Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Pfam	36	7	7	0.285714328.6%	Show methods

Class Pfam

Class Pfam	Line # 36	Total Statements 7	Complexity 7	TOTAL Coverage 0.285714328.6%
Pfam()   Pfam()	4747	1.01	1.01	1.0 1.0100%
getAccessionSeparator() : String   getAccessionSeparator() : String	5757	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	6868	1.01	1.01	0.0 0.00%
getDbVersion() : String   getDbVersion() : String	9898	1.01	1.01	0.0 0.00%
getURLPrefix() : String   getURLPrefix() : String	104104	1.01	1.01	1.0 1.0100%
isValidReference(String) : boolean   isValidReference(String) : boolean	115115	1.01	1.01	0.0 0.00%
getXfamSource() : String   getXfamSource() : String	125125	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.2857143	jalview.ws.dbsources.PfamFullTest.testGetURLjalview.ws.dbsources.PfamFullTest.testGetURL	1PASS
	0.2857143	jalview.ws.dbsources.PfamSeedTest.testGetURLjalview.ws.dbsources.PfamSeedTest.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		* TODO: later PFAM is a complex datasource - it could return a tree in addition
30		* to an alignment TODO: create interface to pass alignment properties and tree
31		* back to sequence fetcher
32		*
33		* @author JimP
34		*
35		*/
		28.6% Uncovered Elements: 10 (14) Complexity: 7 Complexity Density: 1
36		abstract public class Pfam extends Xfam
37		{
38		/*
39		* append to URLs to retrieve as a gzipped file
40		*/
41		protected static final String GZIPPED = "/gzipped";
42
43		static final String PFAM_BASEURL_KEY = "PFAM_BASEURL";
44
45		private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org";
46
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
47	20	public Pfam()...
48		{
49	20	super();
50		}
51
52		/*
53		* (non-Javadoc)
54		*
55		* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
56		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
57	0	@Override...
58		public String getAccessionSeparator()
59		{
60	0	return null;
61		}
62
63		/*
64		* (non-Javadoc)
65		*
66		* @see jalview.ws.DbSourceProxy#getAccessionValidator()
67		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
68	0	@Override...
69		public Regex getAccessionValidator()
70		{
71	0	return null;
72		}
73
74		/*
75		* (non-Javadoc)
76		*
77		* @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
78		* this doesn't work - DbSource is key for the hash of DbSourceProxy instances
79		* - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
80		* 'alignment' source - means proxy is higher level than a sequence source.
81		* return jalview.datamodel.DBRefSource.PFAM; }
82		*/
83
84		/*
85		* (non-Javadoc)
86		*
87		* @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
88		* getDbSourceProperties() {
89		*
90		* return null; }
91		*/
92
93		/*
94		* (non-Javadoc)
95		*
96		* @see jalview.ws.DbSourceProxy#getDbVersion()
97		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
98	0	@Override...
99		public String getDbVersion()
100		{
101	0	return null;
102		}
103
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
104	4	@Override...
105		protected String getURLPrefix()
106		{
107	4	return Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
108		}
109
110		/*
111		* (non-Javadoc)
112		*
113		* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
114		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
115	0	@Override...
116		public boolean isValidReference(String accession)
117		{
118	0	return accession.indexOf("PF") == 0;
119		}
120
121		/*
122		* public String getDbName() { return "PFAM"; // getDbSource(); }
123		*/
124
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
125	0	@Override...
126		public String getXfamSource()
127		{
128	0	return DBRefSource.PFAM;
129		}
130
131		}