Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GeneLocus	39	7	8	0.937593.8%	Show methods

Class GeneLocus

Class GeneLocus	Line # 39	Total Statements 7	Complexity 8	TOTAL Coverage 0.937593.8%
GeneLocus(String,String,String,Mapping)   GeneLocus(String,String,String,Mapping)	5151	1.01	1.01	1.0 1.0100%
GeneLocus(String,String,String)   GeneLocus(String,String,String)	6464	1.01	1.01	1.0 1.0100%
equals(Object) : boolean   equals(Object) : boolean	6969	1.01	1.01	1.0 1.0100%
getMapping() : MapList   getMapping() : MapList	7575	1.01	2.02	0.6666667 0.666666766.7%
getSpeciesId() : String   getSpeciesId() : String	8585	1.01	1.01	1.0 1.0100%
getAssemblyId() : String   getAssemblyId() : String	9595	1.01	1.01	1.0 1.0100%
getChromosomeId() : String   getChromosomeId() : String	105105	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.8125	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS
	0.6875	jalview.io.vcf.VCFLoaderTest.testDoLoadjalview.io.vcf.VCFLoaderTest.testDoLoad	1PASS
	0.6875	jalview.io.vcf.VCFLoaderTest.testDoLoad_reverseStrandjalview.io.vcf.VCFLoaderTest.testDoLoad_reverseStrand	1PASS
	0.6875	jalview.analysis.AlignmentUtilsTests.testTransferGeneLocijalview.analysis.AlignmentUtilsTests.testTransferGeneLoci	1PASS
	0.6875	jalview.io.vcf.VCFLoaderTest.testDoLoad_vepCsqjalview.io.vcf.VCFLoaderTest.testDoLoad_vepCsq	1PASS
	0.375	jalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocusjalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocus	1PASS

 

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 jalview.util.MapList;
24
25		/**
26		* A specialisation of DBRefEntry used to hold the chromosomal coordinates for a
27		* (typically gene) sequence
28		* <ul>
29		* <li>field <code>source</code> is used to hold a species id e.g. human</li>
30		* <li>field <code>version</code> is used to hold assembly id e.g GRCh38</li>
31		* <li>field <code>accession</code> is used to hold the chromosome id</li>
32		* <li>field <code>map</code> is used to hold the mapping from sequence to
33		* chromosome coordinates</li>
34		* </ul>
35		*
36		* @author gmcarstairs
37		*
38		*/
		93.8% Uncovered Elements: 1 (16) Complexity: 8 Complexity Density: 1.14
39		public class GeneLocus extends DBRefEntry implements GeneLociI
40		{
41		/**
42		* Constructor adapts species, assembly, chromosome to DBRefEntry source,
43		* version, accession, respectively, and saves the mapping of sequence to
44		* chromosomal coordinates
45		*
46		* @param speciesId
47		* @param assemblyId
48		* @param chromosomeId
49		* @param mapping
50		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
51	59	public GeneLocus(String speciesId, String assemblyId, String chromosomeId,...
52		Mapping mapping)
53		{
54	59	super(speciesId, assemblyId, chromosomeId, mapping);
55		}
56
57		/**
58		* Constructor
59		*
60		* @param speciesId
61		* @param assemblyId
62		* @param chromosomeId
63		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
64	23	public GeneLocus(String speciesId, String assemblyId, String chromosomeId)...
65		{
66	23	this(speciesId, assemblyId, chromosomeId, null);
67		}
68
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
69	2	@Override...
70		public boolean equals(Object o)
71		{
72	2	return o instanceof GeneLocus && super.equals(o);
73		}
74
		66.7% Uncovered Elements: 1 (3) Complexity: 2 Complexity Density: 2
75	35	@Override...
76		public MapList getMapping()
77		{
78	35	return map == null ? null : map.getMap();
79		}
80
81		/**
82		* Answers the species identifier e.g. "human", stored as field
83		* <code>source</code> of DBRefEntry
84		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
85	34	@Override...
86		public String getSpeciesId()
87		{
88	34	return getSource();
89		}
90
91		/**
92		* Answers the genome assembly id e.g. "GRCh38", stored as field
93		* <code>version</code> of DBRefEntry
94		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
95	35	@Override...
96		public String getAssemblyId()
97		{
98	35	return getVersion();
99		}
100
101		/**
102		* Answers the chromosome identifier e.g. "X", stored as field
103		* <code>accession</code> of DBRefEntry
104		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
105	35	@Override...
106		public String getChromosomeId()
107		{
108	35	return getAccessionId();
109		}
110
111		}