JAL-2629 hmmer searches now read domain rather than full scores

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index f670633..f05823e 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -157,6 +157,8 @@ public class HMMSearch extends Search
               inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
       seqs = file.getSeqsAsArray();
 
+      readDomainTable(searchOutputFile, false);
+
       if (searchAlignment)
       {
         recoverSequences(sequencesHash, seqs);
@@ -179,7 +181,7 @@ public class HMMSearch extends Search
           }
         }
       }
-      readTable(searchOutputFile);
+
 
       int seqCount = Math.min(seqs.length, seqsToReturn);
       SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];