Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EmblFlatFile	48	53	24	0.892473189.2%	Show methods

Class EmblFlatFile

Class EmblFlatFile	Line # 48	Total Statements 53	Complexity 24	TOTAL Coverage 0.892473189.2%
EmblFlatFile(FileParse,String)   EmblFlatFile(FileParse,String)	5757	1.01	1.01	1.0 1.0100%
parse() : void   parse() : void	6868	14.014	7.07	1.0 1.0100%
parseID(String) : String   parseID(String) : String	109109	16.016	6.06	0.7916667 0.791666779.2%
parseDE(String) : String   parseDE(String) : String	163163	8.08	4.04	0.78571427 0.7857142778.6%
parseDR(String) : String   parseDR(String) : String	193193	13.013	5.05	0.9047619 0.904761990.5%
isFeatureContinuationLine(String) : boolean   isFeatureContinuationLine(String) : boolean	224224	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.8817204	jalview.io.EmblFlatFileTest.testParsejalview.io.EmblFlatFileTest.testParse	1PASS
	0.8817204	jalview.io.EmblFlatFileTest.testParseToRNAjalview.io.EmblFlatFileTest.testParseToRNA	1PASS
	0.61290324	jalview.io.EmblFlatFileTest.testParse_noUniprotXrefjalview.io.EmblFlatFileTest.testParse_noUniprotXref	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.io;
22
23		import java.io.IOException;
24
25		import jalview.bin.Console;
26		import jalview.datamodel.DBRefEntry;
27		import jalview.util.DBRefUtils;
28
29		/**
30		* A class that provides selective parsing of the EMBL flatfile format.
31		* <p>
32		* The initial implementation is limited to extracting fields used by Jalview
33		* after fetching an EMBL or EMBLCDS entry:
34		*
35		* <pre>
36		* accession, version, sequence, xref
37		* and (for CDS feature) location, protein_id, product, codon_start, translation
38		* </pre>
39		*
40		* For a complete parser, it may be best to adopt that provided in
41		* https://github.com/enasequence/sequencetools/tree/master/src/main/java/uk/ac/ebi/embl/flatfile
42		* (but note this has a dependency on the Apache Commons library)
43		*
44		* @author gmcarstairs
45		* @see ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/doc/usrman.txt
46		* @see ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html
47		*/
		89.2% Uncovered Elements: 10 (93) Complexity: 24 Complexity Density: 0.45
48		public class EmblFlatFile extends EMBLLikeFlatFile
49		{
50		/**
51		* Constructor given a data source and the id of the source database
52		*
53		* @param fp
54		* @param sourceId
55		* @throws IOException
56		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
57	3	public EmblFlatFile(FileParse fp, String sourceId) throws IOException...
58		{
59	3	super(fp, sourceId);
60		}
61
62		/**
63		* Parses the flatfile, and if successful, saves as an annotated sequence
64		* which may be retrieved by calling {@code getSequence()}
65		*
66		* @throws IOException
67		*/
		100% Uncovered Elements: 0 (26) Complexity: 7 Complexity Density: 0.5
68	3	@Override...
69		public void parse() throws IOException
70		{
71	3	String line = nextLine();
72	121	while (line != null)
73		{
74	118	if (line.startsWith("ID"))
75		{
76	3	line = parseID(line);
77		}
78	115	else if (line.startsWith("DE"))
79		{
80	3	line = parseDE(line);
81		}
82	112	else if (line.startsWith("DR"))
83		{
84	8	line = parseDR(line);
85		}
86	104	else if (line.startsWith("SQ"))
87		{
88	3	line = parseSequence();
89		}
90	101	else if (line.startsWith("FT"))
91		{
92	23	line = parseFeature(line.substring(2));
93		}
94		else
95		{
96	78	line = nextLine();
97		}
98		}
99	3	buildSequence();
100		}
101
102		/**
103		* Extracts and saves the primary accession and version (SV value) from an ID
104		* line, or null if not found. Returns the next line after the one processed.
105		*
106		* @param line
107		* @throws IOException
108		*/
		79.2% Uncovered Elements: 5 (24) Complexity: 6 Complexity Density: 0.38
109	3	String parseID(String line) throws IOException...
110		{
111	3	String[] tokens = line.substring(2).split(";");
112
113		/*
114		* first is primary accession
115		*/
116	3	String token = tokens[0].trim();
117	3	if (!token.isEmpty())
118		{
119	3	this.accession = token;
120		}
121
122		/*
123		* second token is 'SV versionNo'
124		*/
125	3	if (tokens.length > 1)
126		{
127	3	token = tokens[1].trim();
128	3	if (token.startsWith("SV"))
129		{
130	3	String[] bits = token.trim().split(WHITESPACE);
131	3	this.version = bits[bits.length - 1];
132		}
133		}
134
135		/*
136		* seventh token is 'length BP'
137		*/
138	3	if (tokens.length > 6)
139		{
140	3	token = tokens[6].trim();
141	3	String[] bits = token.trim().split(WHITESPACE);
142	3	try
143		{
144	3	this.length = Integer.valueOf(bits[0]);
145		} catch (NumberFormatException e)
146		{
147	0	Console.error("bad length read in flatfile, line: " + line);
148		}
149		}
150
151	3	return nextLine();
152		}
153
154		/**
155		* Reads sequence description from the first DE line found. Any trailing
156		* period is discarded. If there are multiple DE lines, only the first (short
157		* description) is read, the rest are ignored.
158		*
159		* @param line
160		* @return
161		* @throws IOException
162		*/
		78.6% Uncovered Elements: 3 (14) Complexity: 4 Complexity Density: 0.5
163	3	String parseDE(String line) throws IOException...
164		{
165	3	String desc = line.substring(2).trim();
166	3	if (desc.endsWith("."))
167		{
168	2	desc = desc.substring(0, desc.length() - 1);
169		}
170	3	this.description = desc;
171
172		/*
173		* pass over any additional DE lines
174		*/
175	?	while ((line = nextLine()) != null)
176		{
177	3	if (!line.startsWith("DE"))
178		{
179	3	break;
180		}
181		}
182
183	3	return line;
184		}
185
186		/**
187		* Processes one DR line and saves as a DBRefEntry cross-reference. Returns
188		* the line following the line processed.
189		*
190		* @param line
191		* @throws IOException
192		*/
		90.5% Uncovered Elements: 2 (21) Complexity: 5 Complexity Density: 0.38
193	8	String parseDR(String line) throws IOException...
194		{
195	8	String[] tokens = line.substring(2).split(";");
196	8	if (tokens.length > 1)
197		{
198		/*
199		* ensure UniProtKB/Swiss-Prot converted to UNIPROT
200		*/
201	8	String db = tokens[0].trim();
202	8	db = DBRefUtils.getCanonicalName(db);
203	8	String acc = tokens[1].trim();
204	8	if (acc.endsWith("."))
205		{
206	4	acc = acc.substring(0, acc.length() - 1);
207		}
208	8	String version = "0";
209	8	if (tokens.length > 2)
210		{
211	4	String secondaryId = tokens[2].trim();
212	4	if (!secondaryId.isEmpty())
213		{
214		// todo: is this right? secondary id is not a version number
215		// version = secondaryId;
216		}
217		}
218	8	this.dbrefs.add(new DBRefEntry(db, version, acc));
219		}
220
221	8	return nextLine();
222		}
223
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
224	447	@Override...
225		protected boolean isFeatureContinuationLine(String line)
226		{
227	447	return line.startsWith("FT "); // 4 spaces
228		}
229		}