JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index 07f9bd5..159b206 100644 (file)
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package MCview;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -31,14 +51,14 @@ public class PDBChainTest
 
   final Atom a4 = new Atom(2f, 1f, 7f);
 
-  @BeforeMethod
+  @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());
@@ -46,7 +66,7 @@ public class PDBChainTest
     assertEquals("gaga", c.getNewlineString());
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testPrint()
   {
     c.offset = 7;
@@ -74,7 +94,7 @@ 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()
   {
     /*
@@ -109,7 +129,7 @@ public class PDBChainTest
     assertEquals(3f, b2.end[2], 0.0001f);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testSetChainColours_colour()
   {
     c.makeBond(a1, a2);
@@ -126,7 +146,7 @@ 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);
@@ -154,7 +174,7 @@ public class PDBChainTest
     assertEquals(Color.gray, b.endCol);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testGetChargeColour()
   {
     assertEquals(Color.red, PDBChain.getChargeColour("ASP"));
@@ -169,7 +189,7 @@ 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
@@ -198,7 +218,7 @@ 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>();
@@ -256,35 +276,35 @@ 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>();
     c.atoms = atoms;
     atoms.add(makeAtom(4, "N", "MET"));
-    atoms.get(atoms.size()-1).tfactor = 1f;
+    atoms.get(atoms.size() - 1).tfactor = 1f;
     atoms.add(makeAtom(4, "CA", "MET"));
-    atoms.get(atoms.size()-1).tfactor = 2f;
+    atoms.get(atoms.size() - 1).tfactor = 2f;
     atoms.add(makeAtom(4, "C", "MET"));
-    atoms.get(atoms.size()-1).tfactor = 3f;
+    atoms.get(atoms.size() - 1).tfactor = 3f;
     atoms.add(makeAtom(5, "O", "LYS"));
-    atoms.get(atoms.size()-1).tfactor = 7f;
+    atoms.get(atoms.size() - 1).tfactor = 7f;
     atoms.add(makeAtom(5, "N", "LYS"));
-    atoms.get(atoms.size()-1).tfactor = 8f;
+    atoms.get(atoms.size() - 1).tfactor = 8f;
     atoms.add(makeAtom(5, "CA", "LYS"));
-    atoms.get(atoms.size()-1).tfactor = 9f;
+    atoms.get(atoms.size() - 1).tfactor = 9f;
     atoms.add(makeAtom(6, "O", "LEU"));
-    atoms.get(atoms.size()-1).tfactor = 4f;
+    atoms.get(atoms.size() - 1).tfactor = 4f;
     atoms.add(makeAtom(6, "N", "LEU"));
-    atoms.get(atoms.size()-1).tfactor = 5f;
+    atoms.get(atoms.size() - 1).tfactor = 5f;
     atoms.add(makeAtom(6, "CA", "LEU"));
-    atoms.get(atoms.size()-1).tfactor = 6f;
-  
+    atoms.get(atoms.size() - 1).tfactor = 6f;
+
     /*
      * make residues including temp factor annotation
      */
     c.makeResidueList(true);
-    
+
     /*
      * Verify annotations; note the tempFactor is read from the first atom in
      * each residue i.e. we expect values 1, 7, 4 for the residues
@@ -307,7 +327,7 @@ 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;
@@ -338,7 +358,7 @@ public class PDBChainTest
     assertTrue(c.isNa);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testMakeCaBondList_nucleotide()
   {
     c.isNa = false;
@@ -370,7 +390,7 @@ 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>();