JAL-2937 Cygwin path preference, method refactoring

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

diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
index 44828aa..befdc55 100644 (file)
--- a/src/jalview/hmmer/HMMAlign.java
+++ b/src/jalview/hmmer/HMMAlign.java
@@ -14,6 +14,7 @@ import jalview.gui.JvOptionPane;
 import jalview.gui.SplitFrame;
 import jalview.io.DataSourceType;
 import jalview.io.StockholmFile;
+import jalview.util.FileUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 import jalview.ws.params.ArgumentI;
@@ -86,9 +87,9 @@ public class HMMAlign extends HmmerCommand
       Hashtable sequencesHash = stashSequences(seqs);
       try
       {
-        File modelFile = createTempFile("hmm", ".hmm");
-        File alignmentFile = createTempFile("output", ".sto");
-        File resultFile = createTempFile("input", ".sto");
+        File modelFile = FileUtils.createTempFile("hmm", ".hmm");
+        File alignmentFile = FileUtils.createTempFile("output", ".sto");
+        File resultFile = FileUtils.createTempFile("input", ".sto");
 
         exportStockholm(seqs, alignmentFile.getAbsoluteFile(), null);
         exportHmm(hmm, modelFile.getAbsoluteFile());