Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Rfam	33	7	7	0.285714328.6%	Show methods

Class Rfam

Class Rfam	Line # 33	Total Statements 7	Complexity 7	TOTAL Coverage 0.285714328.6%
getURLPrefix() : String   getURLPrefix() : String	4444	1.01	1.01	1.0 1.0100%
Rfam()   Rfam()	5050	1.01	1.01	1.0 1.0100%
getAccessionSeparator() : String   getAccessionSeparator() : String	6161	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	7272	1.01	1.01	0.0 0.00%
getDbVersion() : String   getDbVersion() : String	9595	1.01	1.01	0.0 0.00%
isValidReference(String) : boolean   isValidReference(String) : boolean	106106	1.01	1.01	0.0 0.00%
getXfamSource() : String   getXfamSource() : String	117117	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.2857143	jalview.ws.dbsources.RfamSeedTest.testGetURLjalview.ws.dbsources.RfamSeedTest.testGetURL	1PASS
	0.2857143	jalview.ws.dbsources.RfamFullTest.testGetURLjalview.ws.dbsources.RfamFullTest.testGetURL	1PASS
	0.14285715	jalview.ws.SequenceFetcherTest.testNoDuplicatesInFetchDbRefsjalview.ws.SequenceFetcherTest.testNoDuplicatesInFetchDbRefs	1PASS
	0.14285715	jalview.ws.seqfetcher.DbRefFetcherTest.testStandardProtDbsjalview.ws.seqfetcher.DbRefFetcherTest.testStandardProtDbs	1PASS
	0.14285715	jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere	1PASS
	0.14285715	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	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.ws.dbsources;
22
23		import jalview.bin.Cache;
24		import jalview.datamodel.DBRefSource;
25
26		import com.stevesoft.pat.Regex;
27
28		/**
29		* Contains methods for fetching sequences from Rfam database
30		*
31		* @author Lauren Michelle Lui
32		*/
		28.6% Uncovered Elements: 10 (14) Complexity: 7 Complexity Density: 1
33		abstract public class Rfam extends Xfam
34		{
35		static final String RFAM_BASEURL_KEY = "RFAM_BASEURL";
36
37		private static final String DEFAULT_RFAM_BASEURL = "https://rfam.xfam.org";
38
39		/*
40		* append to URLs to retrieve as a gzipped file
41		*/
42		protected static final String GZIPPED = "?gzip=1&download=1";
43
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
44	4	@Override...
45		protected String getURLPrefix()
46		{
47	4	return Cache.getDefault(RFAM_BASEURL_KEY, DEFAULT_RFAM_BASEURL);
48		}
49
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
50	12	public Rfam()...
51		{
52	12	super();
53		}
54
55		/*
56		* (non-Javadoc)
57		*
58		* @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for
59		* consistency with Pfam class
60		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
61	0	@Override...
62		public String getAccessionSeparator()
63		{
64	0	return null;
65		}
66
67		/*
68		* (non-Javadoc)
69		*
70		* @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for
71		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
72	0	@Override...
73		public Regex getAccessionValidator()
74		{
75	0	return null;
76		}
77
78		/*
79		* (non-Javadoc)
80		*
81		* Left here for consistency with Pfam class
82		*
83		* @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
84		* this doesn't work - DbSource is key for the hash of DbSourceProxy instances
85		* - 1:many mapping for DbSource to proxy will be lost. * suggest : RFAM is an
86		* 'alignment' source - means proxy is higher level than a sequence source.
87		* return jalview.datamodel.DBRefSource.RFAM; }
88		*/
89
90		/*
91		* (non-Javadoc)
92		*
93		* @see jalview.ws.DbSourceProxy#getDbVersion()
94		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
95	0	@Override...
96		public String getDbVersion()
97		{
98	0	return null;
99		}
100
101		/*
102		* (non-Javadoc)
103		*
104		* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
105		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
106	0	@Override...
107		public boolean isValidReference(String accession)
108		{
109	0	return accession.indexOf("RF") == 0;
110		}
111
112		/*
113		* (non-Javadoc)
114		*
115		* @see jalview.ws.dbsources.Xfam#getXfamSource()
116		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
117	0	@Override...
118		public String getXfamSource()
119		{
120	0	return DBRefSource.RFAM;
121		}
122
123		}