JAL-3285 fix incorrect file paths on HMMAlign/Search results

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

diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
index b5f047e..57e35e7 100644 (file)
--- a/src/jalview/hmmer/HMMAlign.java
+++ b/src/jalview/hmmer/HMMAlign.java
@@ -152,9 +152,9 @@ public class HMMAlign extends HmmerCommand
       }
     }
     args.add("-o");
-    args.add(getFilePath(resultFile));
-    args.add(getFilePath(modelFile));
-    args.add(getFilePath(alignmentFile));
+    args.add(getFilePath(resultFile, true));
+    args.add(getFilePath(modelFile, true));
+    args.add(getFilePath(alignmentFile, true));
     
     return runCommand(args);
   }
@@ -172,7 +172,7 @@ public class HMMAlign extends HmmerCommand
   private SequenceI[] importData(File resultFile,
           List<AlignmentOrder> allOrders) throws IOException
   {
-    StockholmFile file = new StockholmFile(getFilePath(resultFile),
+    StockholmFile file = new StockholmFile(getFilePath(resultFile, false),
             DataSourceType.FILE);
     SequenceI[] result = file.getSeqsAsArray();
     AlignmentOrder msaorder = new AlignmentOrder(result);