Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Pfam	39	13	10	0.00%	Show methods

Class Pfam

Class Pfam	Line # 39	Total Statements 13	Complexity 10	TOTAL Coverage 0.00%
getPfamDownloadURL(String,String) : String   getPfamDownloadURL(String,String) : String	4444	4.04	1.01	0.0 0.00%
<clinit>, line 61()   <clinit>, line 61()	6161	1.01	1.01	0.0 0.00%
Pfam()   Pfam()	6666	1.01	1.01	0.0 0.00%
getURL(String) : String   getURL(String) : String	7171	1.01	1.01	0.0 0.00%
getAccessionSeparator() : String   getAccessionSeparator() : String	8383	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	9494	1.01	1.01	0.0 0.00%
getDbVersion() : String   getDbVersion() : String	124124	1.01	1.01	0.0 0.00%
getURLPrefix() : String   getURLPrefix() : String	130130	1.01	1.01	0.0 0.00%
isValidReference(String) : boolean   isValidReference(String) : boolean	141141	1.01	1.01	0.0 0.00%
getXfamSource() : String   getXfamSource() : String	151151	1.01	1.01	0.0 0.00%

 

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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.ws.dbsources;
22
23		import java.util.Locale;
24
25		import com.stevesoft.pat.Regex;
26
27		import jalview.bin.Cache;
28		import jalview.datamodel.DBRefSource;
29		import jalview.util.Platform;
30
31		/**
32		* TODO: later PFAM is a complex datasource - it could return a tree in addition
33		* to an alignment TODO: create interface to pass alignment properties and tree
34		* back to sequence fetcher
35		*
36		* @author JimP
37		*
38		*/
		0% Uncovered Elements: 23 (23) Complexity: 10 Complexity Density: 0.77
39		abstract public class Pfam extends Xfam
40		{
41		public static final String FULL = "full", RP35 = "rp35", RP15 = "rp15",
42		RP75 = "rp75", RP55 = "rp55", SEED = "seed", UNIPROT = "uniprot";
43
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
44	0	public String getPfamDownloadURL(String id, String alType)...
45		{
46	0	String url = Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
47	0	url = url.replace("$PFAMID$", id);
48	0	url = url.replace("$ALTYPE$", alType);
49	0	return url;
50		}
51
52		static final String PFAM_BASEURL_KEY = "PFAM_INTERPRO_URL_TEMPLATE";
53
54		protected String alignmentType;
55
56		/**
57		* docs are http://www.ebi.ac.uk/interpro/api/
58		*/
59		private static final String DEFAULT_PFAM_BASEURL = "https://www.ebi.ac.uk/interpro/api/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$";
60
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
61	0	static...
62		{
63	0	Platform.addJ2SDirectDatabaseCall(DEFAULT_PFAM_BASEURL);
64		}
65
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
66	0	public Pfam()...
67		{
68	0	super();
69		}
70
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
71	0	@Override...
72		String getURL(String queries)
73		{
74	0	return getPfamDownloadURL(queries.trim().toUpperCase(Locale.ROOT),
75		alignmentType);
76		}
77
78		/*
79		* (non-Javadoc)
80		*
81		* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
82		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	@Override...
84		public String getAccessionSeparator()
85		{
86	0	return null;
87		}
88
89		/*
90		* (non-Javadoc)
91		*
92		* @see jalview.ws.DbSourceProxy#getAccessionValidator()
93		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
94	0	@Override...
95		public Regex getAccessionValidator()
96		{
97	0	return null;
98		}
99
100		/*
101		* (non-Javadoc)
102		*
103		* @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
104		* this doesn't work - DbSource is key for the hash of DbSourceProxy instances
105		* - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
106		* 'alignment' source - means proxy is higher level than a sequence source.
107		* return jalview.datamodel.DBRefSource.PFAM; }
108		*/
109
110		/*
111		* (non-Javadoc)
112		*
113		* @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
114		* getDbSourceProperties() {
115		*
116		* return null; }
117		*/
118
119		/*
120		* (non-Javadoc)
121		*
122		* @see jalview.ws.DbSourceProxy#getDbVersion()
123		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
124	0	@Override...
125		public String getDbVersion()
126		{
127	0	return null;
128		}
129
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
130	0	@Override...
131		protected String getURLPrefix()
132		{
133	0	return Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
134		}
135
136		/*
137		* (non-Javadoc)
138		*
139		* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
140		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
141	0	@Override...
142		public boolean isValidReference(String accession)
143		{
144	0	return accession.indexOf("PF") == 0;
145		}
146
147		/*
148		* public String getDbName() { return "PFAM"; // getDbSource(); }
149		*/
150
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
151	0	@Override...
152		public String getXfamSource()
153		{
154	0	return DBRefSource.PFAM;
155		}
156		}