Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EmblFlatfileSource	46	31	17	0.00%	Show methods

Class EmblFlatfileSource

Class EmblFlatfileSource	Line # 46	Total Statements 31	Complexity 17	TOTAL Coverage 0.00%
getDbVersion() : String   getDbVersion() : String	5050	1.01	1.01	0.0 0.00%
getAccessionSeparator() : String   getAccessionSeparator() : String	5656	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	6262	3.03	2.02	0.0 0.00%
isValidReference(String) : boolean   isValidReference(String) : boolean	7272	3.03	3.03	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	8282	1.01	1.01	0.0 0.00%
getTier() : int   getTier() : int	8888	1.01	1.01	0.0 0.00%
getEmblSequenceRecords(String,String) : AlignmentI   getEmblSequenceRecords(String,String) : AlignmentI	9494	8.08	2.02	0.0 0.00%
getEmblSequenceRecords(String,String,File) : AlignmentI   getEmblSequenceRecords(String,String,File) : AlignmentI	116116	12.012	5.05	0.0 0.00%
isDnaCoding() : boolean   isDnaCoding() : boolean	142142	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 java.io.File;
26		import java.io.IOException;
27
28		import com.stevesoft.pat.Regex;
29
30		import jalview.bin.Console;
31		import jalview.datamodel.Alignment;
32		import jalview.datamodel.AlignmentI;
33		import jalview.datamodel.SequenceI;
34		import jalview.io.DataSourceType;
35		import jalview.io.EmblFlatFile;
36		import jalview.io.FileParse;
37		import jalview.util.Platform;
38		import jalview.ws.ebi.EBIFetchClient;
39
40		/**
41		* A class that does partial parsing of an EMBL flatfile.
42		*
43		* @author gmcarstairs
44		*
45		*/
		0% Uncovered Elements: 50 (50) Complexity: 17 Complexity Density: 0.55
46		public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
47		{
48		private static Regex ACCESSION_REGEX = null;
49
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
50	0	@Override...
51		public String getDbVersion()
52		{
53	0	return "0";
54		}
55
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
56	0	@Override...
57		public String getAccessionSeparator()
58		{
59	0	return null;
60		}
61
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
62	0	@Override...
63		public Regex getAccessionValidator()
64		{
65	0	if (ACCESSION_REGEX == null)
66		{
67	0	ACCESSION_REGEX = Platform.newRegex("^[A-Z]+[0-9]+");
68		}
69	0	return ACCESSION_REGEX;
70		}
71
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
72	0	@Override...
73		public boolean isValidReference(String accession)
74		{
75	0	if (accession == null || accession.length() < 2)
76		{
77	0	return false;
78		}
79	0	return getAccessionValidator().search(accession);
80		}
81
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
82	0	@Override...
83		public AlignmentI getSequenceRecords(String queries) throws Exception
84		{
85	0	return null;
86		}
87
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
88	0	@Override...
89		public int getTier()
90		{
91	0	return 0;
92		}
93
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.25
94	0	protected AlignmentI getEmblSequenceRecords(String dbName, String query)...
95		throws Exception
96		{
97	0	startQuery();
98	0	EBIFetchClient dbFetch = new EBIFetchClient();
99	0	File reply;
100	0	try
101		{
102	0	reply = dbFetch.fetchDataAsFile(
103		dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null,
104		"gz");
105		} catch (Exception e)
106		{
107	0	stopQuery();
108	0	throw new Exception(
109		String.format("EBI EMBL retrieval failed for %s:%s",
110		dbName.toLowerCase(Locale.ROOT), query.trim()),
111		e);
112		}
113	0	return getEmblSequenceRecords(dbName, query, reply);
114		}
115
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.42
116	0	private AlignmentI getEmblSequenceRecords(String dbName, String query,...
117		File reply) throws IOException
118		{
119	0	AlignmentI al = null;
120
121	0	if (reply != null && reply.exists())
122		{
123	0	file = reply.getAbsolutePath();
124	0	FileParse fp = new FileParse(file, DataSourceType.FILE);
125	0	EmblFlatFile emblParser = new EmblFlatFile(fp, getDbSource());
126	0	SequenceI[] seqs = emblParser.getSeqsAsArray();
127	0	if (seqs.length > 0)
128		{
129	0	al = new Alignment(seqs);
130		}
131
132	0	if (al == null)
133		{
134	0	Console.error("No record found for '" + dbName + ":" + query + "'");
135		}
136		}
137
138	0	stopQuery();
139	0	return al;
140		}
141
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
142	0	@Override...
143		public boolean isDnaCoding()
144		{
145	0	return true;
146		}
147		}