JAL-2937 working Cygwin bash execution of hmmbuild on Windows

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

diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
index 163e85b..6300c4b 100644 (file)
--- a/src/jalview/hmmer/HMMAlign.java
+++ b/src/jalview/hmmer/HMMAlign.java
@@ -157,9 +157,9 @@ public class HMMAlign extends HmmerCommand
       }
     }
     args.add("-o");
-    args.add(resultFile.getAbsolutePath());
-    args.add(modelFile.getAbsolutePath());
-    args.add(alignmentFile.getAbsolutePath());
+    args.add(getFilePath(resultFile));
+    args.add(getFilePath(modelFile));
+    args.add(getFilePath(alignmentFile));
     
     return runCommand(args);
   }
@@ -177,7 +177,7 @@ public class HMMAlign extends HmmerCommand
   private SequenceI[] importData(File resultFile,
           List<AlignmentOrder> allOrders) throws IOException
   {
-    StockholmFile file = new StockholmFile(resultFile.getAbsolutePath(),
+    StockholmFile file = new StockholmFile(getFilePath(resultFile),
             DataSourceType.FILE);
     SequenceI[] result = file.getSeqsAsArray();
     AlignmentOrder msaorder = new AlignmentOrder(result);