JAL-2629 fix hmm on alignment being deleted upon running jackhmmer

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 1883fef..64802c7 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -34,37 +34,6 @@ public class HMMSearch extends HmmerCommand
 {
   static final String HMMSEARCH = "hmmsearch";
 
-  /*
-   * constants for i18n lookup of passed parameter names
-   */
-  static final String DATABASE_KEY = "label.database";
-
-  static final String THIS_ALIGNMENT_KEY = "label.this_alignment";
-
-  static final String USE_ACCESSIONS_KEY = "label.use_accessions";
-
-  static final String AUTO_ALIGN_SEQS_KEY = "label.auto_align_seqs";
-
-  static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
-
-  static final String TRIM_TERMINI_KEY = "label.trim_termini";
-
-  static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff";
-
-  static final String CUTOFF_NONE = "None";
-
-  static final String CUTOFF_SCORE = "Score";
-
-  static final String CUTOFF_EVALUE = "E-Value";
-
-  static final String SEQ_EVALUE_KEY = "label.seq_evalue";
-
-  static final String DOM_EVALUE_KEY = "label.dom_evalue";
-
-  static final String SEQ_SCORE_KEY = "label.seq_score";
-
-  static final String DOM_SCORE_KEY = "label.dom_score";
-
   boolean realign = false;
 
   boolean trim = false;
@@ -104,7 +73,7 @@ public class HMMSearch extends HmmerCommand
 
     SequenceI hmmSeq = hmm.getConsensusSequence();
     long msgId = System.currentTimeMillis();
-    af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
+    af.setProgressBar(MessageManager.getString("status.running_search"),
             msgId);
 
     try
@@ -181,9 +150,9 @@ public class HMMSearch extends HmmerCommand
           File hitsAlignmentFile, File hmmFile) throws IOException
   {
     args.add("-o");
-    args.add(getFilePath(searchOutputFile));
+    args.add(getFilePath(searchOutputFile, true));
     args.add("-A");
-    args.add(getFilePath(hitsAlignmentFile));
+    args.add(getFilePath(hitsAlignmentFile, true));
 
     boolean dbFound = false;
     String dbPath = "";
@@ -306,16 +275,12 @@ public class HMMSearch extends HmmerCommand
       databaseFile = FileUtils.createTempFile("database", ".sto");
       AlignmentI al = af.getViewport().getAlignment();
       AlignmentI copy = new Alignment(al);
-      List<SequenceI> hmms = copy.getHmmSequences();
-      for (SequenceI hmmSeq : hmms)
-      {
-        copy.deleteSequence(hmmSeq);
-      }
+      deleteHmmSequences(copy);
       exportStockholm(copy.getSequencesArray(), databaseFile, null);
     }
 
-    args.add(getFilePath(hmmFile));
-    args.add(getFilePath(databaseFile));
+    args.add(getFilePath(hmmFile, true));
+    args.add(getFilePath(databaseFile, true));
   }
 
   /**
@@ -470,27 +435,21 @@ public class HMMSearch extends HmmerCommand
     {
       line = br.readLine();
     }
-    for (int i = 0; i < 5; i++)
+    while (!line.contains("-------"))
     {
       line = br.readLine();
     }
+    line = br.readLine();
 
     int index = 0;
     while (!"  ------ inclusion threshold ------".equals(line)
             && !"".equals(line))
     {
       SequenceI seq = seqs[index];
-      AlignmentAnnotation pp = seq
-              .getAlignmentAnnotations("", "Posterior Probability")
-              .get(0);
       Scanner scanner = new Scanner(line);
-      String str = scanner.next();
-      addScoreAnnotation(str, seq, "hmmsearch E-value",
-              "Full sequence E-value", pp);
-      str = scanner.next();
-      addScoreAnnotation(str, seq, "hmmsearch Score",
-              "Full sequence bit score", pp);
-      seq.removeAlignmentAnnotation(pp);
+      String evalue = scanner.next();
+      String score = scanner.next();
+      addScoreAnnotations(evalue, score, seq);
       scanner.close();
       line = br.readLine();
       index++;
@@ -499,58 +458,35 @@ public class HMMSearch extends HmmerCommand
     br.close();
   }
 
-  /**
-   * A helper method that adds one score-only (non-positional) annotation to a
-   * sequence
-   * 
-   * @param value
-   * @param seq
-   * @param label
-   * @param description
-   */
-  protected void addScoreAnnotation(String value, SequenceI seq,
-          String label, String description)
-  {
-    addScoreAnnotation(value, seq, label, description, null);
-  }
 
-  /**
-   * A helper method that adds one score-only (non-positional) annotation to a
-   * sequence
-   * 
-   * @param value
-   * @param seq
-   * @param label
-   * @param description
-   * @param pp
-   *          existing posterior probability annotation - values copied to new
-   *          annotation row
-   */
-  protected void addScoreAnnotation(String value, SequenceI seq,
-          String label, String description, AlignmentAnnotation pp)
+  protected void addScoreAnnotations(String eValue, String bitScore,
+          SequenceI seq)
   {
+    String label = "Search Scores";
+    String description = "Full sequence bit score and E-Value";
+
     try
     {
-      AlignmentAnnotation annot = null;
-      if (pp == null)
-      {
-        new AlignmentAnnotation(label,
+      AlignmentAnnotation annot = new AlignmentAnnotation(label,
               description, null);
-      }
-      else
-      {
-        annot = new AlignmentAnnotation(pp);
-        annot.label = label;
-        annot.description = description;
-      }
+
+      annot.label = label;
+      annot.description = description;
+
       annot.setCalcId(HMMSEARCH);
-      double eValue = Double.parseDouble(value);
-      annot.setScore(eValue);
+
+      double dEValue = Double.parseDouble(eValue);
+      annot.setEValue(dEValue);
+
+      double dBitScore = Double.parseDouble(bitScore);
+      annot.setBitScore(dBitScore);
+
       annot.setSequenceRef(seq);
       seq.addAlignmentAnnotation(annot);
     } catch (NumberFormatException e)
     {
-      System.err.println("Error parsing " + label + " from " + value);
+      System.err.println("Error parsing " + label + " from " + eValue
+              + " & " + bitScore);
     }
   }