JAL-1769 fixed headless execution mode and created test for all possible outputs

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index f4b38d4..f6d0099 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -225,10 +225,13 @@ public class Jalview
       desktop.checkForNews();
     }
 
-    BioJsHTMLOutput.updateBioJS();
+    if (!isHeadlessMode())
+    {
+      BioJsHTMLOutput.updateBioJS();
+    }
 
     String file = null, protocol = null, format = null, data = null;
-    jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
+    jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless);
     Vector getFeatures = null; // vector of das source nicknames to fetch
     // features from
     // loading is done.
@@ -518,8 +521,10 @@ public class Jalview
           }
           else if (format.equalsIgnoreCase("eps"))
           {
-            System.out.println("Creating EPS file: " + file);
-            af.createEPS(new java.io.File(file));
+            File outputFile = new java.io.File(file);
+            System.out.println("Creating EPS file: "
+                    + outputFile.getAbsolutePath());
+            af.createEPS(outputFile);
             continue;
           }