1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.schemes

File AnnotationColourGradientTest.java

 

Code metrics

38
96
8
1
344
199
27
0.28
12
8
3.38

Classes

Class
Line #
Actions
AnnotationColourGradientTest 38 96 27
1.0100%
 

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.schemes;
22   
23    import static org.testng.Assert.assertEquals;
24   
25    import jalview.datamodel.Alignment;
26    import jalview.datamodel.AlignmentAnnotation;
27    import jalview.datamodel.AlignmentI;
28    import jalview.datamodel.Annotation;
29    import jalview.datamodel.GraphLine;
30    import jalview.datamodel.Sequence;
31    import jalview.datamodel.SequenceI;
32   
33    import java.awt.Color;
34   
35    import org.testng.annotations.BeforeClass;
36    import org.testng.annotations.Test;
37   
 
38    public class AnnotationColourGradientTest
39    {
40    final static int WIDTH = 11;
41   
42    final static int THRESHOLD_FIVE = 5;
43   
44    private AlignmentAnnotation ann;
45   
46    private SequenceI seq;
47   
48    private AlignmentI al;
49   
50    Color minColour = new Color(50, 200, 150);
51   
52    Color maxColour = new Color(150, 100, 250);
53   
54    /**
55    * Setup creates an annotation over 11 columns with values 0-10 and threshold
56    * 5
57    */
 
58  1 toggle @BeforeClass(alwaysRun = true)
59    public void setUp()
60    {
61  1 Annotation[] anns = new Annotation[WIDTH];
62    /*
63    * set annotations with values 0-10, graded colours
64    */
65  12 for (int col = 0; col < WIDTH; col++)
66    {
67  11 int hue = col * 20;
68  11 Color colour = new Color(hue, hue, hue);
69  11 anns[col] = new Annotation("a", "a", 'a', col, colour);
70    }
71   
72  1 seq = new Sequence("Seq", "");
73  1 al = new Alignment(new SequenceI[] { seq });
74   
75    /*
76    * AlignmentAnnotation constructor works out min-max range
77    */
78  1 ann = new AlignmentAnnotation("", "", anns);
79  1 ann.setThreshold(new GraphLine(THRESHOLD_FIVE, "", Color.RED));
80  1 seq.addAlignmentAnnotation(ann);
81    }
82   
 
83  1 toggle @Test(groups = "Functional")
84    public void testShadeCalculation_noThreshold()
85    {
86  1 AnnotationColourGradient testee = new AnnotationColourGradient(ann,
87    minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
88  12 for (int col = 0; col < WIDTH; col++)
89    {
90  11 Color result = testee.shadeCalculation(ann, col);
91    /*
92    * column <n> is n/10 of the way from minCol to maxCol
93    */
94  11 Color expected = new Color(50 + 10 * col, 200 - 10 * col,
95    150 + 10 * col);
96  11 assertEquals(result, expected, "for column " + col);
97    }
98    }
99   
100    /**
101    * Test the 'colour above threshold' case
102    */
 
103  1 toggle @Test(groups = "Functional")
104    public void testShadeCalculation_aboveThreshold()
105    {
106  1 AnnotationColourGradient testee = new AnnotationColourGradient(ann,
107    minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD);
108  12 for (int col = 0; col < WIDTH; col++)
109    {
110  11 Color result = testee.shadeCalculation(ann, col);
111    /*
112    * colour is derived regardless of the threshold value
113    * (the renderer will suppress colouring if above/below threshold)
114    */
115  11 Color expected = new Color(50 + 10 * col, 200 - 10 * col,
116    150 + 10 * col);
117  11 assertEquals(result, expected, "for column " + col);
118    }
119   
120    /*
121    * now make 6-10 the span of the colour range
122    * (annotation value == column number in this test)
123    */
124  1 testee.setThresholdIsMinMax(true);
125  6 for (int col = 0; col < THRESHOLD_FIVE; col++)
126    {
127    /*
128    * colours below the threshold are computed as before
129    */
130  5 Color expected = new Color(50 + 10 * col, 200 - 10 * col,
131    150 + 10 * col);
132  5 Color result = testee.shadeCalculation(ann, col);
133  5 assertEquals(result, expected, "for column " + col);
134    }
135  7 for (int col = THRESHOLD_FIVE; col < WIDTH; col++)
136    {
137    /*
138    * colours for values >= threshold are graduated
139    * range is 6-10 so steps of 100/5 = 20
140    */
141  6 int factor = col - THRESHOLD_FIVE;
142  6 Color expected = new Color(50 + 20 * factor, 200 - 20 * factor,
143    150 + 20 * factor);
144  6 Color result = testee.shadeCalculation(ann, col);
145  6 assertEquals(result, expected, "for column " + col);
146    }
147   
148    /*
149    * test for boundary case threshold == graphMax (JAL-3206)
150    */
151  1 float thresh = ann.threshold.value;
152  1 ann.threshold.value = ann.graphMax;
153  1 Color result = testee.shadeCalculation(ann, WIDTH - 1);
154  1 assertEquals(result, maxColour);
155  1 testee.setThresholdIsMinMax(false);
156  1 result = testee.shadeCalculation(ann, WIDTH - 1);
157  1 assertEquals(result, maxColour);
158  1 ann.threshold.value = thresh; // reset
159    }
160   
161    /**
162    * Test the 'colour below threshold' case
163    */
 
164  1 toggle @Test(groups = "Functional")
165    public void testShadeCalculation_belowThreshold()
166    {
167  1 AnnotationColourGradient testee = new AnnotationColourGradient(ann,
168    minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
169   
170  12 for (int col = 0; col < WIDTH; col++)
171    {
172  11 Color result = testee.shadeCalculation(ann, col);
173    /*
174    * colour is derived regardless of the threshold value
175    * (the renderer will suppress colouring if above/below threshold)
176    */
177  11 Color expected = new Color(50 + 10 * col, 200 - 10 * col,
178    150 + 10 * col);
179  11 assertEquals(result, expected, "for column " + col);
180    }
181   
182    /*
183    * now make 0-5 the span of the colour range
184    * (annotation value == column number in this test)
185    */
186  1 testee.setThresholdIsMinMax(true);
187  6 for (int col = THRESHOLD_FIVE + 1; col < WIDTH; col++)
188    {
189    /*
190    * colours above the threshold are computed as before
191    */
192  5 Color expected = new Color(50 + 10 * col, 200 - 10 * col,
193    150 + 10 * col);
194  5 Color result = testee.shadeCalculation(ann, col);
195  5 assertEquals(result, expected, "for column " + col);
196    }
197   
198  7 for (int col = 0; col <= THRESHOLD_FIVE; col++)
199    {
200    /*
201    * colours for values <= threshold are graduated
202    * range is 0-5 so steps of 100/5 = 20
203    */
204  6 Color expected = new Color(50 + 20 * col, 200 - 20 * col,
205    150 + 20 * col);
206  6 Color result = testee.shadeCalculation(ann, col);
207  6 assertEquals(result, expected, "for column " + col);
208    }
209   
210    /*
211    * test for boundary case threshold == graphMin (JAL-3206)
212    */
213  1 float thresh = ann.threshold.value;
214  1 ann.threshold.value = ann.graphMin;
215  1 Color result = testee.shadeCalculation(ann, 0);
216  1 assertEquals(result, minColour);
217  1 testee.setThresholdIsMinMax(false);
218  1 result = testee.shadeCalculation(ann, 0);
219  1 assertEquals(result, minColour);
220  1 ann.threshold.value = thresh; // reset
221    }
222   
223    /**
224    * Test the 'colour above threshold' case
225    */
 
226  1 toggle @Test(groups = "Functional")
227    public void testFindColour_aboveThreshold()
228    {
229  1 AnnotationColourGradient testee = new AnnotationColourGradient(ann,
230    minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD);
231  1 testee = (AnnotationColourGradient) testee.getInstance(null, al);
232   
233  12 for (int col = 0; col < WIDTH; col++)
234    {
235  11 Color result = testee.findColour('a', col, seq);
236    /*
237    * expect white at or below threshold of 5
238    */
239  11 Color expected = col <= 5 ? Color.white
240    : new Color(50 + 10 * col, 200 - 10 * col, 150 + 10 * col);
241  11 assertEquals(result, expected, "for column " + col);
242    }
243   
244    /*
245    * now make 6-10 the span of the colour range
246    * (annotation value == column number in this test)
247    */
248  1 testee.setThresholdIsMinMax(true);
249  12 for (int col = 0; col < WIDTH; col++)
250    {
251    /*
252    * colours for values > threshold are graduated
253    * range is 6-10 so steps of 100/5 = 20
254    */
255  11 int factor = col - THRESHOLD_FIVE;
256  11 Color expected = col <= 5 ? Color.white
257    : new Color(50 + 20 * factor, 200 - 20 * factor,
258    150 + 20 * factor);
259  11 Color result = testee.findColour('a', col, seq);
260  11 assertEquals(result, expected, "for column " + col);
261    }
262    }
263   
264    /**
265    * Test the 'colour below threshold' case
266    */
 
267  1 toggle @Test(groups = "Functional")
268    public void testFindColour_belowThreshold()
269    {
270  1 AnnotationColourGradient testee = new AnnotationColourGradient(ann,
271    minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
272  1 testee = (AnnotationColourGradient) testee.getInstance(null, al);
273   
274  12 for (int col = 0; col < WIDTH; col++)
275    {
276  11 Color result = testee.findColour('a', col, seq);
277  11 Color expected = col >= 5 ? Color.white
278    : new Color(50 + 10 * col, 200 - 10 * col, 150 + 10 * col);
279  11 assertEquals(result, expected, "for column " + col);
280    }
281   
282    /*
283    * now make 0-5 the span of the colour range
284    * (annotation value == column number in this test)
285    */
286  1 testee.setThresholdIsMinMax(true);
287  12 for (int col = 0; col < WIDTH; col++)
288    {
289    /*
290    * colours for values < threshold are graduated
291    * range is 0-5 so steps of 100/5 = 20
292    */
293  11 Color expected = col >= 5 ? Color.white
294    : new Color(50 + 20 * col, 200 - 20 * col, 150 + 20 * col);
295  11 Color result = testee.findColour('a', col, seq);
296  11 assertEquals(result, expected, "for column " + col);
297    }
298    }
299   
 
300  1 toggle @Test(groups = "Functional")
301    public void testFindColour_noThreshold()
302    {
303  1 AnnotationColourGradient testee = new AnnotationColourGradient(ann,
304    minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
305  1 testee = (AnnotationColourGradient) testee.getInstance(null, al);
306   
307  12 for (int col = 0; col < WIDTH; col++)
308    {
309  11 Color result = testee.findColour('a', col, seq);
310    /*
311    * column <n> is n/10 of the way from minCol to maxCol
312    */
313  11 Color expected = new Color(50 + 10 * col, 200 - 10 * col,
314    150 + 10 * col);
315  11 assertEquals(result, expected, "for column " + col);
316    }
317    }
318   
 
319  1 toggle @Test(groups = "Functional")
320    public void testFindColour_originalColours()
321    {
322  1 AnnotationColourGradient testee = new AnnotationColourGradient(ann,
323    minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
324  1 testee = (AnnotationColourGradient) testee.getInstance(null, al);
325   
326    /*
327    * flag corresponding to 'use original colours' checkbox
328    * - just use the individual annotation colours
329    */
330  1 testee.setPredefinedColours(true);
331   
332    /*
333    * the annotation colour is returned, except for column 0 where it is
334    * black - in this case the colour scheme colour overrides it
335    */
336  12 for (int col = 0; col < WIDTH; col++)
337    {
338  11 int hue = col * 20;
339  11 Color c = col == 0 ? minColour : new Color(hue, hue, hue);
340  11 assertEquals(testee.findColour('a', col, seq), c,
341    "for column " + col);
342    }
343    }
344    }