Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblProtein	38	15	13	0.4285714342.9%	Show methods

Class EnsemblProtein

Class EnsemblProtein	Line # 38	Total Statements 15	Complexity 13	TOTAL Coverage 0.4285714342.9%
EnsemblProtein()   EnsemblProtein()	5151	1.01	1.01	1.0 1.0100%
EnsemblProtein(String)   EnsemblProtein(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%
isDnaCoding() : boolean   isDnaCoding() : boolean	8181	1.01	1.01	0.0 0.00%
getTestQuery() : String   getTestQuery() : String	9090	1.01	1.01	0.0 0.00%
addFeaturesAndProduct(String,AlignmentI) : void   addFeaturesAndProduct(String,AlignmentI) : void	100100	0.00	1.01	-1.0 -1.0 -
getFeaturesToFetch() : EnsemblFeatureType[]   getFeaturesToFetch() : EnsemblFeatureType[]	105105	1.01	1.01	0.0 0.00%
getIdentifyingFeatures(SequenceI,String) : List<SequenceFeature>   getIdentifyingFeatures(SequenceI,String) : List<SequenceFeature>	112112	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	119119	1.01	1.01	1.0 1.0100%
getAccessionIdFromQuery(String) : String   getAccessionIdFromQuery(String) : String	130130	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
27		import java.util.ArrayList;
28		import java.util.List;
29
30		import com.stevesoft.pat.Regex;
31
32		/**
33		* A client to fetch protein translated sequence for an Ensembl identifier
34		*
35		* @author gmcarstairs
36		*
37		*/
		42.9% Uncovered Elements: 16 (28) Complexity: 13 Complexity Density: 0.87
38		public class EnsemblProtein extends EnsemblSeqProxy
39		{
40		/*
41		* accepts ENSP with 11 digits
42		* or ENSMUSP or similar for other species
43		* or CCDSnnnnn.nn with at least 3 digits
44		*/
45		private static final Regex ACCESSION_REGEX = new Regex(
46		"(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
47
48		/**
49		* Default constructor (to use rest.ensembl.org)
50		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
51	10	public EnsemblProtein()...
52		{
53	10	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 EnsemblProtein(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 (Protein)";
70		}
71
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
72	0	@Override...
73		protected EnsemblSeqType getSourceEnsemblType()
74		{
75	0	return EnsemblSeqType.PROTEIN;
76		}
77
78		/**
79		* Returns false, as this fetcher does not retrieve DNA sequences.
80		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
81	0	@Override...
82		public boolean isDnaCoding()
83		{
84	0	return false;
85		}
86
87		/**
88		* Test query is to the protein translation of transcript ENST00000288602
89		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
90	0	@Override...
91		public String getTestQuery()
92		{
93	0	return "ENSP00000288602";
94		}
95
96		/**
97		* Overrides base class method to do nothing - genomic features are not
98		* applicable to the protein product sequence
99		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
100	0	@Override...
101		protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
102		{
103		}
104
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
105	0	@Override...
106		protected EnsemblFeatureType[] getFeaturesToFetch()
107		{
108		// not applicable - can't fetch genomic features for a protein sequence
109	0	return null;
110		}
111
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
112	0	@Override...
113		protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
114		String accId)
115		{
116	0	return new ArrayList<>();
117		}
118
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
119	5	@Override...
120		public Regex getAccessionValidator()
121		{
122	5	return ACCESSION_REGEX;
123		}
124
125		/**
126		* Returns an accession id for a query, including conversion of ENST* to
127		* ENSP*. This supports querying for the protein sequence for a transcript
128		* (ENST identifier) and returning the ENSP identifier.
129		*/
		87.5% Uncovered Elements: 1 (8) Complexity: 3 Complexity Density: 0.5
130	6	@Override...
131		public String getAccessionIdFromQuery(String query)
132		{
133	6	String accId = super.getAccessionIdFromQuery(query);
134
135		/*
136		* ensure last character before (11) digits is P
137		* ENST00000288602 -> ENSP00000288602
138		* ENSMUST00000288602 -> ENSMUSP00000288602
139		*/
140	6	if (accId != null && accId.length() >= 12)
141		{
142	6	char[] chars = accId.toCharArray();
143	6	chars[chars.length - 12] = 'P';
144	6	accId = new String(chars);
145		}
146	6	return accId;
147		}
148
149		}