Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblCdna	40	17	11	0.666666766.7%	Show methods

Class EnsemblCdna

Class EnsemblCdna	Line # 40	Total Statements 17	Complexity 11	TOTAL Coverage 0.666666766.7%
EnsemblCdna()   EnsemblCdna()	6161	1.01	1.01	1.0 1.0100%
EnsemblCdna(String)   EnsemblCdna(String)	7171	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	7676	1.01	1.01	0.0 0.00%
getSourceEnsemblType() : EnsemblSeqType   getSourceEnsemblType() : EnsemblSeqType	8282	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	8888	1.01	1.01	1.0 1.0100%
getFeaturesToFetch() : EnsemblFeatureType[]   getFeaturesToFetch() : EnsemblFeatureType[]	9494	1.01	1.01	0.0 0.00%
retainFeature(SequenceFeature,String) : boolean   retainFeature(SequenceFeature,String) : boolean	104104	3.03	2.02	1.0 1.0100%
getIdentifyingFeatures(SequenceI,String) : List<SequenceFeature>   getIdentifyingFeatures(SequenceI,String) : List<SequenceFeature>	119119	7.07	2.02	1.0 1.0100%
getObjectType() : String   getObjectType() : String	142142	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.testGetIdentifyingFeaturesjalview.ext.ensembl.EnsemblCdnaTest.testGetIdentifyingFeatures	1PASS
	0.4	jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_reverseStrandjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_reverseStrand	1PASS
	0.4	jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures	1PASS
	0.33333334	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.datamodel.SequenceI;
25		import jalview.io.gff.SequenceOntologyI;
26
27		import java.util.ArrayList;
28		import java.util.List;
29
30		import com.stevesoft.pat.Regex;
31
32		/**
33		* A client to fetch CDNA sequence from Ensembl (i.e. that part of the genomic
34		* sequence that is transcribed to RNA, but not necessarily translated to
35		* protein)
36		*
37		* @author gmcarstairs
38		*
39		*/
		66.7% Uncovered Elements: 10 (30) Complexity: 11 Complexity Density: 0.65
40		public class EnsemblCdna extends EnsemblSeqProxy
41		{
42		/*
43		* accepts ENST or ENSTG with 11 digits
44		* or ENSMUST or similar for other species
45		* or CCDSnnnnn.nn with at least 3 digits
46		*/
47		private static final Regex ACCESSION_REGEX = new Regex(
48		"(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
49
50		/*
51		* fetch exon features on genomic sequence (to identify the cdna regions)
52		* and cds and variation features (to retain)
53		*/
54		private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
55		EnsemblFeatureType.exon, EnsemblFeatureType.cds,
56		EnsemblFeatureType.variation };
57
58		/**
59		* Default constructor (to use rest.ensembl.org)
60		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
61	10	public EnsemblCdna()...
62		{
63	10	super();
64		}
65
66		/**
67		* Constructor given the target domain to fetch data from
68		*
69		* @param d
70		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
71	0	public EnsemblCdna(String d)...
72		{
73	0	super(d);
74		}
75
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
76	0	@Override...
77		public String getDbName()
78		{
79	0	return "ENSEMBL (CDNA)";
80		}
81
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
82	0	@Override...
83		protected EnsemblSeqType getSourceEnsemblType()
84		{
85	0	return EnsemblSeqType.CDNA;
86		}
87
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
88	6	@Override...
89		public Regex getAccessionValidator()
90		{
91	6	return ACCESSION_REGEX;
92		}
93
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
94	0	@Override...
95		protected EnsemblFeatureType[] getFeaturesToFetch()
96		{
97	0	return FEATURES_TO_FETCH;
98		}
99
100		/**
101		* Answers true unless the feature type is 'transcript' (or a sub-type in the
102		* Sequence Ontology).
103		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
104	7	@Override...
105		protected boolean retainFeature(SequenceFeature sf, String accessionId)
106		{
107	7	if (isTranscript(sf.getType()))
108		{
109	3	return false;
110		}
111	4	return featureMayBelong(sf, accessionId);
112		}
113
114		/**
115		* Answers a list of sequence features (if any) whose type is 'exon' (or a
116		* subtype of exon in the Sequence Ontology), and whose Parent is the
117		* transcript we are retrieving
118		*/
		100% Uncovered Elements: 0 (9) Complexity: 2 Complexity Density: 0.29
119	4	@Override...
120		protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
121		String accId)
122		{
123	4	List<SequenceFeature> result = new ArrayList<>();
124	4	List<SequenceFeature> sfs = seq.getFeatures()
125		.getFeaturesByOntology(SequenceOntologyI.EXON);
126	4	for (SequenceFeature sf : sfs)
127		{
128	12	String parentFeature = (String) sf.getValue(PARENT);
129	12	if (accId.equals(parentFeature))
130		{
131	6	result.add(sf);
132		}
133		}
134
135	4	return result;
136		}
137
138		/**
139		* Parameter object_type=Transcaript added to ensure cdna and not peptide is
140		* returned (JAL-2529)
141		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
142	0	@Override...
143		protected String getObjectType()
144		{
145	0	return OBJECT_TYPE_TRANSCRIPT;
146		}
147
148		}