From 549cdd8bcac48cade7880c4a800d9c90b4d02632 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 12 Mar 2019 09:04:21 +0000
Subject: [PATCH] JAL-1270 missing 'alwaysRun=true' added to setup/teardown

---
 test/jalview/analysis/CrossRefTest.java         |    2 +-
 test/jalview/datamodel/AllColsIteratorTest.java |    4 ++--
 test/jalview/datamodel/AllRowsIteratorTest.java |    2 +-
 test/jalview/gui/ColourMenuHelperTest.java      |   10 +++++-----
 test/jalview/io/vcf/VCFLoaderTest.java          |    2 +-
 5 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index b3c78be..81ec443 100644
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -454,7 +454,7 @@ public class CrossRefTest
     assertSame(pep2, xrefs.getSequenceAt(1));
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceFetcherFactory.setSequenceFetcher(null);
diff --git a/test/jalview/datamodel/AllColsIteratorTest.java b/test/jalview/datamodel/AllColsIteratorTest.java
index 3942f0b..0dfcc21 100644
--- a/test/jalview/datamodel/AllColsIteratorTest.java
+++ b/test/jalview/datamodel/AllColsIteratorTest.java
@@ -31,11 +31,11 @@ public class AllColsIteratorTest
 {
   HiddenColumns hiddenCols;
   
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setup()
   {
     hiddenCols = new HiddenColumns();
-   hiddenCols.hideColumns(2,4);
+    hiddenCols.hideColumns(2, 4);
   }
   
 
diff --git a/test/jalview/datamodel/AllRowsIteratorTest.java b/test/jalview/datamodel/AllRowsIteratorTest.java
index aeff71d..90ed891 100644
--- a/test/jalview/datamodel/AllRowsIteratorTest.java
+++ b/test/jalview/datamodel/AllRowsIteratorTest.java
@@ -36,7 +36,7 @@ public class AllRowsIteratorTest
 
   Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<>();
 
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setup()
   {
     // create random alignment
diff --git a/test/jalview/gui/ColourMenuHelperTest.java b/test/jalview/gui/ColourMenuHelperTest.java
index 9d4ed6c..e685155 100644
--- a/test/jalview/gui/ColourMenuHelperTest.java
+++ b/test/jalview/gui/ColourMenuHelperTest.java
@@ -34,13 +34,13 @@ public class ColourMenuHelperTest
   /**
    * Use a properties file with a user-defined colour scheme
    */
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testAddMenuItems_peptide()
   {
     SequenceI s1 = new Sequence("s1", "KFRQSILM");
@@ -105,7 +105,7 @@ public class ColourMenuHelperTest
     assertFalse(bgElements.hasMoreElements());
   }
 
-  @Test
+  @Test(groups = "Functional")
   public void testAddMenuItems_nucleotide()
   {
     SequenceI s1 = new Sequence("s1", "GAATAATCCATAACAG");
@@ -182,7 +182,7 @@ public class ColourMenuHelperTest
    * <li>only simple colour schemes (colour per residue)</li>
    * </ul>
    */
-  @Test
+  @Test(groups = "Functional")
   public void testAddMenuItems_simpleOnly()
   {
     SequenceI s1 = new Sequence("s1", "KFRQSILM");
@@ -220,7 +220,7 @@ public class ColourMenuHelperTest
   /*
    * menu for AlignFrame includes 'User Defined Colour'
    */
-  @Test
+  @Test(groups = "Functional")
   public void testAddMenuItems_forAlignFrame()
   {
     SequenceI s1 = new Sequence("s1", "KFRQSILM");
diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index 58c73dd..9e0efe6 100644
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -66,7 +66,7 @@ public class VCFLoaderTest
       // insertion G/GA is transferred to nucleotide but not to peptide
       "17\t45051613\t.\tG\tGA,C\t1666.64\tRF\tAC=15;AF=3.0e-03,2.0e-03" };
 
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     /*
-- 
1.7.10.2