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  1. Project Clover database Tue Mar 10 2026 14:58:44 GMT
  2. Package mc_view

File PDBChainTest.java

 

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PDBChainTest 46 228 15
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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package mc_view;
22   
23    import static org.testng.AssertJUnit.assertEquals;
24    import static org.testng.AssertJUnit.assertFalse;
25    import static org.testng.AssertJUnit.assertSame;
26    import static org.testng.AssertJUnit.assertTrue;
27   
28    import jalview.analysis.AlignSeq;
29    import jalview.datamodel.AlignmentAnnotation;
30    import jalview.datamodel.Sequence;
31    import jalview.datamodel.SequenceFeature;
32    import jalview.datamodel.SequenceI;
33    import jalview.gui.JvOptionPane;
34    import jalview.schemes.ColourSchemeI;
35    import jalview.schemes.TaylorColourScheme;
36    import jalview.structure.StructureImportSettings;
37   
38    import java.awt.Color;
39    import java.util.List;
40    import java.util.Vector;
41   
42    import org.testng.annotations.BeforeClass;
43    import org.testng.annotations.BeforeMethod;
44    import org.testng.annotations.Test;
45   
 
46    public class PDBChainTest
47    {
48   
 
49  0 toggle @BeforeClass(alwaysRun = true)
50    public void setUpJvOptionPane()
51    {
52  0 JvOptionPane.setInteractiveMode(false);
53  0 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
54    }
55   
56    PDBChain c;
57   
58    final Atom a1 = new Atom(1f, 2f, 3f);
59   
60    final Atom a2 = new Atom(5f, 6f, 4f);
61   
62    final Atom a3 = new Atom(2f, 5f, 6f);
63   
64    final Atom a4 = new Atom(2f, 1f, 7f);
65   
 
66  0 toggle @BeforeMethod(alwaysRun = true)
67    public void setUp()
68    {
69  0 System.out.println("setup");
70  0 StructureImportSettings.setShowSeqFeatures(true);
71  0 c = new PDBChain("1GAQ", "A");
72    }
73   
 
74  0 toggle @Test(groups = { "Functional" })
75    public void testGetNewlineString()
76    {
77  0 assertEquals(System.lineSeparator(), c.getNewlineString());
78  0 c.setNewlineString("gaga");
79  0 assertEquals("gaga", c.getNewlineString());
80    }
81   
 
82  0 toggle @Test(groups = { "Functional" })
83    public void testPrint()
84    {
85  0 c.offset = 7;
86   
87  0 a1.resName = "GLY";
88  0 a1.resNumber = 23;
89  0 a2.resName = "GLU";
90  0 a2.resNumber = 34;
91  0 a3.resName = "ASP";
92  0 a3.resNumber = 41;
93   
94  0 Vector<Bond> v = new Vector<>();
95  0 v.add(new Bond(a1, a2));
96  0 v.add(new Bond(a2, a3));
97  0 v.add(new Bond(a3, a1));
98  0 c.bonds = v;
99   
100  0 String printed = c.print();
101  0 String nl = System.lineSeparator();
102  0 assertEquals("GLY 23 7" + nl + "GLU 34 7" + nl + "ASP 41 7" + nl,
103    printed);
104    }
105   
106    /**
107    * Test the method that constructs a Bond between two atoms and adds it to the
108    * chain's list of bonds
109    */
 
110  0 toggle @Test(groups = { "Functional" })
111    public void testMakeBond()
112    {
113    /*
114    * Add a bond from a1 to a2
115    */
116  0 c.makeBond(a1, a2);
117  0 assertEquals(1, c.bonds.size());
118  0 Bond b1 = c.bonds.get(0);
119  0 assertSame(a1, b1.at1);
120  0 assertSame(a2, b1.at2);
121  0 assertEquals(1f, b1.start[0], 0.0001f);
122  0 assertEquals(2f, b1.start[1], 0.0001f);
123  0 assertEquals(3f, b1.start[2], 0.0001f);
124  0 assertEquals(5f, b1.end[0], 0.0001f);
125  0 assertEquals(6f, b1.end[1], 0.0001f);
126  0 assertEquals(4f, b1.end[2], 0.0001f);
127   
128    /*
129    * Add another bond from a2 to a1
130    */
131  0 c.makeBond(a2, a1);
132  0 assertEquals(2, c.bonds.size());
133  0 assertSame(b1, c.bonds.get(0));
134  0 Bond b2 = c.bonds.get(1);
135  0 assertSame(a2, b2.at1);
136  0 assertSame(a1, b2.at2);
137  0 assertEquals(5f, b2.start[0], 0.0001f);
138  0 assertEquals(6f, b2.start[1], 0.0001f);
139  0 assertEquals(4f, b2.start[2], 0.0001f);
140  0 assertEquals(1f, b2.end[0], 0.0001f);
141  0 assertEquals(2f, b2.end[1], 0.0001f);
142  0 assertEquals(3f, b2.end[2], 0.0001f);
143    }
144   
 
145  0 toggle @Test(groups = { "Functional" })
146    public void testSetChainColours_colour()
147    {
148  0 c.makeBond(a1, a2);
149  0 c.makeBond(a2, a3);
150  0 c.setChainColours(Color.PINK);
151  0 assertEquals(2, c.bonds.size());
152  0 assertEquals(Color.PINK, c.bonds.get(0).startCol);
153  0 assertEquals(Color.PINK, c.bonds.get(0).endCol);
154  0 assertEquals(Color.PINK, c.bonds.get(1).startCol);
155  0 assertEquals(Color.PINK, c.bonds.get(1).endCol);
156    }
157   
158    /**
159    * Test setting bond start/end colours based on a colour scheme i.e. colour by
160    * residue
161    */
 
162  0 toggle @Test(groups = { "Functional" })
163    public void testSetChainColours_colourScheme()
164    {
165  0 Color alaColour = new Color(204, 255, 0);
166  0 Color glyColour = new Color(255, 153, 0);
167  0 a1.resName = "ALA";
168  0 a2.resName = "GLY";
169  0 a3.resName = "XXX"; // no colour defined
170  0 c.makeBond(a1, a2);
171  0 c.makeBond(a2, a1);
172  0 c.makeBond(a2, a3);
173  0 ColourSchemeI cs = new TaylorColourScheme();
174  0 c.setChainColours(cs);
175    // bond a1 to a2
176  0 Bond b = c.bonds.get(0);
177  0 assertEquals(alaColour, b.startCol);
178  0 assertEquals(glyColour, b.endCol);
179    // bond a2 to a1
180  0 b = c.bonds.get(1);
181  0 assertEquals(glyColour, b.startCol);
182  0 assertEquals(alaColour, b.endCol);
183    // bond a2 to a3 - no colour found for a3
184    // exception handling defaults to gray
185  0 b = c.bonds.get(2);
186  0 assertEquals(Color.gray, b.startCol);
187  0 assertEquals(Color.gray, b.endCol);
188    }
189   
 
190  0 toggle @Test(groups = { "Functional" })
191    public void testGetChargeColour()
192    {
193  0 assertEquals(Color.red, PDBChain.getChargeColour("ASP"));
194  0 assertEquals(Color.red, PDBChain.getChargeColour("GLU"));
195  0 assertEquals(Color.blue, PDBChain.getChargeColour("LYS"));
196  0 assertEquals(Color.blue, PDBChain.getChargeColour("ARG"));
197  0 assertEquals(Color.yellow, PDBChain.getChargeColour("CYS"));
198  0 assertEquals(Color.lightGray, PDBChain.getChargeColour("ALA"));
199  0 assertEquals(Color.lightGray, PDBChain.getChargeColour(null));
200    }
201   
202    /**
203    * Test the method that sets bond start/end colours by residue charge property
204    */
 
205  0 toggle @Test(groups = { "Functional" })
206    public void testSetChargeColours()
207    {
208  0 a1.resName = "ASP"; // red
209  0 a2.resName = "LYS"; // blue
210  0 a3.resName = "CYS"; // yellow
211  0 a4.resName = "ALA"; // no colour (light gray)
212  0 c.makeBond(a1, a2);
213  0 c.makeBond(a2, a3);
214  0 c.makeBond(a3, a4);
215  0 c.setChargeColours();
216  0 assertEquals(3, c.bonds.size());
217    // bond a1 to a2
218  0 Bond b = c.bonds.get(0);
219  0 assertEquals(Color.red, b.startCol);
220  0 assertEquals(Color.blue, b.endCol);
221    // bond a2 to a3
222  0 b = c.bonds.get(1);
223  0 assertEquals(Color.blue, b.startCol);
224  0 assertEquals(Color.yellow, b.endCol);
225    // bond a3 to a4
226  0 b = c.bonds.get(2);
227  0 assertEquals(Color.yellow, b.startCol);
228  0 assertEquals(Color.lightGray, b.endCol);
229    }
230   
231    /**
232    * Test the method that converts the raw list of atoms to a list of residues
233    */
 
234  0 toggle @Test(groups = { "Functional" })
235    public void testMakeResidueList_noAnnotation()
236    {
237  0 Vector<Atom> atoms = new Vector<>();
238  0 c.atoms = atoms;
239  0 c.isNa = true;
240  0 atoms.add(makeAtom(4, "N", "MET"));
241  0 atoms.add(makeAtom(4, "CA", "MET"));
242  0 atoms.add(makeAtom(4, "C", "MET"));
243  0 atoms.add(makeAtom(5, "O", "LYS"));
244  0 atoms.add(makeAtom(5, "N", "LYS"));
245  0 atoms.add(makeAtom(5, "CA", "LYS"));
246  0 atoms.add(makeAtom(6, "O", "LEU"));
247  0 atoms.add(makeAtom(6, "N", "LEU"));
248  0 atoms.add(makeAtom(6, "CA", "LEU"));
249   
250  0 c.makeResidueList(false);
251   
252    /*
253    * check sequence constructed
254    */
255  0 assertEquals("MKL", c.sequence.getSequenceAsString());
256  0 assertFalse(c.isNa);
257  0 assertEquals(3, c.residues.size());
258   
259    /*
260    * check sequence features
261    */
262  0 List<SequenceFeature> sfs = c.sequence.getSequenceFeatures();
263  0 assertEquals(3, sfs.size());
264  0 assertEquals("RESNUM", sfs.get(0).type);
265  0 assertEquals("MET:4 1gaqA", sfs.get(0).description);
266  0 assertEquals(4, sfs.get(0).begin);
267  0 assertEquals(4, sfs.get(0).end);
268  0 assertEquals("RESNUM", sfs.get(0).type);
269  0 assertEquals("LYS:5 1gaqA", sfs.get(1).description);
270  0 assertEquals(5, sfs.get(1).begin);
271  0 assertEquals(5, sfs.get(1).end);
272  0 assertEquals("LEU:6 1gaqA", sfs.get(2).description);
273  0 assertEquals(6, sfs.get(2).begin);
274  0 assertEquals(6, sfs.get(2).end);
275    }
276   
 
277  0 toggle private Atom makeAtom(int resnum, String name, String resname)
278    {
279  0 Atom a = new Atom(1f, 2f, 3f);
280  0 a.resNumber = resnum;
281  0 a.resNumIns = String.valueOf(resnum);
282  0 a.name = name;
283  0 a.resName = resname;
284  0 a.chain = "A";
285  0 return a;
286    }
287   
288    /**
289    * Test the method that converts the raw list of atoms to a list of residues,
290    * including parsing of tempFactor to an alignment annotation
291    */
 
292  0 toggle @Test(groups = { "Functional" })
293    public void testMakeResidueList_withTempFactor()
294    {
295  0 Vector<Atom> atoms = new Vector<>();
296  0 c.atoms = atoms;
297  0 atoms.add(makeAtom(4, "N", "MET"));
298  0 atoms.get(atoms.size() - 1).tfactor = 1f;
299  0 atoms.add(makeAtom(4, "CA", "MET"));
300  0 atoms.get(atoms.size() - 1).tfactor = 2f;
301  0 atoms.add(makeAtom(4, "C", "MET"));
302  0 atoms.get(atoms.size() - 1).tfactor = 3f;
303  0 atoms.add(makeAtom(5, "O", "LYS"));
304  0 atoms.get(atoms.size() - 1).tfactor = 7f;
305  0 atoms.add(makeAtom(5, "N", "LYS"));
306  0 atoms.get(atoms.size() - 1).tfactor = 8f;
307  0 atoms.add(makeAtom(5, "CA", "LYS"));
308  0 atoms.get(atoms.size() - 1).tfactor = 9f;
309  0 atoms.add(makeAtom(6, "O", "LEU"));
310  0 atoms.get(atoms.size() - 1).tfactor = -4f;
311  0 atoms.add(makeAtom(6, "N", "LEU"));
312  0 atoms.get(atoms.size() - 1).tfactor = 5f;
313  0 atoms.add(makeAtom(6, "CA", "LEU"));
314  0 atoms.get(atoms.size() - 1).tfactor = 6f;
315   
316    /*
317    * make residues including temp factor annotation
318    */
319  0 c.makeResidueList(true);
320   
321    /*
322    * Verify annotations; note the tempFactor is read from the first atom in
323    * each residue i.e. we expect values 1, 7, -4 for the residues
324    */
325  0 AlignmentAnnotation[] ann = c.sequence.getAnnotation();
326  0 assertEquals(1, ann.length);
327  0 assertEquals("Temperature Factor", ann[0].label);
328  0 assertEquals("Temperature Factor for 1gaqA", ann[0].description);
329  0 assertSame(c.sequence, ann[0].sequenceRef);
330  0 assertEquals(AlignmentAnnotation.LINE_GRAPH, ann[0].graph);
331  0 assertEquals(-4f, ann[0].graphMin, 0.001f);
332  0 assertEquals(7f, ann[0].graphMax, 0.001f);
333  0 assertEquals(3, ann[0].annotations.length);
334  0 assertEquals(1f, ann[0].annotations[0].value, 0.001f);
335  0 assertEquals(7f, ann[0].annotations[1].value, 0.001f);
336  0 assertEquals(-4f, ann[0].annotations[2].value, 0.001f);
337    }
338   
339    /**
340    * Test the method that constructs bonds between successive residues' CA or P
341    * atoms
342    */
 
343  0 toggle @Test(groups = { "Functional" })
344    public void testMakeCaBondList()
345    {
346  0 c.isNa = true;
347  0 Vector<Atom> atoms = new Vector<>();
348  0 c.atoms = atoms;
349  0 atoms.add(makeAtom(4, "N", "MET"));
350  0 atoms.add(makeAtom(4, "CA", "MET"));
351  0 atoms.add(makeAtom(5, "CA", "ASP"));
352  0 atoms.add(makeAtom(5, "O", "ASP"));
353  0 atoms.add(makeAtom(6, "CA", "GLY"));
354  0 atoms.add(makeAtom(6, "N", "GLY"));
355   
356    // have to make residue list first!
357  0 c.makeResidueList(false);
358  0 assertFalse(c.isNa);
359  0 c.isNa = true;
360   
361  0 c.makeCaBondList();
362  0 assertEquals(2, c.bonds.size());
363  0 Bond b = c.bonds.get(0);
364  0 assertSame(c.atoms.get(1), b.at1);
365  0 assertSame(c.atoms.get(2), b.at2);
366  0 b = c.bonds.get(1);
367  0 assertSame(c.atoms.get(2), b.at1);
368  0 assertSame(c.atoms.get(4), b.at2);
369   
370    // isNa flag is _not_ reset by this method!
371  0 assertTrue(c.isNa);
372    }
373   
 
374  0 toggle @Test(groups = { "Functional" })
375    public void testMakeCaBondList_nucleotide()
376    {
377  0 c.isNa = false;
378  0 Vector<Atom> atoms = new Vector<>();
379  0 c.atoms = atoms;
380  0 atoms.add(makeAtom(4, "N", "G"));
381  0 atoms.add(makeAtom(4, "P", "G"));
382  0 atoms.add(makeAtom(5, "P", "C"));
383  0 atoms.add(makeAtom(5, "O", "C"));
384  0 atoms.add(makeAtom(6, "P", "T"));
385  0 atoms.add(makeAtom(6, "N", "T"));
386   
387    // have to make residue list first!
388  0 c.makeResidueList(false);
389  0 assertEquals("GCT", c.sequence.getSequenceAsString());
390   
391  0 c.makeCaBondList();
392  0 assertEquals(2, c.bonds.size());
393  0 Bond b = c.bonds.get(0);
394  0 assertSame(c.atoms.get(1), b.at1);
395  0 assertSame(c.atoms.get(2), b.at2);
396  0 b = c.bonds.get(1);
397  0 assertSame(c.atoms.get(2), b.at1);
398  0 assertSame(c.atoms.get(4), b.at2);
399   
400  0 assertTrue(c.isNa);
401    }
402   
403    /**
404    * Test the method that updates atoms with their alignment positions
405    */
 
406  0 toggle @Test(groups = { "Functional" })
407    public void testMakeExactMapping()
408    {
409  0 Vector<Atom> atoms = new Vector<>();
410  0 c.atoms = atoms;
411  0 atoms.add(makeAtom(4, "N", "MET"));
412  0 atoms.add(makeAtom(4, "CA", "MET"));
413  0 atoms.add(makeAtom(5, "CA", "ASP"));
414  0 atoms.add(makeAtom(5, "O", "ASP"));
415  0 atoms.add(makeAtom(6, "CA", "GLY"));
416  0 atoms.add(makeAtom(6, "N", "GLY"));
417  0 c.makeResidueList(false);
418  0 assertEquals("MDG", c.sequence.getSequenceAsString());
419  0 SequenceI s1 = new Sequence("Seq1", "MDG");
420  0 SequenceI s2 = new Sequence("Seq2", "MDG");
421  0 AlignSeq alignSeq = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
422  0 SequenceI seq3 = new Sequence("Seq3", "--M-DG");
423  0 c.makeExactMapping(alignSeq, seq3);
424   
425  0 int pos = 0;
426  0 for (Residue res : c.residues)
427    {
428  0 for (Atom a : res.atoms)
429    {
430  0 assertEquals(pos, a.alignmentMapping);
431    }
432  0 pos++;
433    }
434    }
435    }
  • Report generated by OpenClover v 4.4.1 on Tue Mar 10 2026 14:59:17 GMT using coverage data from Thu Jan 1 1970 01:00:00 GMT.
  • OpenClover is free and open-source software.