", ".sto");
       AlignmentI al = af.getViewport().getAlignment();
       AlignmentI copy = new Alignment(al);
-      SequenceI hmms = copy.getHmmConsensus();
-      if (hmms != null)
+      List<SequenceI> hmms = copy.getHmmSequences();
+      for (SequenceI hmmSeq : hmms)
       {
-        copy.deleteSequence(hmms);
+        copy.deleteSequence(hmmSeq);
       }
       exportStockholm(copy.getSequencesArray(), databaseFile, null);
       // StockholmFile stoFile = new StockholmFile(copy);
@@ -213,8 +222,8 @@ public class HMMSearch extends HmmerCommand
       // writer.close();
     }
 
-    args.add(hmmFile.getAbsolutePath());
-    args.add(databaseFile.getAbsolutePath());
+    args.add(getFilePath(hmmFile));
+    args.add(getFilePath(databaseFile));
 
     return runCommand(args);
   }
@@ -250,10 +259,17 @@ public class HMMSearch extends HmmerCommand
       hmmAndSeqs[0] = hmmSeq;
       System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
 
-      AlignmentI alignment = new Alignment(hmmAndSeqs);
-      AlignFrame frame = new AlignFrame(alignment, 1, 1);
-      frame.setSelectedHMMSequence(hmmSeq);
+      /*
+       * and align the search results to the HMM profile
+       */
+      AlignmentI al = new Alignment(hmmAndSeqs);
+      AlignFrame frame = new AlignFrame(al, 1, 1);
       List<ArgumentI> alignArgs = new ArrayList<>();
+      String defSeq = hmmSeq.getName();
+      List<String> options = Collections.singletonList(defSeq);
+      Option option = new Option(MessageManager.getString("label.use_hmm"),
+              "", true, defSeq, defSeq, options, null);
+      alignArgs.add(option);
       if (trim)
       {
         alignArgs.add(new BooleanOption(
@@ -261,7 +277,7 @@ public class HMMSearch extends HmmerCommand
                 MessageManager.getString("label.trim_termini_desc"), true,
                 true, true, null));
       }
-      HMMAlign hmmalign = new HMMAlign(frame, alignArgs);
+      HmmerCommand hmmalign = new HMMAlign(frame, alignArgs);
       hmmalign.run();
       frame = null;
       hmmTemp.delete();