X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2FMCview%2FPDBChainTest.java;h=907c50020b029ffa445e258c3565e9826c1e718a;hb=52288466dd1e71946a06fd1e6ea15fa8e652c693;hp=5be43b3808de2070fc37cc36541839fe18cc9949;hpb=c777b335d0332979123446f431b7f0c160eb4880;p=jalview.git diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java index 5be43b3..907c500 100644 --- a/test/MCview/PDBChainTest.java +++ b/test/MCview/PDBChainTest.java @@ -1,14 +1,9 @@ package MCview; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertSame; -import static org.junit.Assert.assertTrue; - -import java.awt.Color; -import java.util.Vector; - -import org.junit.Test; +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 jalview.analysis.AlignSeq; import jalview.datamodel.AlignmentAnnotation; @@ -18,18 +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); - @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()); @@ -37,7 +46,7 @@ public class PDBChainTest assertEquals("gaga", c.getNewlineString()); } - @Test + @Test(groups = { "Functional" }) public void testPrint() { c.offset = 7; @@ -65,7 +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() { /* @@ -100,7 +109,7 @@ public class PDBChainTest assertEquals(3f, b2.end[2], 0.0001f); } - @Test + @Test(groups = { "Functional" }) public void testSetChainColours_colour() { c.makeBond(a1, a2); @@ -117,7 +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); @@ -145,7 +154,7 @@ public class PDBChainTest assertEquals(Color.gray, b.endCol); } - @Test + @Test(groups = { "Functional" }) public void testGetChargeColour() { assertEquals(Color.red, PDBChain.getChargeColour("ASP")); @@ -160,7 +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 @@ -189,7 +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 atoms = new Vector(); @@ -247,35 +256,35 @@ 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 atoms = new Vector(); 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 @@ -298,7 +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; @@ -329,7 +338,7 @@ public class PDBChainTest assertTrue(c.isNa); } - @Test + @Test(groups = { "Functional" }) public void testMakeCaBondList_nucleotide() { c.isNa = false; @@ -361,7 +370,7 @@ public class PDBChainTest /** * Test the method that updates atoms with their alignment positions */ - @Test + @Test(groups = { "Functional" }) public void testMakeExactMapping() { Vector atoms = new Vector();