From: tva <tva@10.205.251.175>
Date: Wed, 3 Jul 2019 12:44:36 +0000 (+0100)
Subject: JAL-2629 fix hmm on alignment being deleted upon running jackhmmer
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=79d76d41dc80b2c5a71201f26f832af337b7809f;p=jalview.git

JAL-2629 fix hmm on alignment being deleted upon running jackhmmer
---

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 3faa4f2..64802c7 100644
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -275,11 +275,7 @@ public class HMMSearch extends HmmerCommand
       databaseFile = FileUtils.createTempFile("database", ".sto");
       AlignmentI al = af.getViewport().getAlignment();
       AlignmentI copy = new Alignment(al);
-      List<SequenceI> hmms = copy.getHmmSequences();
-      for (SequenceI hmmSeq : hmms)
-      {
-        copy.deleteSequence(hmmSeq);
-      }
+      deleteHmmSequences(copy);
       exportStockholm(copy.getSequencesArray(), databaseFile, null);
     }
 
diff --git a/src/jalview/hmmer/JackHMMER.java b/src/jalview/hmmer/JackHMMER.java
index 1815ac4..1731439 100644
--- a/src/jalview/hmmer/JackHMMER.java
+++ b/src/jalview/hmmer/JackHMMER.java
@@ -246,8 +246,9 @@ public class JackHMMER extends HmmerCommand
        */
       databaseFile = FileUtils.createTempFile("database", ".fa");
       AlignmentI al = af.getViewport().getAlignment();
-      deleteHmmSequences(al);
-      exportFasta(al, databaseFile);
+      AlignmentI copy = new Alignment(al);
+      deleteHmmSequences(copy);
+      exportFasta(copy, databaseFile);
     }
 
     args.add(getFilePath(seqFile, true));