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;
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());
assertEquals("gaga", c.getNewlineString());
}
- @Test
+ @Test(groups ={ "Functional" })
public void testPrint()
{
c.offset = 7;
* 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()
{
/*
assertEquals(3f, b2.end[2], 0.0001f);
}
- @Test
+ @Test(groups ={ "Functional" })
public void testSetChainColours_colour()
{
c.makeBond(a1, a2);
* 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);
assertEquals(Color.gray, b.endCol);
}
- @Test
+ @Test(groups ={ "Functional" })
public void testGetChargeColour()
{
assertEquals(Color.red, PDBChain.getChargeColour("ASP"));
/**
* Test the method that sets bond start/end colours by residue charge property
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSetChargeColours()
{
a1.resName = "ASP"; // red
/**
* 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>();
* 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>();
* Test the method that constructs bonds between successive residues' CA or P
* atoms
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMakeCaBondList()
{
c.isNa = true;
assertTrue(c.isNa);
}
- @Test
+ @Test(groups ={ "Functional" })
public void testMakeCaBondList_nucleotide()
{
c.isNa = false;
/**
* Test the method that updates atoms with their alignment positions
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMakeExactMapping()
{
Vector<Atom> atoms = new Vector<Atom>();