Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureProperties	29	6	5	0.3333333433.3%	Show methods

Class FeatureProperties

Class FeatureProperties	Line # 29	Total Statements 6	Complexity 5	TOTAL Coverage 0.3333333433.3%
isCodingFeature(String,String) : boolean   isCodingFeature(String,String) : boolean	4545	3.03	2.02	0.6 0.660%
getCodingFeature(String) : String   getCodingFeature(String) : String	6363	3.03	3.03	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.33333334	jalview.ws.dbsources.EmblXmlSourceTest.testGetSequencejalview.ws.dbsources.EmblXmlSourceTest.testGetSequence	1PASS

 

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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.datamodel;
22
23		/**
24		* A set of feature property constants used by jalview
25		*
26		* @author JimP
27		*
28		*/
		33.3% Uncovered Elements: 8 (12) Complexity: 5 Complexity Density: 0.83
29		public class FeatureProperties
30		{
31		public static final String EMBL_CODING_FEATURE = "CDS";
32
33		public static final String EXONPOS = "exon number";
34
35		public static final String EXONPRODUCT = "product";
36
37		/**
38		* lookup feature type for a particular database to see if its a coding region
39		* feature
40		*
41		* @param dbrefsource
42		* @param string
43		* @return
44		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
45	3	public static boolean isCodingFeature(String dbrefsource, String type)...
46		{
47	3	if (type.equalsIgnoreCase(EMBL_CODING_FEATURE))
48		{
49	3	return (dbrefsource == null
50		|| dbrefsource.equalsIgnoreCase(DBRefSource.EMBL)
51		|| dbrefsource.equalsIgnoreCase(DBRefSource.EMBLCDS));
52		}
53	0	return false;
54		}
55
56		/**
57		* Returns the coding feature name for a database source. Currently just
58		* hard-coded to return CDS for EMBL/EMBLCDS, else null.
59		*
60		* @param dbrefsource
61		* @return
62		*/
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
63	0	public static String getCodingFeature(String dbrefsource)...
64		{
65	0	if (DBRefSource.EMBL.equalsIgnoreCase(dbrefsource)
66		|| DBRefSource.EMBLCDS.equalsIgnoreCase(dbrefsource))
67		{
68	0	return EMBL_CODING_FEATURE;
69		}
70	0	return null;
71		}
72		}