Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EmblFlatfileSource	45	29	16	0.00%	Show methods

Class EmblFlatfileSource

Class EmblFlatfileSource	Line # 45	Total Statements 29	Complexity 16	TOTAL Coverage 0.00%
getDbVersion() : String   getDbVersion() : String	4949	1.01	1.01	0.0 0.00%
getAccessionSeparator() : String   getAccessionSeparator() : String	5555	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	6161	1.01	1.01	0.0 0.00%
isValidReference(String) : boolean   isValidReference(String) : boolean	6767	3.03	3.03	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	7777	1.01	1.01	0.0 0.00%
getTier() : int   getTier() : int	8383	1.01	1.01	0.0 0.00%
getEmblSequenceRecords(String,String) : AlignmentI   getEmblSequenceRecords(String,String) : AlignmentI	8989	8.08	2.02	0.0 0.00%
getEmblSequenceRecords(String,String,File) : AlignmentI   getEmblSequenceRecords(String,String,File) : AlignmentI	111111	12.012	5.05	0.0 0.00%
isDnaCoding() : boolean   isDnaCoding() : boolean	137137	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.ws.ebi.EBIFetchClient;
38
39		/**
40		* A class that does partial parsing of an EMBL flatfile.
41		*
42		* @author gmcarstairs
43		*
44		*/
		0% Uncovered Elements: 46 (46) Complexity: 16 Complexity Density: 0.55
45		public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
46		{
47		private static final Regex ACCESSION_REGEX = new Regex("^[A-Z]+[0-9]+");
48
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
49	0	@Override...
50		public String getDbVersion()
51		{
52	0	return "0";
53		}
54
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
55	0	@Override...
56		public String getAccessionSeparator()
57		{
58	0	return null;
59		}
60
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
61	0	@Override...
62		public Regex getAccessionValidator()
63		{
64	0	return ACCESSION_REGEX;
65		}
66
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
67	0	@Override...
68		public boolean isValidReference(String accession)
69		{
70	0	if (accession == null || accession.length() < 2)
71		{
72	0	return false;
73		}
74	0	return getAccessionValidator().search(accession);
75		}
76
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
77	0	@Override...
78		public AlignmentI getSequenceRecords(String queries) throws Exception
79		{
80	0	return null;
81		}
82
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	@Override...
84		public int getTier()
85		{
86	0	return 0;
87		}
88
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.25
89	0	protected AlignmentI getEmblSequenceRecords(String dbName, String query)...
90		throws Exception
91		{
92	0	startQuery();
93	0	EBIFetchClient dbFetch = new EBIFetchClient();
94	0	File reply;
95	0	try
96		{
97	0	reply = dbFetch.fetchDataAsFile(
98		dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null,
99		"gz");
100		} catch (Exception e)
101		{
102	0	stopQuery();
103	0	throw new Exception(
104		String.format("EBI EMBL retrieval failed for %s:%s",
105		dbName.toLowerCase(Locale.ROOT), query.trim()),
106		e);
107		}
108	0	return getEmblSequenceRecords(dbName, query, reply);
109		}
110
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.42
111	0	private AlignmentI getEmblSequenceRecords(String dbName, String query,...
112		File reply) throws IOException
113		{
114	0	AlignmentI al = null;
115
116	0	if (reply != null && reply.exists())
117		{
118	0	file = reply.getAbsolutePath();
119	0	FileParse fp = new FileParse(file, DataSourceType.FILE);
120	0	EmblFlatFile emblParser = new EmblFlatFile(fp, getDbSource());
121	0	SequenceI[] seqs = emblParser.getSeqsAsArray();
122	0	if (seqs.length > 0)
123		{
124	0	al = new Alignment(seqs);
125		}
126
127	0	if (al == null)
128		{
129	0	Console.error("No record found for '" + dbName + ":" + query + "'");
130		}
131		}
132
133	0	stopQuery();
134	0	return al;
135		}
136
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
137	0	@Override...
138		public boolean isDnaCoding()
139		{
140	0	return true;
141		}
142		}