JAL-2629 add checks for executing hmmer commands as .exe

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

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index 5d55f84..ed074a8 100644 (file)
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -149,10 +149,16 @@ public class HMMBuildThread implements Runnable
   
   private boolean runCommand() throws IOException, InterruptedException
   {
-    File file = new File(cmds.HMMERFOLDER + "/binaries/hmmbuild");
+    File file = new File(cmds.HMMERFOLDER + "/hmmbuild");
     if (!file.canExecute())
     {
-      return false;
+      file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe");
+      {
+        if (!file.canExecute())
+        {
+          return false;
+        }
+      }
     }
     String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME;
     if (forGroup)