From bc12a8c2d3727216f12bbf9ffd49cd137d19ad9a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 25 Mar 2015 14:06:58 +0000
Subject: [PATCH] JAL-1270 System.exit(0) changed to fail() so as not to abort
 test suite

---
 .../ws/jabaws/JpredJabaStructExportImport.java     |   25 ++++++++++----------
 test/jalview/ws/jabaws/RNAStructExportImport.java  |   23 +++++++++---------
 2 files changed, 25 insertions(+), 23 deletions(-)

diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
index cf98e33..c522bc3 100644
--- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@ -23,17 +23,6 @@ package jalview.ws.jabaws;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
-import jalview.datamodel.AlignmentI;
-import jalview.gui.Jalview2XML;
-import jalview.io.AnnotationFile;
-import jalview.io.FormatAdapter;
-import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.JPred301Client;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Component;
 import java.util.ArrayList;
@@ -49,6 +38,18 @@ import org.junit.Test;
 import compbio.metadata.Argument;
 import compbio.metadata.WrongParameterException;
 
+import jalview.datamodel.AlignmentI;
+import jalview.gui.Jalview2XML;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.JPred301Client;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.SequenceAnnotationWSClient;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
 public class JpredJabaStructExportImport
 {
   public static String testseqs = "examples/uniref50.fa";
@@ -81,7 +82,7 @@ public class JpredJabaStructExportImport
 
     if (jpredws == null)
     {
-      System.exit(0);
+      fail("jpredws is null");
     }
 
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index c052b0b..7046b55 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -23,16 +23,6 @@ package jalview.ws.jabaws;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
-import jalview.datamodel.AlignmentI;
-import jalview.gui.Jalview2XML;
-import jalview.io.AnnotationFile;
-import jalview.io.FormatAdapter;
-import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.RNAalifoldClient;
-import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Component;
 import java.util.ArrayList;
@@ -47,6 +37,17 @@ import org.junit.Test;
 
 import compbio.metadata.WrongParameterException;
 
+import jalview.datamodel.AlignmentI;
+import jalview.gui.Jalview2XML;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.RNAalifoldClient;
+import jalview.ws.jws2.SequenceAnnotationWSClient;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
 public class RNAStructExportImport
 {
   public static String testseqs = "examples/unfolded_RF00031.aln";
@@ -79,7 +80,7 @@ public class RNAStructExportImport
 
     if (rnaalifoldws == null)
     {
-      System.exit(0);
+      fail("rnaalifoldws is null");
     }
 
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
-- 
1.7.10.2