Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblProtein	39	15	13	0.4285714342.9%	Show methods

Class EnsemblProtein

Class EnsemblProtein	Line # 39	Total Statements 15	Complexity 13	TOTAL Coverage 0.4285714342.9%
EnsemblProtein()   EnsemblProtein()	5252	1.01	1.01	1.0 1.0100%
EnsemblProtein(String)   EnsemblProtein(String)	6262	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	6767	1.01	1.01	0.0 0.00%
getSourceEnsemblType() : EnsemblSeqType   getSourceEnsemblType() : EnsemblSeqType	7373	1.01	1.01	0.0 0.00%
isDnaCoding() : boolean   isDnaCoding() : boolean	8282	1.01	1.01	0.0 0.00%
getTestQuery() : String   getTestQuery() : String	9191	1.01	1.01	0.0 0.00%
addFeaturesAndProduct(String,AlignmentI) : void   addFeaturesAndProduct(String,AlignmentI) : void	101101	0.00	1.01	-1.0 -1.0 -
getFeaturesToFetch() : EnsemblFeatureType[]   getFeaturesToFetch() : EnsemblFeatureType[]	106106	1.01	1.01	0.0 0.00%
getIdentifyingFeatures(SequenceI,String) : List<SequenceFeature>   getIdentifyingFeatures(SequenceI,String) : List<SequenceFeature>	113113	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	120120	1.01	1.01	1.0 1.0100%
getAccessionIdFromQuery(String) : String   getAccessionIdFromQuery(String) : String	131131	6.06	3.03	0.875 0.87587.5%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.35714287	jalview.ext.ensembl.EnsemblProteinTest.testGetAccesionIdFromQueryjalview.ext.ensembl.EnsemblProteinTest.testGetAccesionIdFromQuery	1PASS
	0.14285715	jalview.ext.ensembl.EnsemblProteinTest.testIsValidReferencejalview.ext.ensembl.EnsemblProteinTest.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.AlignmentI;
24		import jalview.datamodel.SequenceFeature;
25		import jalview.datamodel.SequenceI;
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 protein translated sequence for an Ensembl identifier
35		*
36		* @author gmcarstairs
37		*
38		*/
		42.9% Uncovered Elements: 16 (28) Complexity: 13 Complexity Density: 0.87
39		public class EnsemblProtein extends EnsemblSeqProxy
40		{
41		/*
42		* accepts ENSP with 11 digits
43		* or ENSMUSP or similar for other species
44		* or CCDSnnnnn.nn with at least 3 digits
45		*/
46		private static final Regex ACCESSION_REGEX = Platform.newRegex(
47		"(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
48
49		/**
50		* Default constructor (to use rest.ensembl.org)
51		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
52	10	public EnsemblProtein()...
53		{
54	10	super();
55		}
56
57		/**
58		* Constructor given the target domain to fetch data from
59		*
60		* @param d
61		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
62	0	public EnsemblProtein(String d)...
63		{
64	0	super(d);
65		}
66
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
67	0	@Override...
68		public String getDbName()
69		{
70	0	return "ENSEMBL (Protein)";
71		}
72
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
73	0	@Override...
74		protected EnsemblSeqType getSourceEnsemblType()
75		{
76	0	return EnsemblSeqType.PROTEIN;
77		}
78
79		/**
80		* Returns false, as this fetcher does not retrieve DNA sequences.
81		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
82	0	@Override...
83		public boolean isDnaCoding()
84		{
85	0	return false;
86		}
87
88		/**
89		* Test query is to the protein translation of transcript ENST00000288602
90		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
91	0	@Override...
92		public String getTestQuery()
93		{
94	0	return "ENSP00000288602";
95		}
96
97		/**
98		* Overrides base class method to do nothing - genomic features are not
99		* applicable to the protein product sequence
100		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
101	0	@Override...
102		protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
103		{
104		}
105
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
106	0	@Override...
107		protected EnsemblFeatureType[] getFeaturesToFetch()
108		{
109		// not applicable - can't fetch genomic features for a protein sequence
110	0	return null;
111		}
112
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
113	0	@Override...
114		protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
115		String accId)
116		{
117	0	return new ArrayList<>();
118		}
119
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
120	5	@Override...
121		public Regex getAccessionValidator()
122		{
123	5	return ACCESSION_REGEX;
124		}
125
126		/**
127		* Returns an accession id for a query, including conversion of ENST* to
128		* ENSP*. This supports querying for the protein sequence for a transcript
129		* (ENST identifier) and returning the ENSP identifier.
130		*/
		87.5% Uncovered Elements: 1 (8) Complexity: 3 Complexity Density: 0.5
131	6	@Override...
132		public String getAccessionIdFromQuery(String query)
133		{
134	6	String accId = super.getAccessionIdFromQuery(query);
135
136		/*
137		* ensure last character before (11) digits is P
138		* ENST00000288602 -> ENSP00000288602
139		* ENSMUST00000288602 -> ENSMUSP00000288602
140		*/
141	6	if (accId != null && accId.length() >= 12)
142		{
143	6	char[] chars = accId.toCharArray();
144	6	chars[chars.length - 12] = 'P';
145	6	accId = new String(chars);
146		}
147	6	return accId;
148		}
149
150		}