X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FJackHMMER.java;h=12c049216655da4ed9b36bc24d15c216433cfc28;hb=72404f561ccd190eab1990874f017bbe94bf9e10;hp=d822439485fd12163cadb30a6b5b979ccf939156;hpb=a3bed79406073da41d03e8278733e4beae172e6e;p=jalview.git

diff --git a/src/jalview/hmmer/JackHMMER.java b/src/jalview/hmmer/JackHMMER.java
index d822439..12c0492 100644
--- a/src/jalview/hmmer/JackHMMER.java
+++ b/src/jalview/hmmer/JackHMMER.java
@@ -26,6 +26,8 @@ import javax.swing.JOptionPane;
 public class JackHMMER extends Search
 {
 
+  SequenceI seq = null;
+
   /**
    * Constructor for the JackhmmerThread
    * 
@@ -45,7 +47,7 @@ public class JackHMMER extends Search
   @Override
   public void run()
   {
-    SequenceI seq = getSequence();
+    seq = getSequence();
     if (seq == null)
     {
       // shouldn't happen if we got this far
@@ -138,15 +140,18 @@ public class JackHMMER extends Search
               inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
       seqs = file.getSeqsAsArray();
 
+      readDomainTable(searchOutputFile, true);
+
       if (searchAlignment)
       {
         recoverSequences(sequencesHash, seqs);
       }
 
-      readTable(searchOutputFile);
+
 
       int seqCount = seqs.length;
 
+
       AlignmentI al = new Alignment(seqs);
 
       AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,