Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GenBankFile	39	43	22	0.00%	Show methods

Class GenBankFile

Class GenBankFile	Line # 39	Total Statements 43	Complexity 22	TOTAL Coverage 0.00%
GenBankFile(FileParse,String)   GenBankFile(FileParse,String)	5050	1.01	1.01	0.0 0.00%
parse() : void   parse() : void	6262	19.019	9.09	0.0 0.00%
parseLocus(String) : String   parseLocus(String) : String	112112	7.07	4.04	0.0 0.00%
parseDefinition(String) : String   parseDefinition(String) : String	145145	9.09	4.04	0.0 0.00%
parseVersion(String) : String   parseVersion(String) : String	185185	6.06	3.03	0.0 0.00%
isFeatureContinuationLine(String) : boolean   isFeatureContinuationLine(String) : boolean	204204	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.io;
22
23		import java.io.IOException;
24
25		/**
26		* A class that provides selective parsing of the GenBank flatfile format.
27		* <p>
28		* The initial implementation is limited to extracting fields used by Jalview
29		* after fetching an EMBL or EMBLCDS entry:
30		*
31		* <pre>
32		* accession, version, sequence, xref
33		* and (for CDS feature) location, protein_id, product, codon_start, translation
34		* </pre>
35		*
36		* @author gmcarstairs
37		* @see https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
38		*/
		0% Uncovered Elements: 79 (79) Complexity: 22 Complexity Density: 0.51
39		public class GenBankFile extends EMBLLikeFlatFile
40		{
41		private static final String DEFINITION = "DEFINITION";
42
43		/**
44		* Constructor given a data source and the id of the source database
45		*
46		* @param fp
47		* @param sourceId
48		* @throws IOException
49		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
50	0	public GenBankFile(FileParse fp, String sourceId) throws IOException...
51		{
52	0	super(fp, sourceId);
53		}
54
55		/**
56		* Parses the flatfile, and if successful, saves as an annotated sequence
57		* which may be retrieved by calling {@code getSequence()}
58		*
59		* @throws IOException
60		* @see https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
61		*/
		0% Uncovered Elements: 35 (35) Complexity: 9 Complexity Density: 0.47
62	0	@Override...
63		public void parse() throws IOException
64		{
65	0	String line = nextLine();
66	0	while (line != null)
67		{
68	0	if (line.startsWith("LOCUS"))
69		{
70	0	line = parseLocus(line);
71		}
72	0	else if (line.startsWith(DEFINITION))
73		{
74	0	line = parseDefinition(line);
75		}
76	0	else if (line.startsWith("ACCESSION"))
77		{
78	0	this.accession = line.split(WHITESPACE)[1];
79	0	line = nextLine();
80		}
81	0	else if (line.startsWith("VERSION"))
82		{
83	0	line = parseVersion(line);
84		}
85	0	else if (line.startsWith("ORIGIN"))
86		{
87	0	line = parseSequence();
88		}
89	0	else if (line.startsWith("FEATURES"))
90		{
91	0	line = nextLine();
92	0	while (line.startsWith(" "))
93		{
94	0	line = parseFeature(line);
95		}
96		}
97		else
98		{
99	0	line = nextLine();
100		}
101		}
102	0	buildSequence();
103		}
104
105		/**
106		* Extracts and saves the primary accession and version (SV value) from an ID
107		* line, or null if not found. Returns the next line after the one processed.
108		*
109		* @param line
110		* @throws IOException
111		*/
		0% Uncovered Elements: 11 (11) Complexity: 4 Complexity Density: 0.57
112	0	String parseLocus(String line) throws IOException...
113		{
114	0	String[] tokens = line.split(WHITESPACE);
115
116		/*
117		* first should be "LOCUS"
118		*/
119	0	if (tokens.length < 2 || !"LOCUS".equals(tokens[0]))
120		{
121	0	return nextLine();
122		}
123		/*
124		* second is primary accession
125		*/
126	0	String token = tokens[1].trim();
127	0	if (!token.isEmpty())
128		{
129	0	this.accession = token;
130		}
131
132		// not going to guess the rest just yet, but third is length with unit (bp)
133
134	0	return nextLine();
135		}
136
137		/**
138		* Reads sequence description from DEFINITION lines. Any trailing period is
139		* discarded. Returns the next line after the definition line(s).
140		*
141		* @param line
142		* @return
143		* @throws IOException
144		*/
		0% Uncovered Elements: 15 (15) Complexity: 4 Complexity Density: 0.44
145	0	String parseDefinition(String line) throws IOException...
146		{
147	0	String desc = line.substring(DEFINITION.length()).trim();
148	0	if (desc.endsWith("."))
149		{
150	0	desc = desc.substring(0, desc.length() - 1);
151		}
152
153		/*
154		* pass over any additional DE lines
155		*/
156	0	while ((line = nextLine()) != null)
157		{
158	0	if (line.startsWith(" "))
159		{
160		// definition continuation line
161	0	desc += line.trim();
162		}
163		else
164		{
165	0	break;
166		}
167		}
168	0	this.description = desc;
169
170	0	return line;
171		}
172
173		/**
174		* Parses the VERSION line e.g.
175		*
176		* <pre>
177		* VERSION X81322.1
178		* </pre>
179		*
180		* and returns the next line
181		*
182		* @param line
183		* @throws IOException
184		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
185	0	String parseVersion(String line) throws IOException...
186		{
187		/*
188		* extract version part of <accession>.<version>
189		* https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#VersionB
190		*/
191	0	String[] tokens = line.split(WHITESPACE);
192	0	if (tokens.length > 1)
193		{
194	0	tokens = tokens[1].split("\\.");
195	0	if (tokens.length > 1)
196		{
197	0	this.version = tokens[1];
198		}
199		}
200
201	0	return nextLine();
202		}
203
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
204	0	@Override...
205		protected boolean isFeatureContinuationLine(String line)
206		{
207	0	return line.startsWith(" "); // 6 spaces
208		}
209		}