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JAL-2629 uniquify all hmmer command sequence outputs
[jalview.git]
/
src
/
jalview
/
hmmer
/
HMMBuild.java
diff --git
a/src/jalview/hmmer/HMMBuild.java
b/src/jalview/hmmer/HMMBuild.java
index
85abd50
..
7c14858
100644
(file)
--- a/
src/jalview/hmmer/HMMBuild.java
+++ b/
src/jalview/hmmer/HMMBuild.java
@@
-199,10
+199,11
@@
public class HMMBuild extends HmmerCommand
// TODO rather than copy alignment data we should anonymize in situ -
// export/File import could use anonymization hash to reinstate references
// at import level ?
// TODO rather than copy alignment data we should anonymize in situ -
// export/File import could use anonymization hash to reinstate references
// at import level ?
+
SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
Hashtable sequencesHash = stashSequences(copyArray);
SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
Hashtable sequencesHash = stashSequences(copyArray);
- exportStockholm(copyArray, alignmentFile, ac, false);
+ exportStockholm(copyArray, alignmentFile, ac);
recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));
recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));