JAL-2937 working Cygwin bash execution of hmmbuild on Windows

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 6f73f2f..b4e7427 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -125,9 +125,9 @@ public class HMMSearch extends HmmerCommand
     List<String> args = new ArrayList<>();
     args.add(command);
     args.add("-o");
-    args.add(searchOutputFile.getAbsolutePath());
+    args.add(getFilePath(searchOutputFile));
     args.add("-A");
-    args.add(hitsAlignmentFile.getAbsolutePath());
+    args.add(getFilePath(hitsAlignmentFile));
 
     boolean dbFound = false;
     String dbPath = "";
@@ -216,8 +216,8 @@ public class HMMSearch extends HmmerCommand
       // writer.close();
     }
 
-    args.add(hmmFile.getAbsolutePath());
-    args.add(databaseFile.getAbsolutePath());
+    args.add(getFilePath(hmmFile));
+    args.add(getFilePath(databaseFile));
 
     return runCommand(args);
   }
@@ -264,7 +264,7 @@ public class HMMSearch extends HmmerCommand
                 MessageManager.getString("label.trim_termini_desc"), true,
                 true, true, null));
       }
-      HMMAlign hmmalign = new HMMAlign(frame, alignArgs);
+      HmmerCommand hmmalign = new HMMAlign(frame, alignArgs);
       hmmalign.run();
       frame = null;
       hmmTemp.delete();