Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblGenome	38	15	9	0.692307769.2%	Show methods

Class EnsemblGenome

Class EnsemblGenome	Line # 38	Total Statements 15	Complexity 9	TOTAL Coverage 0.692307769.2%
EnsemblGenome()   EnsemblGenome()	5151	1.01	1.01	1.0 1.0100%
EnsemblGenome(String)   EnsemblGenome(String)	6161	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	6666	1.01	1.01	0.0 0.00%
getSourceEnsemblType() : EnsemblSeqType   getSourceEnsemblType() : EnsemblSeqType	7272	1.01	1.01	0.0 0.00%
getFeaturesToFetch() : EnsemblFeatureType[]   getFeaturesToFetch() : EnsemblFeatureType[]	7878	1.01	1.01	0.0 0.00%
retainFeature(SequenceFeature,String) : boolean   retainFeature(SequenceFeature,String) : boolean	9191	3.03	2.02	1.0 1.0100%
getIdentifyingFeatures(SequenceI,String) : List<SequenceFeature>   getIdentifyingFeatures(SequenceI,String) : List<SequenceFeature>	110110	7.07	2.02	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.46153846	jalview.ext.ensembl.EnsemblGenomeTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblGenomeTest.testGetGenomicRangesFromFeatures	1PASS
	0.46153846	jalview.ext.ensembl.EnsemblGenomeTest.testGetIdentifyingFeaturesjalview.ext.ensembl.EnsemblGenomeTest.testGetIdentifyingFeatures	1PASS
	0.30769232	jalview.ext.ensembl.EnsemblGenomeTest.testRetainFeaturejalview.ext.ensembl.EnsemblGenomeTest.testRetainFeature	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		/**
31		* A client to fetch genomic sequence from Ensembl
32		*
33		* TODO: not currently used - delete?
34		*
35		* @author gmcarstairs
36		*
37		*/
		69.2% Uncovered Elements: 8 (26) Complexity: 9 Complexity Density: 0.6
38		public class EnsemblGenome extends EnsemblSeqProxy
39		{
40		/*
41		* fetch transcript features on genomic sequence (to identify the transcript
42		* regions) and cds, exon and variation features (to retain)
43		*/
44		private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
45		EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
46		EnsemblFeatureType.cds, EnsemblFeatureType.variation };
47
48		/**
49		* Default constructor (to use rest.ensembl.org)
50		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
51	3	public EnsemblGenome()...
52		{
53	3	super();
54		}
55
56		/**
57		* Constructor given the target domain to fetch data from
58		*
59		* @param d
60		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
61	0	public EnsemblGenome(String d)...
62		{
63	0	super(d);
64		}
65
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
66	0	@Override...
67		public String getDbName()
68		{
69	0	return "ENSEMBL (Genomic)";
70		}
71
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
72	0	@Override...
73		protected EnsemblSeqType getSourceEnsemblType()
74		{
75	0	return EnsemblSeqType.GENOMIC;
76		}
77
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
78	0	@Override...
79		protected EnsemblFeatureType[] getFeaturesToFetch()
80		{
81	0	return FEATURES_TO_FETCH;
82		}
83
84		/**
85		* Answers true unless the feature type is 'transcript' (or a sub-type of
86		* transcript in the Sequence Ontology), or has a parent other than the given
87		* accession id. Transcript features are only retrieved in order to identify
88		* the transcript sequence range, and are redundant information on the
89		* transcript sequence itself.
90		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
91	6	@Override...
92		protected boolean retainFeature(SequenceFeature sf, String accessionId)
93		{
94	6	if (isTranscript(sf.getType()))
95		{
96	3	return false;
97		}
98	3	return featureMayBelong(sf, accessionId);
99		}
100
101		/**
102		* Answers a list of sequence features (if any) whose type is 'transcript' (or
103		* a subtype of transcript in the Sequence Ontology), and whose ID is the
104		* accession we are retrieving.
105		* <p>
106		* Note we also include features of type "NMD_transcript_variant", although
107		* not strictly 'transcript' in the SO, as they used in Ensembl as if they
108		* were.
109		*/
		100% Uncovered Elements: 0 (9) Complexity: 2 Complexity Density: 0.29
110	2	@Override...
111		protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
112		String accId)
113		{
114	2	List<SequenceFeature> result = new ArrayList<>();
115	2	List<SequenceFeature> sfs = seq.getFeatures().getFeaturesByOntology(
116		SequenceOntologyI.TRANSCRIPT,
117		SequenceOntologyI.NMD_TRANSCRIPT_VARIANT);
118	2	for (SequenceFeature sf : sfs)
119		{
120	9	String id = (String) sf.getValue(JSON_ID);
121	9	if (accId.equals(id))
122		{
123	6	result.add(sf);
124		}
125		}
126	2	return result;
127		}
128
129		}