JAL-2629 current hmmer commands are now executed in threads

[jalview.git] / src / jalview / io / HMMFile.java

diff --git a/src/jalview/io/HMMFile.java b/src/jalview/io/HMMFile.java
index e7f8030..02d9229 100644 (file)
--- a/src/jalview/io/HMMFile.java
+++ b/src/jalview/io/HMMFile.java
@@ -27,9 +27,6 @@ public class HMMFile extends AlignFile
   // HMM to store file data
   private HiddenMarkovModel hmm = new HiddenMarkovModel();
 
-
-
-
   // number of possible transitions
   private final int NUMBER_OF_TRANSITIONS = 7;
 
@@ -48,13 +45,15 @@ public class HMMFile extends AlignFile
   private static final String TRANSITIONTYPELINE = "m->m     m->i     m->d     i->m     i->i     d->m     d->d";
 
   /**
-   * Constructor for HMMFile
+   * Constructor for HMMFile, parses immediately
+   * 
    * @param source
    * @throws IOException
    */
   public HMMFile(FileParse source) throws IOException
   {
     super(false, source);
+    parse();
   }
 
   /**