Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index f670633..767a56e 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -1,6 +1,7 @@
 package jalview.hmmer;
 
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -64,7 +65,7 @@ public class HMMSearch extends Search
     if (hmm == null)
     {
       // shouldn't happen if we got this far
-      Cache.log.error("Error: no hmm for hmmsearch");
+      Console.error("Error: no hmm for hmmsearch");
       return;
     }
 
@@ -157,6 +158,8 @@ public class HMMSearch extends Search
               inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
       seqs = file.getSeqsAsArray();
 
+      readDomainTable(searchOutputFile, false);
+
       if (searchAlignment)
       {
         recoverSequences(sequencesHash, seqs);
@@ -179,7 +182,7 @@ public class HMMSearch extends Search
           }
         }
       }
-      readTable(searchOutputFile);
+
 
       int seqCount = Math.min(seqs.length, seqsToReturn);
       SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];