Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblCds	41	19	10	0.5806451458.1%	Show methods

Class EnsemblCds

Class EnsemblCds	Line # 41	Total Statements 19	Complexity 10	TOTAL Coverage 0.5806451458.1%
EnsemblCds()   EnsemblCds()	5454	1.01	1.01	1.0 1.0100%
EnsemblCds(String)   EnsemblCds(String)	6464	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	6969	1.01	1.01	0.0 0.00%
getSourceEnsemblType() : EnsemblSeqType   getSourceEnsemblType() : EnsemblSeqType	7575	1.01	1.01	0.0 0.00%
getFeaturesToFetch() : EnsemblFeatureType[]   getFeaturesToFetch() : EnsemblFeatureType[]	8181	1.01	1.01	0.0 0.00%
retainFeature(SequenceFeature,String) : boolean   retainFeature(SequenceFeature,String) : boolean	9393	3.03	2.02	1.0 1.0100%
getIdentifyingFeatures(SequenceI,String) : List<SequenceFeature>   getIdentifyingFeatures(SequenceI,String) : List<SequenceFeature>	109109	7.07	2.02	1.0 1.0100%
getCdsRanges(SequenceI) : List<int[]>   getCdsRanges(SequenceI) : List<int[]>	133133	4.04	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.38709676	jalview.ext.ensembl.EnsemblCdsTest.testGetIdentifyingFeaturesjalview.ext.ensembl.EnsemblCdsTest.testGetIdentifyingFeatures	1PASS
	0.38709676	jalview.ext.ensembl.EnsemblCdsTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblCdsTest.testGetGenomicRangesFromFeatures	1PASS
	0.2580645	jalview.ext.ensembl.EnsemblCdsTest.testRetainFeaturejalview.ext.ensembl.EnsemblCdsTest.testRetainFeature	1PASS
	0.06451613	jalview.ext.ensembl.EnsemblCdsTest.testIsValidReferencejalview.ext.ensembl.EnsemblCdsTest.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.SequenceOntologyFactory;
26		import jalview.io.gff.SequenceOntologyI;
27
28		import java.util.ArrayList;
29		import java.util.List;
30
31		/**
32		* A client for direct fetching of CDS sequences from Ensembl (i.e. that part of
33		* the genomic sequence that is translated to protein)
34		*
35		* TODO: not currently used as CDS sequences are computed from CDS features on
36		* transcripts - delete this class?
37		*
38		* @author gmcarstairs
39		*
40		*/
		58.1% Uncovered Elements: 13 (31) Complexity: 10 Complexity Density: 0.53
41		public class EnsemblCds extends EnsemblSeqProxy
42		{
43		/*
44		* fetch cds features on genomic sequence (to identify the CDS regions)
45		* and exon and variation features (to retain for display)
46		*/
47		private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
48		EnsemblFeatureType.cds, EnsemblFeatureType.exon,
49		EnsemblFeatureType.variation };
50
51		/**
52		* Default constructor (to use rest.ensembl.org)
53		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
54	4	public EnsemblCds()...
55		{
56	4	super();
57		}
58
59		/**
60		* Constructor given the target domain to fetch data from
61		*
62		* @param d
63		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
64	0	public EnsemblCds(String d)...
65		{
66	0	super(d);
67		}
68
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
69	0	@Override...
70		public String getDbName()
71		{
72	0	return "ENSEMBL (CDS)";
73		}
74
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
75	0	@Override...
76		protected EnsemblSeqType getSourceEnsemblType()
77		{
78	0	return EnsemblSeqType.CDS;
79		}
80
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
81	0	@Override...
82		protected EnsemblFeatureType[] getFeaturesToFetch()
83		{
84	0	return FEATURES_TO_FETCH;
85		}
86
87		/**
88		* Answers true unless the feature type is 'CDS' (or a sub-type of CDS in the
89		* Sequence Ontology). CDS features are only retrieved in order to identify
90		* the cds sequence range, and are redundant information on the cds sequence
91		* itself.
92		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
93	5	@Override...
94		protected boolean retainFeature(SequenceFeature sf, String accessionId)
95		{
96	5	if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
97		SequenceOntologyI.CDS))
98		{
99	2	return false;
100		}
101	3	return featureMayBelong(sf, accessionId);
102		}
103
104		/**
105		* Answers a list of sequence features (if any) whose type is 'CDS' (or a
106		* subtype of CDS in the Sequence Ontology), and whose Parent is the
107		* transcript we are retrieving
108		*/
		100% Uncovered Elements: 0 (9) Complexity: 2 Complexity Density: 0.29
109	2	@Override...
110		protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
111		String accId)
112		{
113	2	List<SequenceFeature> result = new ArrayList<>();
114	2	List<SequenceFeature> sfs = seq.getFeatures()
115		.getFeaturesByOntology(SequenceOntologyI.CDS);
116	2	for (SequenceFeature sf : sfs)
117		{
118	7	String parentFeature = (String) sf.getValue(PARENT);
119	7	if (accId.equals(parentFeature))
120		{
121	4	result.add(sf);
122		}
123		}
124	2	return result;
125		}
126
127		/**
128		* Overrides this method to trivially return a range which is the whole of the
129		* nucleotide sequence. This is both faster than scanning for CDS features,
130		* and also means we don't need to keep CDS features on CDS sequence (where
131		* they are redundant information).
132		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
133	0	protected List<int[]> getCdsRanges(SequenceI dnaSeq)...
134		{
135	0	int len = dnaSeq.getLength();
136	0	List<int[]> ranges = new ArrayList<>();
137	0	ranges.add(new int[] { 1, len });
138	0	return ranges;
139		}
140
141		}