+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package MCview;
import static org.testng.AssertJUnit.assertEquals;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.TaylorColourScheme;
+import jalview.structure.StructureImportSettings;
import java.awt.Color;
+import java.util.List;
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PDBChainTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
PDBChain c;
final Atom a1 = new Atom(1f, 2f, 3f);
final Atom a4 = new Atom(2f, 1f, 7f);
- @BeforeMethod
+ @BeforeMethod(alwaysRun = true)
public void setUp()
{
System.out.println("setup");
+ StructureImportSettings.setShowSeqFeatures(true);
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;
a3.resName = "ASP";
a3.resNumber = 41;
- Vector<Bond> v = new Vector<Bond>();
+ Vector<Bond> v = new Vector<>();
v.add(new Bond(a1, a2));
v.add(new Bond(a2, a3));
v.add(new Bond(a3, a1));
* 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>();
+ Vector<Atom> atoms = new Vector<>();
c.atoms = atoms;
c.isNa = true;
atoms.add(makeAtom(4, "N", "MET"));
/*
* check sequence features
*/
- SequenceFeature[] sfs = c.sequence.getSequenceFeatures();
- assertEquals(3, sfs.length);
- assertEquals("RESNUM", sfs[0].type);
- assertEquals("MET:4 1gaqA", sfs[0].description);
- assertEquals(4, sfs[0].begin);
- assertEquals(4, sfs[0].end);
- assertEquals("RESNUM", sfs[0].type);
- assertEquals("LYS:5 1gaqA", sfs[1].description);
- assertEquals(5, sfs[1].begin);
- assertEquals(5, sfs[1].end);
- assertEquals("LEU:6 1gaqA", sfs[2].description);
- assertEquals(6, sfs[2].begin);
- assertEquals(6, sfs[2].end);
+ List<SequenceFeature> sfs = c.sequence.getSequenceFeatures();
+ assertEquals(3, sfs.size());
+ assertEquals("RESNUM", sfs.get(0).type);
+ assertEquals("MET:4 1gaqA", sfs.get(0).description);
+ assertEquals(4, sfs.get(0).begin);
+ assertEquals(4, sfs.get(0).end);
+ assertEquals("RESNUM", sfs.get(0).type);
+ assertEquals("LYS:5 1gaqA", sfs.get(1).description);
+ assertEquals(5, sfs.get(1).begin);
+ assertEquals(5, sfs.get(1).end);
+ assertEquals("LEU:6 1gaqA", sfs.get(2).description);
+ assertEquals(6, sfs.get(2).begin);
+ assertEquals(6, sfs.get(2).end);
}
private Atom makeAtom(int resnum, String name, String resname)
* 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>();
+ Vector<Atom> 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
+ * each residue i.e. we expect values 1, 7, -4 for the residues
*/
AlignmentAnnotation[] ann = c.sequence.getAnnotation();
assertEquals(1, ann.length);
assertEquals("Temperature Factor for 1gaqA", ann[0].description);
assertSame(c.sequence, ann[0].sequenceRef);
assertEquals(AlignmentAnnotation.LINE_GRAPH, ann[0].graph);
- assertEquals(0f, ann[0].graphMin, 0.001f);
+ assertEquals(-4f, ann[0].graphMin, 0.001f);
assertEquals(7f, ann[0].graphMax, 0.001f);
assertEquals(3, ann[0].annotations.length);
assertEquals(1f, ann[0].annotations[0].value, 0.001f);
assertEquals(7f, ann[0].annotations[1].value, 0.001f);
- assertEquals(4f, ann[0].annotations[2].value, 0.001f);
+ assertEquals(-4f, ann[0].annotations[2].value, 0.001f);
}
/**
* Test the method that constructs bonds between successive residues' CA or P
* atoms
*/
- @Test
+ @Test(groups = { "Functional" })
public void testMakeCaBondList()
{
c.isNa = true;
- Vector<Atom> atoms = new Vector<Atom>();
+ Vector<Atom> atoms = new Vector<>();
c.atoms = atoms;
atoms.add(makeAtom(4, "N", "MET"));
atoms.add(makeAtom(4, "CA", "MET"));
assertTrue(c.isNa);
}
- @Test
+ @Test(groups = { "Functional" })
public void testMakeCaBondList_nucleotide()
{
c.isNa = false;
- Vector<Atom> atoms = new Vector<Atom>();
+ Vector<Atom> atoms = new Vector<>();
c.atoms = atoms;
atoms.add(makeAtom(4, "N", "G"));
atoms.add(makeAtom(4, "P", "G"));
/**
* Test the method that updates atoms with their alignment positions
*/
- @Test
+ @Test(groups = { "Functional" })
public void testMakeExactMapping()
{
- Vector<Atom> atoms = new Vector<Atom>();
+ Vector<Atom> atoms = new Vector<>();
c.atoms = atoms;
atoms.add(makeAtom(4, "N", "MET"));
atoms.add(makeAtom(4, "CA", "MET"));
git://source.jalview.org / jalview.git / blobdiff