JAL-2629 uniquify all hmmer command sequence outputs

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

diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
index 13bbba4..d66ec33 100644 (file)
--- a/src/jalview/hmmer/HMMAlign.java
+++ b/src/jalview/hmmer/HMMAlign.java
@@ -87,7 +87,7 @@ public class HMMAlign extends HmmerCommand
         File alignmentFile = FileUtils.createTempFile("output", ".sto");
         File resultFile = FileUtils.createTempFile("input", ".sto");
 
-        exportStockholm(seqs, alignmentFile.getAbsoluteFile(), null, false);
+        exportStockholm(seqs, alignmentFile.getAbsoluteFile(), null);
         exportHmm(hmm, modelFile.getAbsoluteFile());
 
         boolean ran = runCommand(modelFile, alignmentFile, resultFile);