Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentSorterTest	38	48	2	1.0100%	Show methods

Class AlignmentSorterTest

Class AlignmentSorterTest	Line # 38	Total Statements 48	Complexity 2	TOTAL Coverage 1.0100%
testSortByFeature_score() : void   testSortByFeature_score() : void	4040	48.048	1.01	1.0 1.0100%
testSortByFeature_density() : void   testSortByFeature_density() : void	148148	0.00	1.01	-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

 

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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.analysis;
22
23		import static org.testng.Assert.assertSame;
24
25		import jalview.datamodel.Alignment;
26		import jalview.datamodel.AlignmentI;
27		import jalview.datamodel.Sequence;
28		import jalview.datamodel.SequenceFeature;
29		import jalview.datamodel.SequenceI;
30
31		import java.util.Arrays;
32		import java.util.List;
33
34		import junit.extensions.PA;
35
36		import org.testng.annotations.Test;
37
		100% Uncovered Elements: 0 (50) Complexity: 2 Complexity Density: 0.04
38		public class AlignmentSorterTest
39		{
		100% Uncovered Elements: 0 (48) Complexity: 1 Complexity Density: 0.02 1PASS
40	1	@Test(groups = "Functional")...
41		public void testSortByFeature_score()
42		{
43	1	SequenceI seq1 = new Sequence("Seq1", "ABC--D-EFGHIJ");
44	1	SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
45	1	SequenceI seq3 = new Sequence("Seq3", "ABCDE-FGHIJ");
46	1	SequenceI seq4 = new Sequence("Seq4", "ABCDEFGHIJ");
47	1	SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
48	1	AlignmentI al = new Alignment(seqs);
49	1	al.setDataset(null);
50
51		/*
52		* sort with no score features does nothing
53		*/
54	1	PA.setValue(AlignmentSorter.class, "sortByFeatureCriteria", null);
55
56	1	AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
57		AlignmentSorter.FEATURE_SCORE);
58	1	assertSame(al.getSequenceAt(0), seq1);
59	1	assertSame(al.getSequenceAt(1), seq2);
60	1	assertSame(al.getSequenceAt(2), seq3);
61	1	assertSame(al.getSequenceAt(3), seq4);
62
63		/*
64		* add score and non-score features
65		* seq1 Cath(2.0) Pfam(4.0) average 3.0
66		* seq2 Cath(2.5) Metal(NaN) average 2.5
67		* seq3 KD(-4), KD(3.0) average -0.5
68		* seq4 Helix(NaN) - should sort as if largest score
69		*/
70	1	seq1.addSequenceFeature(
71		new SequenceFeature("Cath", "", 2, 3, 2.0f, "g1"));
72	1	seq1.addSequenceFeature(
73		new SequenceFeature("Pfam", "", 4, 5, 4.0f, "g2"));
74	1	seq2.addSequenceFeature(
75		new SequenceFeature("Cath", "", 2, 3, 2.5f, "g3"));
76	1	seq2.addSequenceFeature(
77		new SequenceFeature("Metal", "", 2, 3, Float.NaN, "g4"));
78	1	seq3.addSequenceFeature(new SequenceFeature("kD", "", 2, 3, -4f, "g5"));
79	1	seq3.addSequenceFeature(
80		new SequenceFeature("kD", "", 5, 6, 3.0f, "g6"));
81	1	seq4.addSequenceFeature(
82		new SequenceFeature("Helix", "", 2, 3, Float.NaN, "g7"));
83
84		/*
85		* sort by ascending score, no filter on feature type or group
86		* NB sort order for the same feature set (none) gets toggled, so descending
87		*/
88	1	PA.setValue(AlignmentSorter.class, "sortByFeatureAscending", true);
89	1	AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
90		AlignmentSorter.FEATURE_SCORE);
91	1	assertSame(al.getSequenceAt(3), seq3); // -0.5
92	1	assertSame(al.getSequenceAt(2), seq2); // 2.5
93	1	assertSame(al.getSequenceAt(1), seq1); // 3.0
94	1	assertSame(al.getSequenceAt(0), seq4); // maximum 'score'
95
96		/*
97		* repeat sort toggles order - now ascending
98		*/
99	1	AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
100		AlignmentSorter.FEATURE_SCORE);
101	1	assertSame(al.getSequenceAt(0), seq3); // -0.5
102	1	assertSame(al.getSequenceAt(1), seq2); // 2.5
103	1	assertSame(al.getSequenceAt(2), seq1); // 3.0
104	1	assertSame(al.getSequenceAt(3), seq4);
105
106		/*
107		* specify features, excluding Pfam
108		* seq1 average is now 2.0
109		* next sort is ascending (not toggled) as for a different feature set
110		*/
111	1	List<String> types = Arrays.asList(new String[] { "Cath", "kD" });
112	1	AlignmentSorter.sortByFeature(types, null, 0, al.getWidth(), al,
113		AlignmentSorter.FEATURE_SCORE);
114	1	assertSame(al.getSequenceAt(0), seq3); // -0.5
115	1	assertSame(al.getSequenceAt(1), seq1); // 2.0
116	1	assertSame(al.getSequenceAt(2), seq2); // 2.5
117	1	assertSame(al.getSequenceAt(3), seq4);
118
119		/*
120		* specify groups, excluding g5 (kD -4 score)
121		* seq3 average is now 3.0
122		* next sort is ascending (not toggled) as for a different group spec
123		*/
124	1	List<String> groups = Arrays
125		.asList(new String[]
126		{ "g1", "g2", "g3", "g6" });
127	1	AlignmentSorter.sortByFeature(types, groups, 0, al.getWidth(), al,
128		AlignmentSorter.FEATURE_SCORE);
129	1	assertSame(al.getSequenceAt(0), seq1); // 2.0
130	1	assertSame(al.getSequenceAt(1), seq2); // 2.5
131	1	assertSame(al.getSequenceAt(2), seq3); // 3.0
132	1	assertSame(al.getSequenceAt(3), seq4);
133
134		/*
135		* limit to columns 0-4, excluding 2nd feature of seq1 and seq3
136		* seq1 is now 2.0, seq3 is now -4
137		*/
138		// fails because seq1.findPosition(4) returns 4
139		// although residue 4 is in column 5! - JAL-2544
140	1	AlignmentSorter.sortByFeature(null, null, 0, 4, al,
141		AlignmentSorter.FEATURE_SCORE);
142	1	assertSame(al.getSequenceAt(0), seq3); // -4
143	1	assertSame(al.getSequenceAt(1), seq1); // 2.0
144	1	assertSame(al.getSequenceAt(2), seq2); // 2.5
145	1	assertSame(al.getSequenceAt(3), seq4);
146		}
147
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: - 1PASS
148	1	@Test(groups = "Functional")...
149		public void testSortByFeature_density()
150		{
151		// TODO
152		}
153		}