X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2FMCview%2FPDBChainTest.java;h=b84ca2848789b8e2e9508de862e838e4af6cb425;hb=06e3a52df5af8243cdb67c023c8ddd834711ad36;hp=193d294357b639417927e248147b98b9c14bfb86;hpb=3412b273e964fb1a9d22564b04a5f0c827ec2461;p=jalview.git

diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index 193d294..b84ca28 100644
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.java
@@ -1,12 +1,9 @@
 package MCview;
 
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import java.awt.Color;
-import java.util.Vector;
 
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
@@ -16,18 +13,32 @@ import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.TaylorColourScheme;
 
+import java.awt.Color;
+import java.util.Vector;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class PDBChainTest
 {
-  PDBChain c = new PDBChain("1GAQ", "A");
-  Atom a1 = new Atom(1f, 2f, 3f);
+  PDBChain c;
+
+  final Atom a1 = new Atom(1f, 2f, 3f);
 
-  Atom a2 = new Atom(5f, 6f, 4f);
+  final Atom a2 = new Atom(5f, 6f, 4f);
 
-  Atom a3 = new Atom(2f, 5f, 6f);
+  final Atom a3 = new Atom(2f, 5f, 6f);
 
-  Atom a4 = new Atom(2f, 1f, 7f);
+  final Atom a4 = new Atom(2f, 1f, 7f);
+
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    System.out.println("setup");
+    c = new PDBChain("1GAQ", "A");
+  }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetNewlineString()
   {
     assertEquals(System.lineSeparator(), c.getNewlineString());
@@ -35,7 +46,7 @@ public class PDBChainTest
     assertEquals("gaga", c.getNewlineString());
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testPrint()
   {
     c.offset = 7;
@@ -63,7 +74,7 @@ public class PDBChainTest
    * Test the method that constructs a Bond between two atoms and adds it to the
    * chain's list of bonds
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeBond()
   {
     /*
@@ -98,7 +109,7 @@ public class PDBChainTest
     assertEquals(3f, b2.end[2], 0.0001f);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSetChainColours_colour()
   {
     c.makeBond(a1, a2);
@@ -115,7 +126,7 @@ public class PDBChainTest
    * Test setting bond start/end colours based on a colour scheme i.e. colour by
    * residue
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSetChainColours_colourScheme()
   {
     Color alaColour = new Color(204, 255, 0);
@@ -143,7 +154,7 @@ public class PDBChainTest
     assertEquals(Color.gray, b.endCol);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetChargeColour()
   {
     assertEquals(Color.red, PDBChain.getChargeColour("ASP"));
@@ -158,7 +169,7 @@ public class PDBChainTest
   /**
    * Test the method that sets bond start/end colours by residue charge property
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSetChargeColours()
   {
     a1.resName = "ASP"; // red
@@ -187,7 +198,7 @@ public class PDBChainTest
   /**
    * Test the method that converts the raw list of atoms to a list of residues
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeResidueList_noAnnotation()
   {
     Vector<Atom> atoms = new Vector<Atom>();
@@ -245,7 +256,7 @@ public class PDBChainTest
    * Test the method that converts the raw list of atoms to a list of residues,
    * including parsing of tempFactor to an alignment annotation
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeResidueList_withTempFactor()
   {
     Vector<Atom> atoms = new Vector<Atom>();
@@ -296,7 +307,7 @@ public class PDBChainTest
    * Test the method that constructs bonds between successive residues' CA or P
    * atoms
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeCaBondList()
   {
     c.isNa = true;
@@ -327,7 +338,7 @@ public class PDBChainTest
     assertTrue(c.isNa);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeCaBondList_nucleotide()
   {
     c.isNa = false;
@@ -359,7 +370,7 @@ public class PDBChainTest
   /**
    * Test the method that updates atoms with their alignment positions
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeExactMapping()
   {
     Vector<Atom> atoms = new Vector<Atom>();