Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Rfam	34	8	8	0.37537.5%	Show methods

Class Rfam

Class Rfam	Line # 34	Total Statements 8	Complexity 8	TOTAL Coverage 0.37537.5%
<clinit>, line 40()   <clinit>, line 40()	4040	1.01	1.01	1.0 1.0100%
getURLPrefix() : String   getURLPrefix() : String	5050	1.01	1.01	1.0 1.0100%
Rfam()   Rfam()	5656	1.01	1.01	1.0 1.0100%
getAccessionSeparator() : String   getAccessionSeparator() : String	6767	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	7878	1.01	1.01	0.0 0.00%
getDbVersion() : String   getDbVersion() : String	101101	1.01	1.01	0.0 0.00%
isValidReference(String) : boolean   isValidReference(String) : boolean	112112	1.01	1.01	0.0 0.00%
getXfamSource() : String   getXfamSource() : String	123123	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.25	jalview.ws.dbsources.RfamSeedTest.testGetURLjalview.ws.dbsources.RfamSeedTest.testGetURL	1PASS
	0.25	jalview.ws.dbsources.RfamFullTest.testGetURLjalview.ws.dbsources.RfamFullTest.testGetURL	1PASS
	0.125	jalview.gui.AnnotationLabelsTest2.testIdWidthChangesjalview.gui.AnnotationLabelsTest2.testIdWidthChanges	1PASS
	0.125	jalview.ws.SequenceFetcherTest.testNoDuplicatesInFetchDbRefsjalview.ws.SequenceFetcherTest.testNoDuplicatesInFetchDbRefs	1PASS
	0.125	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS
	0.125	jalview.ws.seqfetcher.DbRefFetcherTest.testStandardProtDbsjalview.ws.seqfetcher.DbRefFetcherTest.testStandardProtDbs	1PASS
	0.125	jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest	1PASS
	0.125	jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest	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		import jalview.util.Platform;
26
27		import com.stevesoft.pat.Regex;
28
29		/**
30		* Contains methods for fetching sequences from Rfam database
31		*
32		* @author Lauren Michelle Lui
33		*/
		37.5% Uncovered Elements: 10 (16) Complexity: 8 Complexity Density: 1
34		abstract public class Rfam extends Xfam
35		{
36		static final String RFAM_BASEURL_KEY = "RFAM_BASEURL";
37
38		private static final String DEFAULT_RFAM_BASEURL = "https://rfam.org";
39
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
40	7	static...
41		{
42	7	Platform.addJ2SDirectDatabaseCall(DEFAULT_RFAM_BASEURL);
43		}
44
45		/*
46		* append to URLs to retrieve as a gzipped file
47		*/
48		protected static final String GZIPPED = "?gzip=1&download=1";
49
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
50	4	@Override...
51		protected String getURLPrefix()
52		{
53	4	return Cache.getDefault(RFAM_BASEURL_KEY, DEFAULT_RFAM_BASEURL);
54		}
55
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
56	20	public Rfam()...
57		{
58	20	super();
59		}
60
61		/*
62		* (non-Javadoc)
63		*
64		* @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for
65		* consistency with Pfam class
66		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
67	0	@Override...
68		public String getAccessionSeparator()
69		{
70	0	return null;
71		}
72
73		/*
74		* (non-Javadoc)
75		*
76		* @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for
77		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
78	0	@Override...
79		public Regex getAccessionValidator()
80		{
81	0	return null;
82		}
83
84		/*
85		* (non-Javadoc)
86		*
87		* Left here for consistency with Pfam class
88		*
89		* @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
90		* this doesn't work - DbSource is key for the hash of DbSourceProxy instances
91		* - 1:many mapping for DbSource to proxy will be lost. * suggest : RFAM is an
92		* 'alignment' source - means proxy is higher level than a sequence source.
93		* return jalview.datamodel.DBRefSource.RFAM; }
94		*/
95
96		/*
97		* (non-Javadoc)
98		*
99		* @see jalview.ws.DbSourceProxy#getDbVersion()
100		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
101	0	@Override...
102		public String getDbVersion()
103		{
104	0	return null;
105		}
106
107		/*
108		* (non-Javadoc)
109		*
110		* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
111		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
112	0	@Override...
113		public boolean isValidReference(String accession)
114		{
115	0	return accession.indexOf("RF") == 0;
116		}
117
118		/*
119		* (non-Javadoc)
120		*
121		* @see jalview.ws.dbsources.Xfam#getXfamSource()
122		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
123	0	@Override...
124		public String getXfamSource()
125		{
126	0	return DBRefSource.RFAM;
127		}
128
129		}