Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AlignmentSorterTest	18	48	2	0	1.0100%	Show methods

Class AlignmentSorterTest

Class AlignmentSorterTest	Line # 18	Total Statements 48	Complexity 2	Uncovered Elements 0	TOTAL Coverage 1.0100%
testSortByFeature_score() : void   testSortByFeature_score() : void	2020	48.048	1.01	0.00	1.0 1.0100%
testSortByFeature_density() : void   testSortByFeature_density() : void	126126	0.00	1.01	0.00	-1.0 -1.0 -

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.98	jalview.analysis.AlignmentSorterTest.testSortByFeature_scorejalview.analysis.AlignmentSorterTest.testSortByFeature_score	1PASS
	0.02	jalview.analysis.AlignmentSorterTest.testSortByFeature_densityjalview.analysis.AlignmentSorterTest.testSortByFeature_density	1PASS

 

Source view

1		package jalview.analysis;
2
3		import static org.testng.Assert.assertSame;
4
5		import jalview.datamodel.Alignment;
6		import jalview.datamodel.AlignmentI;
7		import jalview.datamodel.Sequence;
8		import jalview.datamodel.SequenceFeature;
9		import jalview.datamodel.SequenceI;
10
11		import java.util.Arrays;
12		import java.util.List;
13
14		import junit.extensions.PA;
15
16		import org.testng.annotations.Test;
17
		100% Uncovered Elements: 0 (50) Complexity: 2 Complexity Density: 0.04
18		public class AlignmentSorterTest
19		{
		100% Uncovered Elements: 0 (48) Complexity: 1 Complexity Density: 0.02 1PASS
20	1	@Test(groups = "Functional")...
21		public void testSortByFeature_score()
22		{
23	1	SequenceI seq1 = new Sequence("Seq1", "ABC--D-EFGHIJ");
24	1	SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
25	1	SequenceI seq3 = new Sequence("Seq3", "ABCDE-FGHIJ");
26	1	SequenceI seq4 = new Sequence("Seq4", "ABCDEFGHIJ");
27	1	SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
28	1	AlignmentI al = new Alignment(seqs);
29	1	al.setDataset(null);
30
31		/*
32		* sort with no score features does nothing
33		*/
34	1	PA.setValue(AlignmentSorter.class, "sortByFeatureCriteria", null);
35
36	1	AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
37		AlignmentSorter.FEATURE_SCORE);
38	1	assertSame(al.getSequenceAt(0), seq1);
39	1	assertSame(al.getSequenceAt(1), seq2);
40	1	assertSame(al.getSequenceAt(2), seq3);
41	1	assertSame(al.getSequenceAt(3), seq4);
42
43		/*
44		* add score and non-score features
45		* seq1 Cath(2.0) Pfam(4.0) average 3.0
46		* seq2 Cath(2.5) Metal(NaN) average 2.5
47		* seq3 KD(-4), KD(3.0) average -0.5
48		* seq4 Helix(NaN) - should sort as if largest score
49		*/
50	1	seq1.addSequenceFeature(new SequenceFeature("Cath", "", 2, 3, 2.0f,
51		"g1"));
52	1	seq1.addSequenceFeature(new SequenceFeature("Pfam", "", 4, 5, 4.0f,
53		"g2"));
54	1	seq2.addSequenceFeature(new SequenceFeature("Cath", "", 2, 3, 2.5f,
55		"g3"));
56	1	seq2.addSequenceFeature(new SequenceFeature("Metal", "", 2, 3,
57		Float.NaN, "g4"));
58	1	seq3.addSequenceFeature(new SequenceFeature("kD", "", 2, 3, -4f, "g5"));
59	1	seq3.addSequenceFeature(new SequenceFeature("kD", "", 5, 6, 3.0f, "g6"));
60	1	seq4.addSequenceFeature(new SequenceFeature("Helix", "", 2, 3,
61		Float.NaN, "g7"));
62
63		/*
64		* sort by ascending score, no filter on feature type or group
65		* NB sort order for the same feature set (none) gets toggled, so descending
66		*/
67	1	PA.setValue(AlignmentSorter.class, "sortByFeatureAscending", true);
68	1	AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
69		AlignmentSorter.FEATURE_SCORE);
70	1	assertSame(al.getSequenceAt(3), seq3); // -0.5
71	1	assertSame(al.getSequenceAt(2), seq2); // 2.5
72	1	assertSame(al.getSequenceAt(1), seq1); // 3.0
73	1	assertSame(al.getSequenceAt(0), seq4); // maximum 'score'
74
75		/*
76		* repeat sort toggles order - now ascending
77		*/
78	1	AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
79		AlignmentSorter.FEATURE_SCORE);
80	1	assertSame(al.getSequenceAt(0), seq3); // -0.5
81	1	assertSame(al.getSequenceAt(1), seq2); // 2.5
82	1	assertSame(al.getSequenceAt(2), seq1); // 3.0
83	1	assertSame(al.getSequenceAt(3), seq4);
84
85		/*
86		* specify features, excluding Pfam
87		* seq1 average is now 2.0
88		* next sort is ascending (not toggled) as for a different feature set
89		*/
90	1	List<String> types = Arrays.asList(new String[] { "Cath", "kD" });
91	1	AlignmentSorter.sortByFeature(types, null, 0, al.getWidth(), al,
92		AlignmentSorter.FEATURE_SCORE);
93	1	assertSame(al.getSequenceAt(0), seq3); // -0.5
94	1	assertSame(al.getSequenceAt(1), seq1); // 2.0
95	1	assertSame(al.getSequenceAt(2), seq2); // 2.5
96	1	assertSame(al.getSequenceAt(3), seq4);
97
98		/*
99		* specify groups, excluding g5 (kD -4 score)
100		* seq3 average is now 3.0
101		* next sort is ascending (not toggled) as for a different group spec
102		*/
103	1	List<String> groups = Arrays.asList(new String[] { "g1", "g2", "g3",
104		"g6" });
105	1	AlignmentSorter.sortByFeature(types, groups, 0, al.getWidth(), al,
106		AlignmentSorter.FEATURE_SCORE);
107	1	assertSame(al.getSequenceAt(0), seq1); // 2.0
108	1	assertSame(al.getSequenceAt(1), seq2); // 2.5
109	1	assertSame(al.getSequenceAt(2), seq3); // 3.0
110	1	assertSame(al.getSequenceAt(3), seq4);
111
112		/*
113		* limit to columns 0-4, excluding 2nd feature of seq1 and seq3
114		* seq1 is now 2.0, seq3 is now -4
115		*/
116		// fails because seq1.findPosition(4) returns 4
117		// although residue 4 is in column 5! - JAL-2544
118	1	AlignmentSorter.sortByFeature(null, null, 0, 4, al,
119		AlignmentSorter.FEATURE_SCORE);
120	1	assertSame(al.getSequenceAt(0), seq3); // -4
121	1	assertSame(al.getSequenceAt(1), seq1); // 2.0
122	1	assertSame(al.getSequenceAt(2), seq2); // 2.5
123	1	assertSame(al.getSequenceAt(3), seq4);
124		}
125
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: - 1PASS
126	1	@Test(groups = "Functional")...
127		public void testSortByFeature_density()
128		{
129		// TODO
130		}
131		}