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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.io

File SequenceAnnotationReportTest.java

 

Code metrics

4
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Classes

Class Line # Actions
SequenceAnnotationReportTest 45 150 13 0
1.0100%
 

Contributing tests

This file is covered by 10 tests. .

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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 jalview.io;
22   
23    import static org.testng.AssertJUnit.assertEquals;
24    import static org.testng.AssertJUnit.assertTrue;
25   
26    import jalview.api.FeatureColourI;
27    import jalview.datamodel.DBRefEntry;
28    import jalview.datamodel.Sequence;
29    import jalview.datamodel.SequenceFeature;
30    import jalview.datamodel.SequenceI;
31    import jalview.gui.JvOptionPane;
32    import jalview.io.gff.GffConstants;
33    import jalview.renderer.seqfeatures.FeatureRenderer;
34    import jalview.schemes.FeatureColour;
35    import jalview.viewmodel.seqfeatures.FeatureRendererModel;
36   
37    import java.awt.Color;
38    import java.util.Map;
39   
40    import junit.extensions.PA;
41   
42    import org.testng.annotations.BeforeClass;
43    import org.testng.annotations.Test;
44   
 
45    public class SequenceAnnotationReportTest
46    {
47   
 
48  1 toggle @BeforeClass(alwaysRun = true)
49    public void setUpJvOptionPane()
50    {
51  1 JvOptionPane.setInteractiveMode(false);
52  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
53    }
54   
 
55  1 toggle @Test(groups = "Functional")
56    public void testAppendFeature_disulfideBond()
57    {
58  1 SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
59  1 StringBuilder sb = new StringBuilder();
60  1 sb.append("123456");
61  1 SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
62    3, 1.2f, "group");
63   
64    // residuePos == 2 does not match start or end of feature, nothing done:
65  1 sar.appendFeature(sb, 2, null, sf);
66  1 assertEquals("123456", sb.toString());
67   
68    // residuePos == 1 matches start of feature, text appended (but no <br>)
69    // feature score is not included
70  1 sar.appendFeature(sb, 1, null, sf);
71  1 assertEquals("123456disulfide bond 1:3", sb.toString());
72   
73    // residuePos == 3 matches end of feature, text appended
74    // <br> is prefixed once sb.length() > 6
75  1 sar.appendFeature(sb, 3, null, sf);
76  1 assertEquals("123456disulfide bond 1:3<br>disulfide bond 1:3",
77    sb.toString());
78    }
79   
 
80  1 toggle @Test(groups = "Functional")
81    public void testAppendFeature_status()
82    {
83  1 SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
84  1 StringBuilder sb = new StringBuilder();
85  1 SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
86    Float.NaN, "group");
87  1 sf.setStatus("Confirmed");
88   
89  1 sar.appendFeature(sb, 1, null, sf);
90  1 assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
91    }
92   
 
93  1 toggle @Test(groups = "Functional")
94    public void testAppendFeature_withScore()
95    {
96  1 SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
97  1 StringBuilder sb = new StringBuilder();
98  1 SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
99    "group");
100   
101  1 FeatureRendererModel fr = new FeatureRenderer(null);
102  1 Map<String, float[][]> minmax = fr.getMinMax();
103  1 sar.appendFeature(sb, 1, fr, sf);
104    /*
105    * map has no entry for this feature type - score is not shown:
106    */
107  1 assertEquals("METAL 1 3; Fe2-S", sb.toString());
108   
109    /*
110    * map has entry for this feature type - score is shown:
111    */
112  1 minmax.put("METAL", new float[][] { { 0f, 1f }, null });
113  1 sar.appendFeature(sb, 1, fr, sf);
114    // <br> is appended to a buffer > 6 in length
115  1 assertEquals("METAL 1 3; Fe2-S<br>METAL 1 3; Fe2-S Score=1.3",
116    sb.toString());
117   
118    /*
119    * map has min == max for this feature type - score is not shown:
120    */
121  1 minmax.put("METAL", new float[][] { { 2f, 2f }, null });
122  1 sb.setLength(0);
123  1 sar.appendFeature(sb, 1, fr, sf);
124  1 assertEquals("METAL 1 3; Fe2-S", sb.toString());
125    }
126   
 
127  1 toggle @Test(groups = "Functional")
128    public void testAppendFeature_noScore()
129    {
130  1 SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
131  1 StringBuilder sb = new StringBuilder();
132  1 SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
133    Float.NaN, "group");
134   
135  1 sar.appendFeature(sb, 1, null, sf);
136  1 assertEquals("METAL 1 3; Fe2-S", sb.toString());
137    }
138   
139    /**
140    * A specific attribute value is included if it is used to colour the feature
141    */
 
142  1 toggle @Test(groups = "Functional")
143    public void testAppendFeature_colouredByAttribute()
144    {
145  1 SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
146  1 StringBuilder sb = new StringBuilder();
147  1 SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
148    Float.NaN, "group");
149  1 sf.setValue("clinical_significance", "Benign");
150   
151    /*
152    * first with no colour by attribute
153    */
154  1 FeatureRendererModel fr = new FeatureRenderer(null);
155  1 sar.appendFeature(sb, 1, fr, sf);
156  1 assertEquals("METAL 1 3; Fe2-S", sb.toString());
157   
158    /*
159    * then with colour by an attribute the feature lacks
160    */
161  1 FeatureColourI fc = new FeatureColour(Color.white, Color.black, 5, 10);
162  1 fc.setAttributeName("Pfam");
163  1 fr.setColour("METAL", fc);
164  1 sb.setLength(0);
165  1 sar.appendFeature(sb, 1, fr, sf);
166  1 assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change
167   
168    /*
169    * then with colour by an attribute the feature has
170    */
171  1 fc.setAttributeName("clinical_significance");
172  1 sb.setLength(0);
173  1 sar.appendFeature(sb, 1, fr, sf);
174  1 assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
175    sb.toString());
176    }
177   
 
178  1 toggle @Test(groups = "Functional")
179    public void testAppendFeature_withScoreStatusAttribute()
180    {
181  1 SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
182  1 StringBuilder sb = new StringBuilder();
183  1 SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
184    "group");
185  1 sf.setStatus("Confirmed");
186  1 sf.setValue("clinical_significance", "Benign");
187   
188  1 FeatureRendererModel fr = new FeatureRenderer(null);
189  1 Map<String, float[][]> minmax = fr.getMinMax();
190  1 FeatureColourI fc = new FeatureColour(Color.white, Color.blue, 12, 22);
191  1 fc.setAttributeName("clinical_significance");
192  1 fr.setColour("METAL", fc);
193  1 minmax.put("METAL", new float[][] { { 0f, 1f }, null });
194  1 sar.appendFeature(sb, 1, fr, sf);
195   
196  1 assertEquals(
197    "METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
198    sb.toString());
199    }
200   
 
201  1 toggle @Test(groups = "Functional")
202    public void testAppendFeature_DescEqualsType()
203    {
204  1 SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
205  1 StringBuilder sb = new StringBuilder();
206  1 SequenceFeature sf = new SequenceFeature("METAL", "METAL", 1, 3,
207    Float.NaN, "group");
208   
209    // description is not included if it duplicates type:
210  1 sar.appendFeature(sb, 1, null, sf);
211  1 assertEquals("METAL 1 3", sb.toString());
212   
213  1 sb.setLength(0);
214  1 sf.setDescription("Metal");
215    // test is case-sensitive:
216  1 sar.appendFeature(sb, 1, null, sf);
217  1 assertEquals("METAL 1 3; Metal", sb.toString());
218    }
219   
 
220  1 toggle @Test(groups = "Functional")
221    public void testAppendFeature_stripHtml()
222    {
223  1 SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
224  1 StringBuilder sb = new StringBuilder();
225  1 SequenceFeature sf = new SequenceFeature("METAL",
226    "<html><body>hello<em>world</em></body></html>", 1, 3,
227    Float.NaN, "group");
228   
229  1 sar.appendFeature(sb, 1, null, sf);
230    // !! strips off </body> but not <body> ??
231  1 assertEquals("METAL 1 3; <body>hello<em>world</em>", sb.toString());
232   
233  1 sb.setLength(0);
234  1 sf.setDescription("<br>&kHD>6");
235  1 sar.appendFeature(sb, 1, null, sf);
236    // if no <html> tag, html-encodes > and < (only):
237  1 assertEquals("METAL 1 3; &lt;br&gt;&kHD&gt;6", sb.toString());
238    }
239   
 
240  1 toggle @Test(groups = "Functional")
241    public void testCreateSequenceAnnotationReport()
242    {
243  1 SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
244  1 StringBuilder sb = new StringBuilder();
245   
246  1 SequenceI seq = new Sequence("s1", "MAKLKRFQSSTLL");
247  1 seq.setDescription("SeqDesc");
248   
249  1 sar.createSequenceAnnotationReport(sb, seq, true, true, null);
250   
251    /*
252    * positional features are ignored
253    */
254  1 seq.addSequenceFeature(new SequenceFeature("Domain", "Ferredoxin", 5,
255    10, 1f, null));
256  1 assertEquals("<i><br>SeqDesc</i>", sb.toString());
257   
258    /*
259    * non-positional feature
260    */
261  1 seq.addSequenceFeature(new SequenceFeature("Type1", "Nonpos", 0, 0, 1f,
262    null));
263  1 sb.setLength(0);
264  1 sar.createSequenceAnnotationReport(sb, seq, true, true, null);
265  1 String expected = "<i><br>SeqDesc<br>Type1 ; Nonpos Score=1.0</i>";
266  1 assertEquals(expected, sb.toString());
267   
268    /*
269    * non-positional features not wanted
270    */
271  1 sb.setLength(0);
272  1 sar.createSequenceAnnotationReport(sb, seq, true, false, null);
273  1 assertEquals("<i><br>SeqDesc</i>", sb.toString());
274   
275    /*
276    * add non-pos feature with score inside min-max range for feature type
277    * minmax holds { [positionalMin, positionalMax], [nonPosMin, nonPosMax] }
278    * score is only appended for positional features so ignored here!
279    * minMax are not recorded for non-positional features
280    */
281  1 seq.addSequenceFeature(new SequenceFeature("Metal", "Desc", 0, 0, 5f,
282    null));
283   
284  1 FeatureRendererModel fr = new FeatureRenderer(null);
285  1 Map<String, float[][]> minmax = fr.getMinMax();
286  1 minmax.put("Metal", new float[][] { null, new float[] { 2f, 5f } });
287   
288  1 sb.setLength(0);
289  1 sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
290  1 expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos</i>";
291  1 assertEquals(expected, sb.toString());
292   
293    /*
294    * 'linkonly' features are ignored; this is obsolete, as linkonly
295    * is only set by DasSequenceFetcher, and DAS is history
296    */
297  1 SequenceFeature sf = new SequenceFeature("Metal", "Desc", 0, 0, 5f,
298    null);
299  1 sf.setValue("linkonly", Boolean.TRUE);
300  1 seq.addSequenceFeature(sf);
301  1 sb.setLength(0);
302  1 sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
303  1 assertEquals(expected, sb.toString()); // unchanged!
304   
305    /*
306    * 'clinical_significance' attribute only included when
307    * used for feature colouring
308    */
309  1 SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0,
310    5f, null);
311  1 sf2.setValue(GffConstants.CLINICAL_SIGNIFICANCE, "benign");
312  1 seq.addSequenceFeature(sf2);
313  1 sb.setLength(0);
314  1 sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
315  1 expected = "<i><br>SeqDesc<br>Metal ; Desc<br>Type1 ; Nonpos<br>Variant ; Havana</i>";
316  1 assertEquals(expected, sb.toString());
317   
318    /*
319    * add dbrefs
320    */
321  1 seq.addDBRef(new DBRefEntry("PDB", "0", "3iu1"));
322  1 seq.addDBRef(new DBRefEntry("Uniprot", "1", "P30419"));
323   
324    // with showDbRefs = false
325  1 sb.setLength(0);
326  1 sar.createSequenceAnnotationReport(sb, seq, false, true, fr);
327  1 assertEquals(expected, sb.toString()); // unchanged
328   
329    // with showDbRefs = true, colour Variant features by clinical_significance
330  1 sb.setLength(0);
331  1 FeatureColourI fc = new FeatureColour(Color.green, Color.pink, 2, 3);
332  1 fc.setAttributeName("clinical_significance");
333  1 fr.setColour("Variant", fc);
334  1 sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
335  1 expected = "<i><br>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1<br>Metal ; Desc<br>"
336    + "Type1 ; Nonpos<br>Variant ; Havana; clinical_significance=benign</i>";
337  1 assertEquals(expected, sb.toString());
338    // with showNonPositionalFeatures = false
339  1 sb.setLength(0);
340  1 sar.createSequenceAnnotationReport(sb, seq, true, false, fr);
341  1 expected = "<i><br>SeqDesc<br>UNIPROT P30419<br>PDB 3iu1</i>";
342  1 assertEquals(expected, sb.toString());
343   
344    // see other tests for treatment of status and html
345    }
346   
347    /**
348    * Test that exercises an abbreviated sequence details report, with ellipsis
349    * where there are more than 40 different sources, or more than 4 dbrefs for a
350    * single source
351    */
 
352  1 toggle @Test(groups = "Functional")
353    public void testCreateSequenceAnnotationReport_withEllipsis()
354    {
355  1 SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
356  1 StringBuilder sb = new StringBuilder();
357   
358  1 SequenceI seq = new Sequence("s1", "ABC");
359   
360  1 int maxSources = (int) PA.getValue(sar, "MAX_SOURCES");
361  42 for (int i = 0; i <= maxSources; i++)
362    {
363  41 seq.addDBRef(new DBRefEntry("PDB" + i, "0", "3iu1"));
364    }
365   
366  1 int maxRefs = (int) PA.getValue(sar, "MAX_REFS_PER_SOURCE");
367  6 for (int i = 0; i <= maxRefs; i++)
368    {
369  5 seq.addDBRef(new DBRefEntry("Uniprot", "0", "P3041" + i));
370    }
371   
372  1 sar.createSequenceAnnotationReport(sb, seq, true, true, null, true);
373  1 String report = sb.toString();
374  1 assertTrue(report
375    .startsWith("<i><br>UNIPROT P30410, P30411, P30412, P30413,...<br>PDB0 3iu1"));
376  1 assertTrue(report
377    .endsWith("<br>PDB7 3iu1<br>PDB8,...<br>(Output Sequence Details to list all database references)</i>"));
378    }
379    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.