X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMSearch.java;h=a3ac034cbaa3b4f6961d66161df3c6952999199a;hb=20559094a404933bfa73a9c30a16f3ea3227081f;hp=21a3b208bc14889e78171122efc31fb73c4c12da;hpb=49b68fe2a01763c44661e2012363f9847bfc789f;p=jalview.git

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 21a3b20..a3ac034 100644
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -4,6 +4,7 @@ import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -160,6 +161,25 @@ public class HMMSearch extends HmmerCommand
 
     List<String> args = new ArrayList<>();
     args.add(command);
+    buildArguments(args, searchOutputFile, hitsAlignmentFile, hmmFile);
+
+    return runCommand(args);
+  }
+
+  /**
+   * Appends command line arguments to the given list, to specify input and
+   * output files for the search, and any additional options that may have been
+   * passed from the parameters dialog
+   * 
+   * @param args
+   * @param searchOutputFile
+   * @param hitsAlignmentFile
+   * @param hmmFile
+   * @throws IOException
+   */
+  protected void buildArguments(List<String> args, File searchOutputFile,
+          File hitsAlignmentFile, File hmmFile) throws IOException
+  {
     args.add("-o");
     args.add(getFilePath(searchOutputFile));
     args.add("-A");
@@ -176,6 +196,7 @@ public class HMMSearch extends HmmerCommand
     String seqScoreCutoff = null;
     String domScoreCutoff = null;
     databaseName = "Alignment";
+    boolean searchAlignment = false;
 
     if (params != null)
     {
@@ -187,6 +208,18 @@ public class HMMSearch extends HmmerCommand
         {
           seqsToReturn = Integer.parseInt(arg.getValue());
         }
+        else if (MessageManager.getString("action.search").equals(name))
+        {
+          searchAlignment = arg.getValue().equals(
+                  MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY));
+        }
+        else if (MessageManager.getString(DATABASE_KEY).equals(name))
+        {
+          dbPath = arg.getValue();
+          int pos = dbPath.lastIndexOf(File.separator);
+          databaseName = dbPath.substring(pos + 1);
+          databaseFile = new File(dbPath);
+        }
         else if (MessageManager.getString(AUTO_ALIGN_SEQS_KEY)
                 .equals(name))
         {
@@ -261,8 +294,9 @@ public class HMMSearch extends HmmerCommand
       args.add(domScoreCutoff);
     }
 
-    if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
-            .equals(dbPath))
+//    if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
+//            .equals(dbPath))
+      if (searchAlignment)
     {
       /*
        * no external database specified for search, so
@@ -282,8 +316,6 @@ public class HMMSearch extends HmmerCommand
 
     args.add(getFilePath(hmmFile));
     args.add(getFilePath(databaseFile));
-
-    return runCommand(args);
   }
 
   /**
@@ -309,7 +341,23 @@ public class HMMSearch extends HmmerCommand
       StockholmFile file = new StockholmFile(new FileParse(
               inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
       seqs = file.getSeqsAsArray();
-
+      // look for PP cons and ref seq in alignment only annotation
+      AlignmentAnnotation modelpos = null, ppcons = null;
+      for (AlignmentAnnotation aa : file.getAnnotations())
+      {
+        if (aa.sequenceRef == null)
+        {
+          if (aa.label.equals("Reference Positions")) // RF feature type in
+                                                      // stockholm parser
+          {
+            modelpos = aa;
+          }
+          if (aa.label.equals("Posterior Probability"))
+          {
+            ppcons = aa;
+          }
+        }
+      }
       readTable(searchOutputFile);
 
       int seqCount = Math.min(seqs.length, seqsToReturn);
@@ -324,6 +372,14 @@ public class HMMSearch extends HmmerCommand
       else
       {
         AlignmentI al = new Alignment(hmmAndSeqs);
+        if (ppcons != null)
+        {
+          al.addAnnotation(ppcons);
+        }
+        if (modelpos != null)
+        {
+          al.addAnnotation(modelpos);
+        }
         AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
         String ttl = "hmmSearch of " + databaseName + " using "
@@ -398,24 +454,18 @@ public class HMMSearch extends HmmerCommand
     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(); // full sequence eValue score
-      // float eValue = Float.parseFloat(str);
-      // int seqLength = seqs[index].getLength();
-      // Annotation[] annots = new Annotation[seqLength];
-      // for (int j = 0; j < seqLength; j++)
-      // {
-      // annots[j] = new Annotation(eValue);
-      // }
-      AlignmentAnnotation annot = new AlignmentAnnotation("E-value",
-              "Score", null);
-      annot.setCalcId(HMMSEARCH);
-      double eValue = Double.parseDouble(str);
-      annot.setScore(eValue);
-      annot.setSequenceRef(seqs[index]);
-      seqs[index].addAlignmentAnnotation(annot);
-
+      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);
       scanner.close();
       line = br.readLine();
       index++;
@@ -424,4 +474,59 @@ 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)
+  {
+    try
+    {
+      AlignmentAnnotation annot = null;
+      if (pp == null)
+      {
+        new AlignmentAnnotation(label,
+              description, null);
+      }
+      else
+      {
+        annot = new AlignmentAnnotation(pp);
+        annot.label = label;
+        annot.description = description;
+      }
+      annot.setCalcId(HMMSEARCH);
+      double eValue = Double.parseDouble(value);
+      annot.setScore(eValue);
+      annot.setSequenceRef(seq);
+      seq.addAlignmentAnnotation(annot);
+    } catch (NumberFormatException e)
+    {
+      System.err.println("Error parsing " + label + " from " + value);
+    }
+  }
+
 }