JAL-2629 fix hmmsearch/jackhmmer being unable to search through DB file

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 3faa4f2..d2b469f 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))
         {
@@ -244,6 +238,11 @@ public class HMMSearch extends HmmerCommand
             databaseName = dbPath.substring(pos + 1);
             databaseFile = new File(dbPath);
           }
+          searchAlignment = false;
+        }
+        else if (MessageManager.getString(RETURN_N_NEW_SEQ).equals(name))
+        {
+          returnNoOfNewSeqs = true;
         }
       }
     }
@@ -275,12 +274,12 @@ 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);
+
+      sequencesHash = stashSequences(copy.getSequencesArray());
+
       exportStockholm(copy.getSequencesArray(), databaseFile, null);
+
     }
 
     args.add(getFilePath(hmmFile, true));
@@ -310,6 +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())
@@ -359,6 +364,7 @@ public class HMMSearch extends HmmerCommand
           }
         }
       }
+
       if (realign)
       {
         realignResults(hmmAndSeqs);
@@ -380,8 +386,14 @@ public class HMMSearch extends HmmerCommand
                 + hmmSeq.getName();
         Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
+
+        int nNew = checkForNewSequences();
+        JvOptionPane.showMessageDialog(af.alignPanel, nNew + " "
+                + MessageManager.getString("label.new_returned"));
+
       }
 
+
       hmmTemp.delete();
       inputAlignmentTemp.delete();
       searchOutputFile.delete();
@@ -394,6 +406,25 @@ 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--;
+        }
+      }
+    }
+
+    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
@@ -422,6 +453,10 @@ public class HMMSearch extends HmmerCommand
     }
     HmmerCommand hmmalign = new HMMAlign(frame, alignArgs);
     hmmalign.run();
+
+    int nNew = checkForNewSequences();
+    JvOptionPane.showMessageDialog(frame.alignPanel,
+            nNew + " " + MessageManager.getString("label.new_returned"));
   }
 
   /**