JAL-1805 modified test setup's so the are ran for groups which requires them

[jalview.git] / test / MCview / PDBChainTest.java

diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index 0df7851..fda4e1b 100644 (file)
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.java
@@ -16,21 +16,29 @@ 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");
+  PDBChain c;
 
-  Atom a1 = new Atom(1f, 2f, 3f);
+  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);
 
-  @Test
+ @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    System.out.println("setup");
+    c = new PDBChain("1GAQ", "A");
+  }
+
+  @Test(groups ={ "Functional" })
   public void testGetNewlineString()
   {
     assertEquals(System.lineSeparator(), c.getNewlineString());
@@ -38,7 +46,7 @@ public class PDBChainTest
     assertEquals("gaga", c.getNewlineString());
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testPrint()
   {
     c.offset = 7;
@@ -66,7 +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()
   {
     /*
@@ -101,7 +109,7 @@ public class PDBChainTest
     assertEquals(3f, b2.end[2], 0.0001f);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSetChainColours_colour()
   {
     c.makeBond(a1, a2);
@@ -118,7 +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);
@@ -146,7 +154,7 @@ public class PDBChainTest
     assertEquals(Color.gray, b.endCol);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetChargeColour()
   {
     assertEquals(Color.red, PDBChain.getChargeColour("ASP"));
@@ -161,7 +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
@@ -190,7 +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>();
@@ -248,7 +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>();
@@ -299,7 +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;
@@ -330,7 +338,7 @@ public class PDBChainTest
     assertTrue(c.isNa);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeCaBondList_nucleotide()
   {
     c.isNa = false;
@@ -362,7 +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>();