Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EnsemblCdna	37	15	12	10	0.666666766.7%	Show methods

Class EnsemblCdna

Class EnsemblCdna	Line # 37	Total Statements 15	Complexity 12	Uncovered Elements 10	TOTAL Coverage 0.666666766.7%
EnsemblCdna()   EnsemblCdna()	5858	1.01	1.01	0.00	1.0 1.0100%
EnsemblCdna(String)   EnsemblCdna(String)	6868	1.01	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	7373	1.01	1.01	1.01	0.0 0.00%
getSourceEnsemblType() : EnsemblSeqType   getSourceEnsemblType() : EnsemblSeqType	7979	1.01	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	8585	1.01	1.01	0.00	1.0 1.0100%
getFeaturesToFetch() : EnsemblFeatureType[]   getFeaturesToFetch() : EnsemblFeatureType[]	9191	1.01	1.01	1.01	0.0 0.00%
retainFeature(SequenceFeature,String) : boolean   retainFeature(SequenceFeature,String) : boolean	101101	3.03	2.02	0.00	1.0 1.0100%
identifiesSequence(SequenceFeature,String) : boolean   identifiesSequence(SequenceFeature,String) : boolean	116116	5.05	3.03	0.00	1.0 1.0100%
getObjectType() : String   getObjectType() : String	135135	1.01	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.4	jalview.ext.ensembl.EnsemblCdnaTest.testIdentifiesSequencejalview.ext.ensembl.EnsemblCdnaTest.testIdentifiesSequence	1PASS
	0.4	jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures	1PASS
	0.4	jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_reverseStrandjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_reverseStrand	1PASS
	0.3	jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_mixedStrandjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_mixedStrand	1PASS
	0.26666668	jalview.ext.ensembl.EnsemblCdnaTest.testRetainFeaturejalview.ext.ensembl.EnsemblCdnaTest.testRetainFeature	1PASS
	0.13333334	jalview.ext.ensembl.EnsemblCdnaTest.testIsValidReferencejalview.ext.ensembl.EnsemblCdnaTest.testIsValidReference	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.ext.ensembl;
22
23		import jalview.datamodel.SequenceFeature;
24		import jalview.io.gff.SequenceOntologyFactory;
25		import jalview.io.gff.SequenceOntologyI;
26
27		import com.stevesoft.pat.Regex;
28
29		/**
30		* A client to fetch CDNA sequence from Ensembl (i.e. that part of the genomic
31		* sequence that is transcribed to RNA, but not necessarily translated to
32		* protein)
33		*
34		* @author gmcarstairs
35		*
36		*/
		66.7% Uncovered Elements: 10 (30) Complexity: 12 Complexity Density: 0.8
37		public class EnsemblCdna extends EnsemblSeqProxy
38		{
39		/*
40		* accepts ENST or ENSTG with 11 digits
41		* or ENSMUST or similar for other species
42		* or CCDSnnnnn.nn with at least 3 digits
43		*/
44		private static final Regex ACCESSION_REGEX = new Regex(
45		"(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
46
47		/*
48		* fetch exon features on genomic sequence (to identify the cdna regions)
49		* and cds and variation features (to retain)
50		*/
51		private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
52		EnsemblFeatureType.exon, EnsemblFeatureType.cds,
53		EnsemblFeatureType.variation };
54
55		/**
56		* Default constructor (to use rest.ensembl.org)
57		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
58	7	public EnsemblCdna()...
59		{
60	7	super();
61		}
62
63		/**
64		* Constructor given the target domain to fetch data from
65		*
66		* @param d
67		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
68	0	public EnsemblCdna(String d)...
69		{
70	0	super(d);
71		}
72
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
73	0	@Override...
74		public String getDbName()
75		{
76	0	return "ENSEMBL (CDNA)";
77		}
78
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
79	0	@Override...
80		protected EnsemblSeqType getSourceEnsemblType()
81		{
82	0	return EnsemblSeqType.CDNA;
83		}
84
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
85	6	@Override...
86		public Regex getAccessionValidator()
87		{
88	6	return ACCESSION_REGEX;
89		}
90
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
91	0	@Override...
92		protected EnsemblFeatureType[] getFeaturesToFetch()
93		{
94	0	return FEATURES_TO_FETCH;
95		}
96
97		/**
98		* Answers true unless the feature type is 'transcript' (or a sub-type in the
99		* Sequence Ontology).
100		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
101	7	@Override...
102		protected boolean retainFeature(SequenceFeature sf, String accessionId)
103		{
104	7	if (isTranscript(sf.getType()))
105		{
106	3	return false;
107		}
108	4	return featureMayBelong(sf, accessionId);
109		}
110
111		/**
112		* Answers true if the sequence feature type is 'exon' (or a subtype of exon
113		* in the Sequence Ontology), and the Parent of the feature is the transcript
114		* we are retrieving
115		*/
		100% Uncovered Elements: 0 (9) Complexity: 3 Complexity Density: 0.6
116	16	@Override...
117		protected boolean identifiesSequence(SequenceFeature sf, String accId)
118		{
119	16	if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
120		SequenceOntologyI.EXON))
121		{
122	12	String parentFeature = (String) sf.getValue(PARENT);
123	12	if (("transcript:" + accId).equals(parentFeature))
124		{
125	8	return true;
126		}
127		}
128	8	return false;
129		}
130
131		/**
132		* Parameter object_type=Transcaript added to ensure cdna and not peptide is
133		* returned (JAL-2529)
134		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
135	0	@Override...
136		protected String getObjectType()
137		{
138	0	return OBJECT_TYPE_TRANSCRIPT;
139		}
140
141		}