JAL-2629 fix hmmsearch/jackhmmer assigning incorrect evalues and scores

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index b40b079..a06f186 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -25,6 +25,7 @@ import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
+import java.util.Hashtable;
 import java.util.List;
 import java.util.Scanner;
 
@@ -38,12 +39,18 @@ public class HMMSearch extends HmmerCommand
 
   boolean trim = false;
 
+  boolean returnNoOfNewSeqs = false;
+
   int seqsToReturn = Integer.MAX_VALUE;
 
+  boolean searchAlignment = true;
+
   SequenceI[] seqs;
 
   private String databaseName;
 
+  Hashtable sequencesHash;
+
   /**
    * Constructor for the HMMSearchThread
    * 
@@ -165,7 +172,6 @@ public class HMMSearch extends HmmerCommand
     String seqScoreCutoff = null;
     String domScoreCutoff = null;
     databaseName = "Alignment";
-    boolean searchAlignment = false;
 
     if (params != null)
     {
@@ -177,18 +183,6 @@ 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))
         {
@@ -202,11 +196,13 @@ public class HMMSearch extends HmmerCommand
         else if (MessageManager.getString(REPORTING_CUTOFF_KEY)
                 .equals(name))
         {
-          if (CUTOFF_EVALUE.equals(arg.getValue()))
+          if (MessageManager.getString(CUTOFF_EVALUE)
+                  .equals(arg.getValue()))
           {
             useEvalueCutoff = true;
           }
-          else if (CUTOFF_SCORE.equals(arg.getValue()))
+          else if (MessageManager.getString(CUTOFF_SCORE)
+                  .equals(arg.getValue()))
           {
             useScoreCutoff = true;
           }
@@ -235,16 +231,16 @@ public class HMMSearch extends HmmerCommand
         }
         else if (MessageManager.getString(DATABASE_KEY).equals(name))
         {
-          dbFound = true;
-          dbPath = arg.getValue();
-          if (!MessageManager.getString(THIS_ALIGNMENT_KEY)
-                  .equals(dbPath))
+          databaseFile = new File(arg.getValue());
+          if (!arg.getValue().isEmpty())
           {
-            int pos = dbPath.lastIndexOf(File.separator);
-            databaseName = dbPath.substring(pos + 1);
-            databaseFile = new File(dbPath);
+            searchAlignment = false;
           }
         }
+        else if (MessageManager.getString(RETURN_N_NEW_SEQ).equals(name))
+        {
+          returnNoOfNewSeqs = true;
+        }
       }
     }
 
@@ -277,12 +273,13 @@ public class HMMSearch extends HmmerCommand
       AlignmentI copy = new Alignment(al);
       deleteHmmSequences(copy);
 
-      SequenceI[] seqs = copy.getSequencesArray();
+      if (searchAlignment)
+      {
+        sequencesHash = stashSequences(copy.getSequencesArray());
+      }
 
-      // hmmsearch fails if duplicate sequence names in file
-      renameDuplicates(seqs);
+      exportStockholm(copy.getSequencesArray(), databaseFile, null);
 
-      exportStockholm(copy.getSequencesArray(), databaseFile, null, true);
     }
 
     args.add(getFilePath(hmmFile, true));
@@ -312,6 +309,12 @@ public class HMMSearch extends HmmerCommand
       StockholmFile file = new StockholmFile(new FileParse(
               inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
       seqs = file.getSeqsAsArray();
+
+      if (searchAlignment)
+      {
+        recoverSequences(sequencesHash, seqs);
+      }
+
       // look for PP cons and ref seq in alignment only annotation
       AlignmentAnnotation modelpos = null, ppcons = null;
       for (AlignmentAnnotation aa : file.getAnnotations())
@@ -361,6 +364,7 @@ public class HMMSearch extends HmmerCommand
           }
         }
       }
+
       if (realign)
       {
         realignResults(hmmAndSeqs);
@@ -382,8 +386,17 @@ public class HMMSearch extends HmmerCommand
                 + hmmSeq.getName();
         Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
+
+        if (returnNoOfNewSeqs)
+        {
+          int nNew = checkForNewSequences();
+          JvOptionPane.showMessageDialog(af.alignPanel, nNew + " "
+                  + MessageManager.getString("label.new_returned"));
+        }
+
       }
 
+
       hmmTemp.delete();
       inputAlignmentTemp.delete();
       searchOutputFile.delete();
@@ -396,6 +409,26 @@ public class HMMSearch extends HmmerCommand
     }
   }
 
+  private int checkForNewSequences()
+  {
+    int nNew = seqs.length;
+
+    for (SequenceI resultSeq : seqs)
+    {
+      for (SequenceI aliSeq : alignment.getSequencesArray())
+      {
+        if (resultSeq.getName().equals(aliSeq.getName()))
+        {
+          nNew--;
+          break;
+        }
+      }
+    }
+
+    return nNew;
+
+  }
+
   /**
    * Realigns the given sequences using hmmalign, to the HMM profile sequence
    * which is the first in the array, and opens the results in a new frame
@@ -424,6 +457,13 @@ public class HMMSearch extends HmmerCommand
     }
     HmmerCommand hmmalign = new HMMAlign(frame, alignArgs);
     hmmalign.run();
+
+    if (returnNoOfNewSeqs)
+    {
+      int nNew = checkForNewSequences();
+      JvOptionPane.showMessageDialog(frame.alignPanel,
+              nNew + " " + MessageManager.getString("label.new_returned"));
+    }
   }
 
   /**
@@ -451,10 +491,11 @@ public class HMMSearch extends HmmerCommand
     while (!"  ------ inclusion threshold ------".equals(line)
             && !"".equals(line))
     {
-      SequenceI seq = seqs[index];
       Scanner scanner = new Scanner(line);
       String evalue = scanner.next();
       String score = scanner.next();
+      checkSequenceOrder(index, scanner);
+      SequenceI seq = seqs[index];
       addScoreAnnotations(evalue, score, seq);
       scanner.close();
       line = br.readLine();
@@ -496,4 +537,29 @@ public class HMMSearch extends HmmerCommand
     }
   }
 
+  private void checkSequenceOrder(int index, Scanner scanner)
+  {
+    String seqName = null;
+
+    for (int i = 0; i < 8; i++)
+    {
+      seqName = scanner.next();
+    }
+
+    if (!seqs[index].getName().equals(seqName))
+    {
+      SequenceI temp = seqs[index];
+
+      for (int j = 0; j < seqs.length; j++)
+      {
+        if (seqs[j].getName().equals(seqName))
+        {
+          seqs[index] = seqs[j];
+          seqs[j] = temp;
+          break;
+        }
+      }
+    }
+  }
+    
 }