JAL-2629 fix file loading issues on Mac

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

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index 853b5f1..5d55f84 100644 (file)
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -10,6 +10,7 @@ import jalview.gui.JvOptionPane;
 import jalview.gui.Preferences;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
+import jalview.io.FileLoader;
 import jalview.util.MessageManager;
 
 import java.io.File;
@@ -148,7 +149,7 @@ public class HMMBuildThread implements Runnable
   
   private boolean runCommand() throws IOException, InterruptedException
   {
-    File file = new File(cmds.HMMERFOLDER + "/binaries/hmmbuild.exe");
+    File file = new File(cmds.HMMERFOLDER + "/binaries/hmmbuild");
     if (!file.canExecute())
     {
       return false;
@@ -185,8 +186,10 @@ public class HMMBuildThread implements Runnable
   private void importData() throws IOException, InterruptedException
   {
     cmds.addHMMConsensusSequences(af);
-    af.loadJalviewDataFile(hmmTemp.getAbsolutePath(), DataSourceType.FILE,
-            FileFormat.HMMER3, null);
+    FileLoader loader = new FileLoader();
+    loader.LoadFileOntoAlignmentWaitTillLoaded(af.getViewport(),
+            hmmTemp.getAbsolutePath(), DataSourceType.FILE,
+            FileFormat.HMMER3);
     hmmTemp.delete();
     stoTemp.delete();
   }