Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DBRefSource	39	9	7	1.0100%	Show methods

Class DBRefSource

Class DBRefSource	Line # 39	Total Statements 9	Complexity 7	TOTAL Coverage 1.0100%
getSourceKey(String) : int   getSourceKey(String) : int	9191	4.04	3.03	1.0 1.0100%
isPrimarySource(String) : boolean   isPrimarySource(String) : boolean	139139	1.01	1.01	1.0 1.0100%
isPrimaryCandidate(String) : boolean   isPrimaryCandidate(String) : boolean	144144	4.04	3.03	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.9	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS
	0.8	jalview.datamodel.SequenceTest.testGetPrimaryDBRefs_nucleotidejalview.datamodel.SequenceTest.testGetPrimaryDBRefs_nucleotide	1PASS
	0.7	jalview.datamodel.SequenceTest.testDeriveSequence_existingDatasetjalview.datamodel.SequenceTest.testDeriveSequence_existingDataset	1PASS
	0.7	jalview.datamodel.SequenceTest.testGetPrimaryDBRefs_peptidejalview.datamodel.SequenceTest.testGetPrimaryDBRefs_peptide	1PASS
	0.7	jalview.analysis.AlignmentUtilsTests.testMakeCdsAlignmentjalview.analysis.AlignmentUtilsTests.testMakeCdsAlignment	1PASS
	0.7	jalview.io.StockholmFileTest.dbrefOutputjalview.io.StockholmFileTest.dbrefOutput	1PASS
	0.55	jalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReport_withEllipsisjalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReport_withEllipsis	1PASS
	0.45	jalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReportjalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReport	1PASS
	0.45	jalview.io.StockholmFileTest.pfamFileIOjalview.io.StockholmFileTest.pfamFileIO	1PASS
	0.45	jalview.datamodel.DBRefEntryTest.testIsPrimaryCandidatejalview.datamodel.DBRefEntryTest.testIsPrimaryCandidate	1PASS
	0.35	jalview.io.StockholmFileTest.rfamFileIOjalview.io.StockholmFileTest.rfamFileIO	1PASS
	0.35	jalview.ext.ensembl.EnsemblXrefTest.testGetCrossReferencesjalview.ext.ensembl.EnsemblXrefTest.testGetCrossReferences	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		*/
		100% Uncovered Elements: 0 (20) Complexity: 7 Complexity Density: 0.78
39		public class DBRefSource
40		{
41
42
43
44		public static final String UNIPROT = "UNIPROT";
45		public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
46		/**
47		* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
48		*/
49		public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
50
51		public static final String ENSEMBL = "ENSEMBL";
52		public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
53
54		public static final String EMBL = "EMBL";
55		public static final String EMBLCDS = "EMBLCDS";
56		public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase();
57
58		public static final String PDB = "PDB";
59		public static final String PFAM = "PFAM";
60		public static final String RFAM = "RFAM";
61		public static final String GENEDB = "GeneDB".toUpperCase();
62
63		public static final String PDB_CANONICAL_NAME = PDB;
64
65
66		public static final String[] allSources = new String[] {
67		UNIPROT,
68		UP_NAME, UNIPROTKB,
69		ENSEMBL, ENSEMBLGENOMES,
70		EMBL, EMBLCDS, EMBLCDSProduct,
71		PDB, PFAM, RFAM, GENEDB
72		};
73
74		public static final int UNIPROT_MASK = 1<<0;
75		public static final int UP_NAME_MASK = 1<<1;
76		public static final int UNIPROT_KB_MASK = 1<<2;
77		public static final int ENSEMBL_MASK = 1<<3;
78		public static final int ENSEMBL_GENOMES_MASK = 1<<4;
79		public static final int EMBL_MASK = 1<<5;
80		public static final int EMBL_CDS_MASK = 1<<6;
81		public static final int EMBL_CDS_PRODUCT_MASK = 1<<7;
82		public static final int PDB_MASK = 1<<8;
83		public static final int PFAM_MASK = 1<<9;
84		public static final int RFAM_MASK = 1<<10;
85		public static final int GENE_DB_MASK = 1<<11;
86
87		public static final int MASK_COUNT = 12;
88
89		public static final int ALL_MASKS = (1 << MASK_COUNT) - 1;
90
		100% Uncovered Elements: 0 (8) Complexity: 3 Complexity Density: 0.75
91	614	public static int getSourceKey(String name) {...
92	6189	for (int i = 0; i < MASK_COUNT; i++) {
93	5812	if (name.equals(allSources[i]))
94		{
95	237	return 1<<i;
96		}
97		}
98	377	return 0;
99		}
100
101		public static final int PRIMARY_MASK = UNIPROT_MASK | ENSEMBL_MASK;
102
103		/**
104		* List of databases whose sequences might have coding regions annotated
105		*/
106		public static final String[] DNACODINGDBS = {
107		ENSEMBL, ENSEMBLGENOMES,
108		EMBL, EMBLCDS, GENEDB
109		};
110
111		public static final int DNA_CODING_MASK =
112		ENSEMBL_MASK | ENSEMBL_GENOMES_MASK
113		| EMBL_MASK | EMBL_CDS_MASK | GENE_DB_MASK;
114
115
116
117		public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
118
119		public static final int CODING_MASK = EMBL_CDS_MASK | GENE_DB_MASK | ENSEMBL_MASK;
120
121
122
123		public static final String[] PROTEINDBS = {
124		UNIPROT, UNIPROTKB,
125		ENSEMBL, EMBLCDSProduct }; // Ensembl ENSP* entries are protein
126
127		public static final int PROTEIN_MASK =
128		UNIPROT_MASK | UNIPROT_KB_MASK
129		| ENSEMBL_MASK | EMBL_CDS_PRODUCT_MASK ;
130
131
132		// for SequenceAnnotationReport only
133
134		// public static final String[][] PRIMARY_SOURCES = new String[][] {
135		// CODINGDBS, DNACODINGDBS, PROTEINDBS };
136		//
137		public static final int PRIMARY_SOURCES_MASK = CODING_MASK | DNA_CODING_MASK | PROTEIN_MASK;
138
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
139	290	public static boolean isPrimarySource(String source)...
140		{
141	290	return ((PRIMARY_SOURCES_MASK & getSourceKey(source)) != 0);
142		}
143
		100% Uncovered Elements: 0 (8) Complexity: 3 Complexity Density: 0.75
144	1066	public static boolean isPrimaryCandidate(String ucversion) { ...
145		// tricky - this test really needs to search the sequence's set of dbrefs to
146		// see if there is a primary reference that derived this reference.
147	6534	for (int i = allSources.length; --i >= 0;)
148		{
149	6467	if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources
150		{
151		// by convention, many secondary references inherit the primary
152		// reference's
153		// source string as a prefix for any version information from the
154		// secondary reference.
155	999	return false;
156		}
157		}
158	67	return true;
159		}
160
161
162
163
164		}