Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EnsemblGenome	33	13	10	8	0.692307769.2%	Show methods

Class EnsemblGenome

Class EnsemblGenome	Line # 33	Total Statements 13	Complexity 10	Uncovered Elements 8	TOTAL Coverage 0.692307769.2%
EnsemblGenome()   EnsemblGenome()	4646	1.01	1.01	0.00	1.0 1.0100%
EnsemblGenome(String)   EnsemblGenome(String)	5656	1.01	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	6161	1.01	1.01	1.01	0.0 0.00%
getSourceEnsemblType() : EnsemblSeqType   getSourceEnsemblType() : EnsemblSeqType	6767	1.01	1.01	1.01	0.0 0.00%
getFeaturesToFetch() : EnsemblFeatureType[]   getFeaturesToFetch() : EnsemblFeatureType[]	7373	1.01	1.01	1.01	0.0 0.00%
retainFeature(SequenceFeature,String) : boolean   retainFeature(SequenceFeature,String) : boolean	8686	3.03	2.02	0.00	1.0 1.0100%
identifiesSequence(SequenceFeature,String) : boolean   identifiesSequence(SequenceFeature,String) : boolean	101101	5.05	3.03	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.46153846	jalview.ext.ensembl.EnsemblGenomeTest.testIdentifiesSequencejalview.ext.ensembl.EnsemblGenomeTest.testIdentifiesSequence	1PASS
	0.46153846	jalview.ext.ensembl.EnsemblGenomeTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblGenomeTest.testGetGenomicRangesFromFeatures	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
25		/**
26		* A client to fetch genomic sequence from Ensembl
27		*
28		* TODO: not currently used - delete?
29		*
30		* @author gmcarstairs
31		*
32		*/
		69.2% Uncovered Elements: 8 (26) Complexity: 10 Complexity Density: 0.77
33		public class EnsemblGenome extends EnsemblSeqProxy
34		{
35		/*
36		* fetch transcript features on genomic sequence (to identify the transcript
37		* regions) and cds, exon and variation features (to retain)
38		*/
39		private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
40		EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
41		EnsemblFeatureType.cds, EnsemblFeatureType.variation };
42
43		/**
44		* Default constructor (to use rest.ensembl.org)
45		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
46	3	public EnsemblGenome()...
47		{
48	3	super();
49		}
50
51		/**
52		* Constructor given the target domain to fetch data from
53		*
54		* @param d
55		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
56	0	public EnsemblGenome(String d)...
57		{
58	0	super(d);
59		}
60
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
61	0	@Override...
62		public String getDbName()
63		{
64	0	return "ENSEMBL (Genomic)";
65		}
66
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
67	0	@Override...
68		protected EnsemblSeqType getSourceEnsemblType()
69		{
70	0	return EnsemblSeqType.GENOMIC;
71		}
72
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
73	0	@Override...
74		protected EnsemblFeatureType[] getFeaturesToFetch()
75		{
76	0	return FEATURES_TO_FETCH;
77		}
78
79		/**
80		* Answers true unless the feature type is 'transcript' (or a sub-type of
81		* transcript in the Sequence Ontology), or has a parent other than the given
82		* accession id. Transcript features are only retrieved in order to identify
83		* the transcript sequence range, and are redundant information on the
84		* transcript sequence itself.
85		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
86	6	@Override...
87		protected boolean retainFeature(SequenceFeature sf, String accessionId)
88		{
89	6	if (isTranscript(sf.getType()))
90		{
91	3	return false;
92		}
93	3	return featureMayBelong(sf, accessionId);
94		}
95
96		/**
97		* Answers true if the sequence feature type is 'transcript' (or a subtype of
98		* transcript in the Sequence Ontology), and the ID of the feature is the
99		* transcript we are retrieving
100		*/
		100% Uncovered Elements: 0 (9) Complexity: 3 Complexity Density: 0.6
101	12	@Override...
102		protected boolean identifiesSequence(SequenceFeature sf, String accId)
103		{
104	12	if (isTranscript(sf.getType()))
105		{
106	9	String id = (String) sf.getValue("ID");
107	9	if (("transcript:" + accId).equals(id))
108		{
109	6	return true;
110		}
111		}
112	6	return false;
113		}
114
115		}