Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Xfam	39	14	7	0.00%	Show methods

Class Xfam

Class Xfam	Line # 39	Total Statements 14	Complexity 7	TOTAL Coverage 0.00%
Xfam()   Xfam()	4141	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	5858	10.010	3.03	0.0 0.00%
getURL(String) : String   getURL(String) : String	8888	1.01	1.01	0.0 0.00%
isAlignmentSource() : boolean   isAlignmentSource() : boolean	9797	1.01	1.01	0.0 0.00%
getURLSuffix() : String   getURLSuffix() : String	108108	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 jalview.bin.Console;
26		import jalview.datamodel.AlignmentI;
27		import jalview.datamodel.DBRefEntry;
28		import jalview.io.DataSourceType;
29		import jalview.io.FileFormat;
30		import jalview.io.FormatAdapter;
31		import jalview.ws.seqfetcher.DbSourceProxyImpl;
32
33		/**
34		* Acts as a superclass for the Rfam and Pfam classes
35		*
36		* @author Lauren Michelle Lui
37		*
38		*/
		0% Uncovered Elements: 23 (23) Complexity: 7 Complexity Density: 0.5
39		public abstract class Xfam extends DbSourceProxyImpl
40		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
41	0	public Xfam()...
42		{
43	0	super();
44		}
45
46		/**
47		* the base URL for this Xfam-like service
48		*
49		* @return
50		*/
51		protected abstract String getURLPrefix();
52
53		@Override
54		public abstract String getDbVersion();
55
56		abstract String getXfamSource();
57
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
58	0	@Override...
59		public AlignmentI getSequenceRecords(String queries) throws Exception
60		{
61		// TODO: this is not a perfect implementation. We need to be able to add
62		// individual references to each sequence in each family alignment that's
63		// retrieved.
64	0	startQuery();
65		// TODO: trap HTTP 404 exceptions and return null
66	0	String xfamUrl = getURL(queries);
67
68	0	Console.debug("XFAM URL for retrieval is: " + xfamUrl);
69
70	0	AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
71		DataSourceType.URL, FileFormat.Stockholm);
72
73	0	for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
74		{
75	0	rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
76		// getDbSource(),
77		getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
78	0	if (!getDbSource().equals(getXfamSource()))
79		{ // add the specific ref too
80	0	rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
81		getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
82		}
83		}
84	0	stopQuery();
85	0	return rcds;
86		}
87
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
88	0	String getURL(String queries)...
89		{
90	0	return getURLPrefix() + "/family/"
91		+ queries.trim().toUpperCase(Locale.ROOT) + getURLSuffix();
92		}
93
94		/**
95		* Pfam and Rfam provide alignments
96		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
97	0	@Override...
98		public boolean isAlignmentSource()
99		{
100	0	return true;
101		}
102
103		/**
104		* default suffix to append the retrieval URL for this source.
105		*
106		* @return "" for most Xfam sources
107		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
108	0	public String getURLSuffix()...
109		{
110	0	return "";
111		}
112
113		}