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Coverage Report

  1. Project Clover database Mon Nov 18 2024 09:38:20 GMT
  2. Package jalview.datamodel

File AlignmentAnnotationTests.java

 

Code metrics

26
204
11
1
451
342
25
0.12
18.55
11
2.27

Classes

Class Line # Actions
AlignmentAnnotationTests 37 204 25
0.9336099693.4%
 

Contributing tests

This file is covered by 7 tests. .

Source view

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 jalview.datamodel;
22   
23    import static org.testng.Assert.assertFalse;
24    import static org.testng.Assert.assertNull;
25    import static org.testng.Assert.assertTrue;
26    import static org.testng.AssertJUnit.assertEquals;
27   
28    import jalview.analysis.AlignSeq;
29    import jalview.gui.JvOptionPane;
30    import jalview.io.AppletFormatAdapter;
31    import jalview.io.FileFormat;
32   
33    import org.testng.Assert;
34    import org.testng.annotations.BeforeClass;
35    import org.testng.annotations.Test;
36   
 
37    public class AlignmentAnnotationTests
38    {
39   
 
40  1 toggle @BeforeClass(alwaysRun = true)
41    public void setUpJvOptionPane()
42    {
43  1 JvOptionPane.setInteractiveMode(false);
44  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
45    }
46   
 
47  1 toggle @Test(groups = { "Functional" })
48    public void testCopyConstructor()
49    {
50  1 SequenceI sq = new Sequence("Foo", "ARAARARARAWEAWEAWRAWEAWE");
51  1 createAnnotation(sq);
52  1 AlignmentAnnotation alc, alo = sq.getAnnotation()[0];
53  1 alc = new AlignmentAnnotation(alo);
54  1 for (String key : alo.getProperties())
55    {
56  1 assertEquals("Property mismatch", alo.getProperty(key),
57    alc.getProperty(key));
58    }
59    }
60   
61    /**
62    * create some dummy annotation derived from the sequence
63    *
64    * @param sq
65    */
 
66  3 toggle public static void createAnnotation(SequenceI sq)
67    {
68  3 Annotation[] al = new Annotation[sq.getLength()];
69  41 for (int i = 0; i < al.length; i++)
70    {
71  38 al[i] = new Annotation(new Annotation("" + sq.getCharAt(i), "",
72    (char) 0, sq.findPosition(i)));
73    }
74  3 AlignmentAnnotation alan = new AlignmentAnnotation(
75    "For " + sq.getName(), "Fake alignment annot", al);
76    // create a sequence mapping for the annotation vector in its current state
77  3 alan.createSequenceMapping(sq, sq.getStart(), false);
78  3 alan.setProperty("CreatedBy", "createAnnotation");
79  3 sq.addAlignmentAnnotation(alan);
80    }
81   
82    /**
83    * use this to test annotation derived from method above as it is transferred
84    * across different sequences derived from same dataset coordinate frame
85    *
86    * @param ala
87    */
 
88  0 toggle public static void testAnnotTransfer(AlignmentAnnotation ala)
89    {
90  0 assertEquals(
91    "Failed - need annotation created by createAnnotation method",
92    ala.description, "Fake alignment annot");
93  0 ala.adjustForAlignment();
94  0 for (int p = 0; p < ala.annotations.length; p++)
95    {
96  0 if (ala.annotations[p] != null)
97    {
98  0 assertEquals(
99    "Mismatch at position " + p
100    + " between annotation position value and sequence"
101    + ala.annotations[p],
102    (int) ala.annotations[p].value,
103    ala.sequenceRef.findPosition(p));
104    }
105    }
106    }
107   
108    /**
109    * Tests the liftOver method and also exercises the functions for remapping
110    * annotation across different reference sequences. Here, the test is between
111    * different dataset frames (annotation transferred by mapping between
112    * sequences)
113    */
 
114  1 toggle @Test(groups = { "Functional" })
115    public void testLiftOver()
116    {
117  1 SequenceI sqFrom = new Sequence("fromLong", "QQQCDEWGH");
118  1 sqFrom.setStart(10);
119  1 sqFrom.setEnd(sqFrom.findPosition(sqFrom.getLength() - 1));
120  1 SequenceI sqTo = new Sequence("toShort", "RCDEW");
121  1 sqTo.setStart(20);
122  1 sqTo.setEnd(sqTo.findPosition(sqTo.getLength() - 1));
123  1 createAnnotation(sqTo);
124  1 AlignmentAnnotation origTo = sqTo.getAnnotation()[0];
125  1 createAnnotation(sqFrom);
126  1 AlignmentAnnotation origFrom = sqFrom.getAnnotation()[0];
127  1 AlignSeq align = AlignSeq.doGlobalNWAlignment(sqFrom, sqTo,
128    AlignSeq.PEP);
129  1 SequenceI alSeq1 = new Sequence(sqFrom.getName(), align.getAStr1());
130  1 alSeq1.setStart(sqFrom.getStart() + align.getSeq1Start() - 1);
131  1 alSeq1.setEnd(sqFrom.getStart() + align.getSeq1End() - 1);
132  1 alSeq1.setDatasetSequence(sqFrom);
133  1 SequenceI alSeq2 = new Sequence(sqTo.getName(), align.getAStr2());
134  1 alSeq2.setStart(sqTo.getStart() + align.getSeq2Start() - 1);
135  1 alSeq2.setEnd(sqTo.getStart() + align.getSeq2End() - 1);
136  1 alSeq2.setDatasetSequence(sqTo);
137  1 System.out.println(new AppletFormatAdapter().formatSequences(
138    FileFormat.Stockholm, new Alignment(new SequenceI[]
139    { sqFrom, alSeq1, sqTo, alSeq2 }), true));
140   
141  1 Mapping mp = align.getMappingFromS1(false);
142   
143  1 AlignmentAnnotation almap1 = new AlignmentAnnotation(
144    sqTo.getAnnotation()[0]);
145  1 almap1.liftOver(sqFrom, mp);
146  1 assertEquals(almap1.sequenceRef, sqFrom);
147  1 alSeq1.addAlignmentAnnotation(almap1);
148  1 almap1.setSequenceRef(alSeq1);
149  1 almap1.adjustForAlignment();
150  1 AlignmentAnnotation almap2 = new AlignmentAnnotation(
151    sqFrom.getAnnotation()[0]);
152  1 almap2.liftOver(sqTo, mp);
153  1 assertEquals(almap2.sequenceRef, sqTo);
154   
155  1 alSeq2.addAlignmentAnnotation(almap2);
156  1 almap2.setSequenceRef(alSeq2);
157  1 almap2.adjustForAlignment();
158   
159  1 AlignmentI all = new Alignment(new SequenceI[] { alSeq1, alSeq2 });
160  1 all.addAnnotation(almap1);
161  1 all.addAnnotation(almap2);
162  1 System.out.println(new AppletFormatAdapter()
163    .formatSequences(FileFormat.Stockholm, all, true));
164   
165  6 for (int p = 0; p < alSeq1.getLength(); p++)
166    {
167  5 Annotation orig1, trans1, orig2, trans2;
168  5 trans2 = almap2.annotations[p];
169  5 orig2 = origFrom.annotations[alSeq1.findPosition(p)
170    - sqFrom.getStart()];
171  5 orig1 = origTo.annotations[alSeq2.findPosition(p) - sqTo.getStart()];
172  5 trans1 = almap1.annotations[p];
173  5 if (trans1 == trans2)
174    {
175  1 System.out.println("Pos " + p + " mismatch");
176  1 continue;
177    }
178  4 assertEquals(
179    "Mismatch on Original From and transferred annotation on 2",
180  4 (orig2 != null) ? orig2.toString() : null,
181  4 (trans2 != null) ? trans2.toString() : null);
182  4 assertEquals(
183    "Mismatch on Original To and transferred annotation on 1",
184  4 (orig1 != null) ? orig1.toString() : null,
185  4 (trans1 != null) ? trans1.toString() : null);
186  4 String alm1 = "" + (almap1.annotations.length > p
187    ? almap1.annotations[p].displayCharacter
188    : "Out of range");
189  4 String alm2 = "" + (almap2.annotations.length > p
190    ? almap2.annotations[p].displayCharacter
191    : "Out of range");
192  4 assertEquals("Position " + p + " " + alm1 + " " + alm2, alm1, alm2);
193    }
194    }
195   
 
196  1 toggle @Test(groups = { "Functional" })
197    public void testAdjustForAlignment()
198    {
199  1 SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
200  1 seq.createDatasetSequence();
201   
202    /*
203    * Annotate positions 3/4/5 (CDE) with values 1/2/3
204    */
205  1 Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
206    new Annotation(2), new Annotation(3) };
207  1 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
208    "secondary structure", anns);
209  1 seq.addAlignmentAnnotation(ann);
210   
211    /*
212    * Check annotation map before modifying aligned sequence
213    */
214  1 assertNull(ann.getAnnotationForPosition(1));
215  1 assertNull(ann.getAnnotationForPosition(2));
216  1 assertNull(ann.getAnnotationForPosition(6));
217  1 assertNull(ann.getAnnotationForPosition(7));
218  1 assertEquals(1, ann.getAnnotationForPosition(3).value, 0.001d);
219  1 assertEquals(2, ann.getAnnotationForPosition(4).value, 0.001d);
220  1 assertEquals(3, ann.getAnnotationForPosition(5).value, 0.001d);
221   
222    /*
223    * Trim the displayed sequence to BCD and adjust annotations
224    */
225  1 seq.setSequence("BCD");
226  1 seq.setStart(2);
227  1 seq.setEnd(4);
228  1 ann.adjustForAlignment();
229   
230    /*
231    * Should now have annotations for aligned positions 2, 3Q (CD) only
232    */
233  1 assertEquals(3, ann.annotations.length);
234  1 assertNull(ann.annotations[0]);
235  1 assertEquals(1, ann.annotations[1].value, 0.001);
236  1 assertEquals(2, ann.annotations[2].value, 0.001);
237    }
238   
239    /**
240    * Test the method that defaults rna symbol to the one matching the preceding
241    * unmatched opening bracket (if any)
242    */
 
243  1 toggle @Test(groups = { "Functional" })
244    public void testGetDefaultRnaHelixSymbol()
245    {
246  1 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
247    "secondary structure", null);
248  1 assertEquals("(", ann.getDefaultRnaHelixSymbol(4));
249   
250  1 Annotation[] anns = new Annotation[20];
251  1 ann.annotations = anns;
252  1 assertEquals("(", ann.getDefaultRnaHelixSymbol(4));
253   
254  1 anns[1] = new Annotation("(", "S", '(', 0f);
255  1 assertEquals("(", ann.getDefaultRnaHelixSymbol(0));
256  1 assertEquals("(", ann.getDefaultRnaHelixSymbol(1));
257  1 assertEquals(")", ann.getDefaultRnaHelixSymbol(2));
258  1 assertEquals(")", ann.getDefaultRnaHelixSymbol(3));
259   
260    /*
261    * .(.[.{.<.}.>.).].
262    */
263  1 anns[1] = new Annotation("(", "S", '(', 0f);
264  1 anns[3] = new Annotation("[", "S", '[', 0f);
265  1 anns[5] = new Annotation("{", "S", '{', 0f);
266  1 anns[7] = new Annotation("<", "S", '<', 0f);
267  1 anns[9] = new Annotation("}", "S", '}', 0f);
268  1 anns[11] = new Annotation(">", "S", '>', 0f);
269  1 anns[13] = new Annotation(")", "S", ')', 0f);
270  1 anns[15] = new Annotation("]", "S", ']', 0f);
271   
272  1 String expected = "(())]]}}>>>>]]]](";
273  18 for (int i = 0; i < expected.length(); i++)
274    {
275  17 assertEquals("column " + i, String.valueOf(expected.charAt(i)),
276    ann.getDefaultRnaHelixSymbol(i));
277    }
278   
279    /*
280    * .(.[.(.).{.}.<.].D.
281    */
282  1 anns[1] = new Annotation("(", "S", '(', 0f);
283  1 anns[3] = new Annotation("[", "S", '[', 0f);
284  1 anns[5] = new Annotation("(", "S", '(', 0f);
285  1 anns[7] = new Annotation(")", "S", ')', 0f);
286  1 anns[9] = new Annotation("{", "S", '{', 0f);
287  1 anns[11] = new Annotation("}", "S", '}', 0f);
288  1 anns[13] = new Annotation("<", "S", '>', 0f);
289  1 anns[15] = new Annotation("]", "S", ']', 0f);
290  1 anns[17] = new Annotation("D", "S", 'D', 0f);
291   
292  1 expected = "(())]]))]]}}]]>>>>dd";
293  21 for (int i = 0; i < expected.length(); i++)
294    {
295  20 assertEquals("column " + i, String.valueOf(expected.charAt(i)),
296    ann.getDefaultRnaHelixSymbol(i));
297    }
298    }
299   
 
300  15 toggle public static Annotation newAnnotation(String ann)
301    {
302  15 float val = 0f;
303  15 try
304    {
305  15 val = Float.parseFloat(ann);
306    } catch (NumberFormatException q)
307    {
308    }
309  15 ;
310  15 return new Annotation(ann, ann, '\0', val);
311    }
312   
 
313  1 toggle @Test(groups = { "Functional" })
314    public void testIsQuantitative()
315    {
316  1 AlignmentAnnotation ann = null;
317   
318  1 ann = new AlignmentAnnotation("an", "some an", null);
319  1 Assert.assertFalse(ann.isQuantitative(),
320    "Empty annotation set should not be quantitative.");
321   
322  1 ann = new AlignmentAnnotation("an", "some an",
323    new Annotation[]
324    { newAnnotation("4"), newAnnotation("1"), newAnnotation("1"),
325    newAnnotation("0.1"), newAnnotation("0.3") });
326  1 Assert.assertTrue(ann.isQuantitative(),
327    "All numbers annotation set should be quantitative.");
328   
329  1 ann = new AlignmentAnnotation("an", "some an",
330    new Annotation[]
331    { newAnnotation("E"), newAnnotation("E"), newAnnotation("E"),
332    newAnnotation("E"), newAnnotation("E") });
333  1 Assert.assertFalse(ann.isQuantitative(),
334    "All 'E' annotation set should not be quantitative.");
335   
336  1 ann = new AlignmentAnnotation("an", "some an",
337    new Annotation[]
338    { newAnnotation("E"), newAnnotation("1"), newAnnotation("2"),
339    newAnnotation("3"), newAnnotation("E") });
340  1 Assert.assertTrue(ann.isQuantitative(),
341    "Mixed 'E' annotation set should be quantitative.");
342    }
343   
 
344  1 toggle @Test(groups = "Functional")
345    public void testMakeVisibleAnnotation()
346    {
347  1 HiddenColumns h = new HiddenColumns();
348  1 Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
349    new Annotation(2), new Annotation(3), null, null, new Annotation(4),
350    new Annotation(5), new Annotation(6), new Annotation(7),
351    new Annotation(8) };
352  1 AlignmentAnnotation ann = new AlignmentAnnotation("an", "some an",
353    anns);
354   
355    // null annotations
356  1 AlignmentAnnotation emptyann = new AlignmentAnnotation("an", "some ann",
357    null);
358  1 emptyann.makeVisibleAnnotation(h);
359  1 assertNull(emptyann.annotations);
360   
361  1 emptyann.makeVisibleAnnotation(3, 4, h);
362  1 assertNull(emptyann.annotations);
363   
364    // without bounds, does everything
365  1 ann.makeVisibleAnnotation(h);
366  1 assertEquals(12, ann.annotations.length);
367  1 assertNull(ann.annotations[0]);
368  1 assertNull(ann.annotations[1]);
369  1 assertEquals(1.0f, ann.annotations[2].value);
370  1 assertEquals(2.0f, ann.annotations[3].value);
371  1 assertEquals(3.0f, ann.annotations[4].value);
372  1 assertNull(ann.annotations[5]);
373  1 assertNull(ann.annotations[6]);
374  1 assertEquals(4.0f, ann.annotations[7].value);
375  1 assertEquals(5.0f, ann.annotations[8].value);
376  1 assertEquals(6.0f, ann.annotations[9].value);
377  1 assertEquals(7.0f, ann.annotations[10].value);
378  1 assertEquals(8.0f, ann.annotations[11].value);
379   
380    // without hidden cols, just truncates
381  1 ann.makeVisibleAnnotation(3, 5, h);
382  1 assertEquals(3, ann.annotations.length);
383  1 assertEquals(2.0f, ann.annotations[0].value);
384  1 assertEquals(3.0f, ann.annotations[1].value);
385  1 assertNull(ann.annotations[2]);
386   
387  1 anns = new Annotation[] { null, null, new Annotation(1),
388    new Annotation(2), new Annotation(3), null, null, new Annotation(4),
389    new Annotation(5), new Annotation(6), new Annotation(7),
390    new Annotation(8) };
391  1 ann = new AlignmentAnnotation("an", "some an", anns);
392  1 h.hideColumns(4, 7);
393  1 ann.makeVisibleAnnotation(1, 9, h);
394  1 assertEquals(5, ann.annotations.length);
395  1 assertNull(ann.annotations[0]);
396  1 assertEquals(1.0f, ann.annotations[1].value);
397  1 assertEquals(2.0f, ann.annotations[2].value);
398  1 assertEquals(5.0f, ann.annotations[3].value);
399  1 assertEquals(6.0f, ann.annotations[4].value);
400   
401  1 anns = new Annotation[] { null, null, new Annotation(1),
402    new Annotation(2), new Annotation(3), null, null, new Annotation(4),
403    new Annotation(5), new Annotation(6), new Annotation(7),
404    new Annotation(8) };
405  1 ann = new AlignmentAnnotation("an", "some an", anns);
406  1 h.hideColumns(1, 2);
407  1 ann.makeVisibleAnnotation(1, 9, h);
408  1 assertEquals(3, ann.annotations.length);
409  1 assertEquals(2.0f, ann.annotations[0].value);
410  1 assertEquals(5.0f, ann.annotations[1].value);
411  1 assertEquals(6.0f, ann.annotations[2].value);
412   
413  1 anns = new Annotation[] { null, null, new Annotation(1),
414    new Annotation(2), new Annotation(3), null, null, new Annotation(4),
415    new Annotation(5), new Annotation(6), new Annotation(7),
416    new Annotation(8), new Annotation(9), new Annotation(10),
417    new Annotation(11), new Annotation(12), new Annotation(13),
418    new Annotation(14), new Annotation(15) };
419  1 ann = new AlignmentAnnotation("an", "some an", anns);
420  1 h = new HiddenColumns();
421  1 h.hideColumns(5, 18);
422  1 h.hideColumns(20, 21);
423  1 ann.makeVisibleAnnotation(1, 21, h);
424  1 assertEquals(5, ann.annotations.length);
425  1 assertEquals(1.0f, ann.annotations[1].value);
426  1 assertEquals(2.0f, ann.annotations[2].value);
427  1 assertEquals(3.0f, ann.annotations[3].value);
428  1 assertNull(ann.annotations[0]);
429  1 assertNull(ann.annotations[4]);
430    }
431   
432    /**
433    * test the contact matrix nogroups property methods
434    */
 
435  1 toggle @Test(groups = { "Functional" })
436    public void test_contactMatrixGroups()
437    {
438  1 AlignmentAnnotation aa = new AlignmentAnnotation("foo", "foo desc",
439    null);
440  1 assertTrue(aa.isShowGroupsForContactMatrix());
441  1 aa.setShowGroupsForContactMatrix(false);
442  1 assertFalse(aa.isShowGroupsForContactMatrix());
443  1 AlignmentAnnotation copy = new AlignmentAnnotation(aa);
444  1 assertFalse(copy.isShowGroupsForContactMatrix());
445  1 aa.setShowGroupsForContactMatrix(true);
446  1 assertTrue(aa.isShowGroupsForContactMatrix());
447    // copy should not be updated
448  1 assertFalse(copy.isShowGroupsForContactMatrix());
449   
450    }
451    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 18 2024 09:54:26 GMT using coverage data from Mon Nov 18 2024 09:54:15 GMT.
  • OpenClover is free and open-source software.