X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2FMCview%2FPDBChainTest.java;h=9255e5a85663f23a9e537ecd9fc1e73f179a7c17;hb=6d7ab37f37b09174ec61fee301aed6057ef86605;hp=0df78512c6a2bb978b2764d8e92b4d322c39dc2d;hpb=c93b9ad2ebfab4cad4608a8890132918589576be;p=jalview.git
diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index 0df7851..9255e5a 100644
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package MCview;
import static org.testng.AssertJUnit.assertEquals;
@@ -16,21 +36,29 @@ 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 +66,7 @@ public class PDBChainTest
assertEquals("gaga", c.getNewlineString());
}
- @Test
+ @Test(groups = { "Functional" })
public void testPrint()
{
c.offset = 7;
@@ -66,7 +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()
{
/*
@@ -101,7 +129,7 @@ public class PDBChainTest
assertEquals(3f, b2.end[2], 0.0001f);
}
- @Test
+ @Test(groups = { "Functional" })
public void testSetChainColours_colour()
{
c.makeBond(a1, a2);
@@ -118,7 +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);
@@ -146,7 +174,7 @@ public class PDBChainTest
assertEquals(Color.gray, b.endCol);
}
- @Test
+ @Test(groups = { "Functional" })
public void testGetChargeColour()
{
assertEquals(Color.red, PDBChain.getChargeColour("ASP"));
@@ -161,7 +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
@@ -190,7 +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 atoms = new Vector();
@@ -248,35 +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 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
@@ -299,7 +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;
@@ -330,7 +358,7 @@ public class PDBChainTest
assertTrue(c.isNa);
}
- @Test
+ @Test(groups = { "Functional" })
public void testMakeCaBondList_nucleotide()
{
c.isNa = false;
@@ -362,7 +390,7 @@ public class PDBChainTest
/**
* Test the method that updates atoms with their alignment positions
*/
- @Test
+ @Test(groups = { "Functional" })
public void testMakeExactMapping()
{
Vector atoms = new Vector();