Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblCdna	41	17	11	0.666666766.7%	Show methods

Class EnsemblCdna

Class EnsemblCdna	Line # 41	Total Statements 17	Complexity 11	TOTAL Coverage 0.666666766.7%
EnsemblCdna()   EnsemblCdna()	6262	1.01	1.01	1.0 1.0100%
EnsemblCdna(String)   EnsemblCdna(String)	7272	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	7777	1.01	1.01	0.0 0.00%
getSourceEnsemblType() : EnsemblSeqType   getSourceEnsemblType() : EnsemblSeqType	8383	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	8989	1.01	1.01	1.0 1.0100%
getFeaturesToFetch() : EnsemblFeatureType[]   getFeaturesToFetch() : EnsemblFeatureType[]	9595	1.01	1.01	0.0 0.00%
retainFeature(SequenceFeature,String) : boolean   retainFeature(SequenceFeature,String) : boolean	105105	3.03	2.02	1.0 1.0100%
getIdentifyingFeatures(SequenceI,String) : List<SequenceFeature>   getIdentifyingFeatures(SequenceI,String) : List<SequenceFeature>	120120	7.07	2.02	1.0 1.0100%
getObjectType() : String   getObjectType() : String	143143	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.testGetGenomicRangesFromFeatures_reverseStrandjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_reverseStrand	1PASS
	0.4	jalview.ext.ensembl.EnsemblCdnaTest.testGetIdentifyingFeaturesjalview.ext.ensembl.EnsemblCdnaTest.testGetIdentifyingFeatures	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		import jalview.util.Platform;
27
28		import java.util.ArrayList;
29		import java.util.List;
30
31		import com.stevesoft.pat.Regex;
32
33		/**
34		* A client to fetch CDNA sequence from Ensembl (i.e. that part of the genomic
35		* sequence that is transcribed to RNA, but not necessarily translated to
36		* protein)
37		*
38		* @author gmcarstairs
39		*
40		*/
		66.7% Uncovered Elements: 10 (30) Complexity: 11 Complexity Density: 0.65
41		public class EnsemblCdna extends EnsemblSeqProxy
42		{
43		/*
44		* accepts ENST or ENSTG with 11 digits
45		* or ENSMUST or similar for other species
46		* or CCDSnnnnn.nn with at least 3 digits
47		*/
48		private static final Regex ACCESSION_REGEX = Platform.newRegex(
49		"(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
50
51		/*
52		* fetch exon features on genomic sequence (to identify the cdna regions)
53		* and cds and variation features (to retain)
54		*/
55		private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
56		EnsemblFeatureType.exon, EnsemblFeatureType.cds,
57		EnsemblFeatureType.variation };
58
59		/**
60		* Default constructor (to use rest.ensembl.org)
61		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
62	10	public EnsemblCdna()...
63		{
64	10	super();
65		}
66
67		/**
68		* Constructor given the target domain to fetch data from
69		*
70		* @param d
71		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
72	0	public EnsemblCdna(String d)...
73		{
74	0	super(d);
75		}
76
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
77	0	@Override...
78		public String getDbName()
79		{
80	0	return "ENSEMBL (CDNA)";
81		}
82
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	@Override...
84		protected EnsemblSeqType getSourceEnsemblType()
85		{
86	0	return EnsemblSeqType.CDNA;
87		}
88
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
89	6	@Override...
90		public Regex getAccessionValidator()
91		{
92	6	return ACCESSION_REGEX;
93		}
94
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
95	0	@Override...
96		protected EnsemblFeatureType[] getFeaturesToFetch()
97		{
98	0	return FEATURES_TO_FETCH;
99		}
100
101		/**
102		* Answers true unless the feature type is 'transcript' (or a sub-type in the
103		* Sequence Ontology).
104		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
105	7	@Override...
106		protected boolean retainFeature(SequenceFeature sf, String accessionId)
107		{
108	7	if (isTranscript(sf.getType()))
109		{
110	3	return false;
111		}
112	4	return featureMayBelong(sf, accessionId);
113		}
114
115		/**
116		* Answers a list of sequence features (if any) whose type is 'exon' (or a
117		* subtype of exon in the Sequence Ontology), and whose Parent is the
118		* transcript we are retrieving
119		*/
		100% Uncovered Elements: 0 (9) Complexity: 2 Complexity Density: 0.29
120	4	@Override...
121		protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
122		String accId)
123		{
124	4	List<SequenceFeature> result = new ArrayList<>();
125	4	List<SequenceFeature> sfs = seq.getFeatures()
126		.getFeaturesByOntology(SequenceOntologyI.EXON);
127	4	for (SequenceFeature sf : sfs)
128		{
129	12	String parentFeature = (String) sf.getValue(PARENT);
130	12	if (accId.equals(parentFeature))
131		{
132	6	result.add(sf);
133		}
134		}
135
136	4	return result;
137		}
138
139		/**
140		* Parameter object_type=Transcaript added to ensure cdna and not peptide is
141		* returned (JAL-2529)
142		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
143	0	@Override...
144		protected String getObjectType()
145		{
146	0	return OBJECT_TYPE_TRANSCRIPT;
147		}
148
149		}