Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EnsemblProtein	34	15	13	16	0.4285714342.9%	Show methods

Class EnsemblProtein

Class EnsemblProtein	Line # 34	Total Statements 15	Complexity 13	Uncovered Elements 16	TOTAL Coverage 0.4285714342.9%
EnsemblProtein()   EnsemblProtein()	4747	1.01	1.01	0.00	1.0 1.0100%
EnsemblProtein(String)   EnsemblProtein(String)	5757	1.01	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	6262	1.01	1.01	1.01	0.0 0.00%
getSourceEnsemblType() : EnsemblSeqType   getSourceEnsemblType() : EnsemblSeqType	6868	1.01	1.01	1.01	0.0 0.00%
isDnaCoding() : boolean   isDnaCoding() : boolean	7777	1.01	1.01	1.01	0.0 0.00%
getTestQuery() : String   getTestQuery() : String	8686	1.01	1.01	1.01	0.0 0.00%
addFeaturesAndProduct(String,AlignmentI) : void   addFeaturesAndProduct(String,AlignmentI) : void	9696	0.00	1.01	0.00	-1.0 -1.0 -
getFeaturesToFetch() : EnsemblFeatureType[]   getFeaturesToFetch() : EnsemblFeatureType[]	101101	1.01	1.01	1.01	0.0 0.00%
identifiesSequence(SequenceFeature,String) : boolean   identifiesSequence(SequenceFeature,String) : boolean	108108	1.01	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	115115	1.01	1.01	0.00	1.0 1.0100%
getAccessionIdFromQuery(String) : String   getAccessionIdFromQuery(String) : String	126126	6.06	3.03	1.01	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
26		import com.stevesoft.pat.Regex;
27
28		/**
29		* A client to fetch protein translated sequence for an Ensembl identifier
30		*
31		* @author gmcarstairs
32		*
33		*/
		42.9% Uncovered Elements: 16 (28) Complexity: 13 Complexity Density: 0.87
34		public class EnsemblProtein extends EnsemblSeqProxy
35		{
36		/*
37		* accepts ENSP with 11 digits
38		* or ENSMUSP or similar for other species
39		* or CCDSnnnnn.nn with at least 3 digits
40		*/
41		private static final Regex ACCESSION_REGEX = new Regex(
42		"(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
43
44		/**
45		* Default constructor (to use rest.ensembl.org)
46		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
47	4	public EnsemblProtein()...
48		{
49	4	super();
50		}
51
52		/**
53		* Constructor given the target domain to fetch data from
54		*
55		* @param d
56		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
57	0	public EnsemblProtein(String d)...
58		{
59	0	super(d);
60		}
61
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
62	0	@Override...
63		public String getDbName()
64		{
65	0	return "ENSEMBL (Protein)";
66		}
67
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
68	0	@Override...
69		protected EnsemblSeqType getSourceEnsemblType()
70		{
71	0	return EnsemblSeqType.PROTEIN;
72		}
73
74		/**
75		* Returns false, as this fetcher does not retrieve DNA sequences.
76		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
77	0	@Override...
78		public boolean isDnaCoding()
79		{
80	0	return false;
81		}
82
83		/**
84		* Test query is to the protein translation of transcript ENST00000288602
85		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
86	0	@Override...
87		public String getTestQuery()
88		{
89	0	return "ENSP00000288602";
90		}
91
92		/**
93		* Overrides base class method to do nothing - genomic features are not
94		* applicable to the protein product sequence
95		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
96	0	@Override...
97		protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
98		{
99		}
100
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
101	0	@Override...
102		protected EnsemblFeatureType[] getFeaturesToFetch()
103		{
104		// not applicable - can't fetch genomic features for a protein sequence
105	0	return null;
106		}
107
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
108	0	@Override...
109		protected boolean identifiesSequence(SequenceFeature sf, String accId)
110		{
111		// not applicable - protein sequence is not a 'subset' of genomic sequence
112	0	return false;
113		}
114
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
115	5	@Override...
116		public Regex getAccessionValidator()
117		{
118	5	return ACCESSION_REGEX;
119		}
120
121		/**
122		* Returns an accession id for a query, including conversion of ENST* to
123		* ENSP*. This supports querying for the protein sequence for a transcript
124		* (ENST identifier) and returning the ENSP identifier.
125		*/
		87.5% Uncovered Elements: 1 (8) Complexity: 3 Complexity Density: 0.5
126	6	@Override...
127		public String getAccessionIdFromQuery(String query)
128		{
129	6	String accId = super.getAccessionIdFromQuery(query);
130
131		/*
132		* ensure last character before (11) digits is P
133		* ENST00000288602 -> ENSP00000288602
134		* ENSMUST00000288602 -> ENSMUSP00000288602
135		*/
136	6	if (accId != null && accId.length() >= 12)
137		{
138	6	char[] chars = accId.toCharArray();
139	6	chars[chars.length - 12] = 'P';
140	6	accId = new String(chars);
141		}
142	6	return accId;
143		}
144
145		}