JAL-2937 Cygwin path preference, method refactoring

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 30299e9..6f73f2f 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -11,6 +11,7 @@ import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StockholmFile;
+import jalview.util.FileUtils;
 import jalview.util.MessageManager;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.simple.BooleanOption;
@@ -71,9 +72,11 @@ public class HMMSearch extends HmmerCommand
 
     try
     {
-      File hmmFile = createTempFile("hmm", ".hmm");
-      File hitsAlignmentFile = createTempFile("hitAlignment", ".sto");
-      File searchOutputFile = createTempFile("searchOutput", ".sto");
+      File hmmFile = FileUtils.createTempFile("hmm", ".hmm");
+      File hitsAlignmentFile = FileUtils.createTempFile("hitAlignment",
+              ".sto");
+      File searchOutputFile = FileUtils.createTempFile("searchOutput",
+              ".sto");
 
       exportHmm(hmm, hmmFile.getAbsoluteFile());
 
@@ -196,7 +199,7 @@ public class HMMSearch extends HmmerCommand
        * no external database specified for search, so
        * export current alignment as 'database' to search
        */
-      databaseFile = createTempFile("database", ".sto");
+      databaseFile = FileUtils.createTempFile("database", ".sto");
       AlignmentI al = af.getViewport().getAlignment();
       AlignmentI copy = new Alignment(al);
       SequenceI hmms = copy.getHmmConsensus();