Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DBRefSource	41	11	8	0.916666791.7%	Show methods

Class DBRefSource

Class DBRefSource	Line # 41	Total Statements 11	Complexity 8	TOTAL Coverage 0.916666791.7%
getSourceKey(String) : int   getSourceKey(String) : int	108108	4.04	3.03	1.0 1.0100%
isPrimarySource(String) : boolean   isPrimarySource(String) : boolean	150150	1.01	1.01	1.0 1.0100%
isPrimaryCandidate(String) : boolean   isPrimaryCandidate(String) : boolean	155155	6.06	4.04	0.8333333 0.833333383.3%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.8333333	jalview.ws.dbsources.UniprotTest.testGetUniprotSequencejalview.ws.dbsources.UniprotTest.testGetUniprotSequence	1PASS
	0.8333333	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS
	0.75	jalview.datamodel.SequenceTest.testGetPrimaryDBRefs_nucleotidejalview.datamodel.SequenceTest.testGetPrimaryDBRefs_nucleotide	1PASS
	0.6666667	jalview.datamodel.SequenceTest.testDeriveSequence_existingDatasetjalview.datamodel.SequenceTest.testDeriveSequence_existingDataset	1PASS
	0.6666667	jalview.io.StockholmFileTest.dbrefOutputjalview.io.StockholmFileTest.dbrefOutput	1PASS
	0.6666667	jalview.analysis.AlignmentUtilsTests.testMakeCdsAlignmentjalview.analysis.AlignmentUtilsTests.testMakeCdsAlignment	1PASS
	0.6666667	jalview.datamodel.SequenceTest.testGetPrimaryDBRefs_peptidejalview.datamodel.SequenceTest.testGetPrimaryDBRefs_peptide	1PASS
	0.45833334	jalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReport_withEllipsisjalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReport_withEllipsis	1PASS
	0.45833334	jalview.datamodel.DBRefEntryTest.testIsPrimaryCandidatejalview.datamodel.DBRefEntryTest.testIsPrimaryCandidate	1PASS
	0.45833334	jalview.io.StockholmFileTest.pfamFileIOjalview.io.StockholmFileTest.pfamFileIO	1PASS
	0.375	jalview.io.StockholmFileTest.rfamFileIOjalview.io.StockholmFileTest.rfamFileIO	1PASS
	0.375	jalview.ext.ensembl.EnsemblXrefTest.testGetCrossReferencesjalview.ext.ensembl.EnsemblXrefTest.testGetCrossReferences	1PASS
	0.375	jalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReportjalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReport	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		/**
24		* BH 2018 SwingJS note: If additional final static Strings are added to this
25		* file, they should be added to public static final String[] allTypes.
26		*
27		* Defines internal constants for unambiguous annotation of DbRefEntry source
28		* strings and describing the data retrieved from external database sources (see
29		* jalview.ws.DbSourcProxy) <br/>
30		* TODO: replace with ontology to allow recognition of particular attributes
31		* (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
32		* genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
33		*
34		*
35		*
36		* @author JimP
37		*
38		*/
39		import java.util.Locale;
40
		91.7% Uncovered Elements: 2 (24) Complexity: 8 Complexity Density: 0.73
41		public class DBRefSource
42		{
43
44		public static final String UNIPROT = "UNIPROT";
45
46		public static final String UP_NAME = "UNIPROT_NAME"
47		.toUpperCase(Locale.ROOT);
48
49		/**
50		* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
51		*/
52		public static final String UNIPROTKB = "UniProtKB/TrEMBL"
53		.toUpperCase(Locale.ROOT);
54
55		public static final String ENSEMBL = "ENSEMBL";
56
57		public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
58
59		public static final String EMBL = "EMBL";
60
61		public static final String EMBLCDS = "EMBLCDS";
62
63		public static final String EMBLCDSProduct = "EMBLCDSProtein"
64		.toUpperCase(Locale.ROOT);
65
66		public static final String PDB = "PDB";
67
68		public static final String PFAM = "PFAM";
69
70		public static final String RFAM = "RFAM";
71
72		public static final String GENEDB = "GeneDB".toUpperCase(Locale.ROOT);
73
74		public static final String PDB_CANONICAL_NAME = PDB;
75
76		public static final String[] allSources = new String[] { UNIPROT, UP_NAME,
77		UNIPROTKB, ENSEMBL, ENSEMBLGENOMES, EMBL, EMBLCDS, EMBLCDSProduct,
78		PDB, PFAM, RFAM, GENEDB };
79
80		public static final int UNIPROT_MASK = 1 << 0;
81
82		public static final int UP_NAME_MASK = 1 << 1;
83
84		public static final int UNIPROT_KB_MASK = 1 << 2;
85
86		public static final int ENSEMBL_MASK = 1 << 3;
87
88		public static final int ENSEMBL_GENOMES_MASK = 1 << 4;
89
90		public static final int EMBL_MASK = 1 << 5;
91
92		public static final int EMBL_CDS_MASK = 1 << 6;
93
94		public static final int EMBL_CDS_PRODUCT_MASK = 1 << 7;
95
96		public static final int PDB_MASK = 1 << 8;
97
98		public static final int PFAM_MASK = 1 << 9;
99
100		public static final int RFAM_MASK = 1 << 10;
101
102		public static final int GENE_DB_MASK = 1 << 11;
103
104		public static final int MASK_COUNT = 12;
105
106		public static final int ALL_MASKS = (1 << MASK_COUNT) - 1;
107
		100% Uncovered Elements: 0 (8) Complexity: 3 Complexity Density: 0.75
108	356	public static int getSourceKey(String name)...
109		{
110	3148	for (int i = 0; i < MASK_COUNT; i++)
111		{
112	2999	if (name.equals(allSources[i]))
113		{
114	207	return 1 << i;
115		}
116		}
117	149	return 0;
118		}
119
120		public static final int PRIMARY_MASK = UNIPROT_MASK | ENSEMBL_MASK;
121
122		/**
123		* List of databases whose sequences might have coding regions annotated
124		*/
125		public static final String[] DNACODINGDBS = { ENSEMBL, ENSEMBLGENOMES,
126		EMBL, EMBLCDS, GENEDB };
127
128		public static final int DNA_CODING_MASK = ENSEMBL_MASK
129		| ENSEMBL_GENOMES_MASK | EMBL_MASK | EMBL_CDS_MASK | GENE_DB_MASK;
130
131		public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
132
133		public static final int CODING_MASK = EMBL_CDS_MASK | GENE_DB_MASK
134		| ENSEMBL_MASK;
135
136		public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB, ENSEMBL,
137		EMBLCDSProduct }; // Ensembl ENSP* entries are protein
138
139		public static final int PROTEIN_MASK = UNIPROT_MASK | UNIPROT_KB_MASK
140		| ENSEMBL_MASK | EMBL_CDS_PRODUCT_MASK;
141
142		// for SequenceAnnotationReport only
143
144		// public static final String[][] PRIMARY_SOURCES = new String[][] {
145		// CODINGDBS, DNACODINGDBS, PROTEINDBS };
146		//
147		public static final int PRIMARY_SOURCES_MASK = CODING_MASK
148		| DNA_CODING_MASK | PROTEIN_MASK;
149
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
150	48	public static boolean isPrimarySource(String source)...
151		{
152	48	return ((PRIMARY_SOURCES_MASK & getSourceKey(source)) != 0);
153		}
154
		83.3% Uncovered Elements: 2 (12) Complexity: 4 Complexity Density: 0.67
155	834	public static boolean isPrimaryCandidate(String ucversion)...
156		{
157	834	if (ucversion == null)
158		{
159		// Null/empty version is not a real reference ?
160	0	return false;
161		}
162		// tricky - this test really needs to search the sequence's set of dbrefs to
163		// see if there is a primary reference that derived this reference.
164	4436	for (int i = allSources.length; --i >= 0;)
165		{
166	4376	if (ucversion.startsWith(allSources[i])) // BH 2019.01.25
167		// .toUpperCase(Locale.ROOT)
168		// unnecessary here for
169		// allSources
170		{
171		// by convention, many secondary references inherit the primary
172		// reference's
173		// source string as a prefix for any version information from the
174		// secondary reference.
175	774	return false;
176		}
177		}
178	60	return true;
179		}
180
181		}