X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=adc24dbc6cef060af67acbaaffe2894860c90958;hb=28fda83cbef0c9c82cd09a343af4e1721085c104;hp=8bd484a24dcfd07c854ca76a536b9949ac4bbffd;hpb=4de381907ba9fbd6b079aaf5f1d089680f0d9c6f;p=jalview.git

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 8bd484a..adc24db 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -109,7 +109,6 @@ public class CommandLineOperations
     {
       BufferedReader outputReader = new BufferedReader(
               new InputStreamReader(ls2_proc.getInputStream()));
-
       BufferedReader errorReader = new BufferedReader(
               new InputStreamReader(ls2_proc.getErrorStream()));
       worker = new Worker(ls2_proc);
@@ -127,20 +126,20 @@ public class CommandLineOperations
     return worker;
   }
 
-  @BeforeTest
+  @BeforeTest(alwaysRun = true)
   public void initialize()
   {
     new CommandLineOperations();
   }
 
   
-  @BeforeTest
+  @BeforeTest(alwaysRun = true)
   public void setUpForHeadlessCommandLineInputOperations()
           throws IOException
   {
     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
-            + "-features examples/uniref50_test_features -annotations examples/uniref50_test_annot -tree examples/uniref50_test_tree";
+            + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
     Worker worker = jalviewDesktopRunner(true, cmds, 9000);
     String ln = null;
     while ((ln = worker.getOutputReader().readLine()) != null)
@@ -150,7 +149,7 @@ public class CommandLineOperations
     }
   }
 
-  @BeforeTest
+  @BeforeTest(alwaysRun = true)
   public void setUpForCommandLineInputOperations() throws IOException
   {
     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
@@ -232,13 +231,14 @@ public class CommandLineOperations
         { "CMD [-dasserver nickname=www.test.com] executed successfully!",
             "Failed command : -dasserver nickname=www.test.com" },
         {
-            "CMD [-features examples/uniref50_test_features]  executed successfully!",
-            "Failed command : -features examples/uniref50_test_features" },
+            "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
+            "Failed command : -features examples/testdata/plantfdx.features" },
+        {
+            "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
+            "Failed command : -annotations examples/testdata/plantfdx.annotations" },
         {
-            "CMD [-annotations examples/uniref50_test_annot] executed successfully!",
-            "Failed command : -annotations examples/uniref50_test_annot" },
-        { "CMD [-tree examples/uniref50_test_tree] executed successfully!",
-            "Failed command : -tree examples/uniref50_test_tree" },
+            "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
+            "Failed command : -tree examples/testdata/uniref50_test_tree" },
         // non headless mode input operations
         { "CMD [-nousagestats] executed successfully!",
             "Failed command : -nousagestats" },