X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMAlign.java;h=6300c4bd060b26b06d2fe44024c32c51acb72ffd;hb=ff638b98db095ffd7dc792f5d91fe5a0de6fc2ba;hp=163e85bffed429737c65f8e99b838ef01c49a6f8;hpb=37f0332f53a8564ba7a9d55b993f8bfd2f368c80;p=jalview.git

diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
index 163e85b..6300c4b 100644
--- 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);