Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/hmmer/JackHMMER.java b/src/jalview/hmmer/JackHMMER.java
index d822439..00314f0 100644 (file)
--- a/src/jalview/hmmer/JackHMMER.java
+++ b/src/jalview/hmmer/JackHMMER.java
@@ -1,6 +1,7 @@
 package jalview.hmmer;
 
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
@@ -26,6 +27,8 @@ import javax.swing.JOptionPane;
 public class JackHMMER extends Search
 {
 
+  SequenceI seq = null;
+
   /**
    * Constructor for the JackhmmerThread
    * 
@@ -45,11 +48,11 @@ 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
-      Cache.log.error("Error: no sequence for jackhmmer");
+      Console.error("Error: no sequence for jackhmmer");
       return;
     }
 
@@ -138,15 +141,18 @@ 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,