Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EmblFile	43	44	20	21	0.695652269.6%	Show methods

Class EmblFile

Class EmblFile	Line # 43	Total Statements 44	Complexity 20	Uncovered Elements 21	TOTAL Coverage 0.695652269.6%
getEntries() : Vector<EmblEntry>   getEntries() : Vector<EmblEntry>	5454	1.01	1.01	0.00	1.0 1.0100%
setEntries(Vector<EmblEntry>) : void   setEntries(Vector<EmblEntry>) : void	6363	1.01	1.01	0.00	1.0 1.0100%
getErrors() : Vector<EmblError>   getErrors() : Vector<EmblError>	7171	1.01	1.01	0.00	1.0 1.0100%
setErrors(Vector<EmblError>) : void   setErrors(Vector<EmblError>) : void	8080	1.01	1.01	1.01	0.0 0.00%
getEmblFile(File) : EmblFile   getEmblFile(File) : EmblFile	9191	7.07	3.03	9.09	0.0 0.00%
getEmblFile(Reader) : EmblFile   getEmblFile(Reader) : EmblFile	108108	18.018	4.04	3.03	0.85 0.8585%
canonicaliseDbRefs(EmblFile) : void   canonicaliseDbRefs(EmblFile) : void	156156	13.013	7.07	4.04	0.84 0.8484%
getText() : String   getText() : String	194194	1.01	1.01	0.00	1.0 1.0100%
setText(String) : void   setText(String) : void	199199	1.01	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.datamodel.xdb.embl;
22
23		import jalview.datamodel.DBRefEntry;
24		import jalview.ws.dbsources.Uniprot;
25
26		import java.io.File;
27		import java.io.FileReader;
28		import java.io.PrintWriter;
29		import java.io.Reader;
30		import java.util.Vector;
31
32		import org.exolab.castor.mapping.Mapping;
33		import org.exolab.castor.xml.Unmarshaller;
34
35		/**
36		* Data model for entries returned from an EMBL query, as marshalled by a Castor
37		* binding file
38		*
39		* For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
40		*
41		* @see embl_mapping.xml
42		*/
		69.6% Uncovered Elements: 21 (69) Complexity: 20 Complexity Density: 0.45
43		public class EmblFile
44		{
45		Vector<EmblEntry> entries;
46
47		Vector<EmblError> errors;
48
49		String text;
50
51		/**
52		* @return the entries
53		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
54	12	public Vector<EmblEntry> getEntries()...
55		{
56	12	return entries;
57		}
58
59		/**
60		* @param entries
61		* the entries to set
62		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
63	2	public void setEntries(Vector<EmblEntry> entries)...
64		{
65	2	this.entries = entries;
66		}
67
68		/**
69		* @return the errors
70		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
71	2	public Vector<EmblError> getErrors()...
72		{
73	2	return errors;
74		}
75
76		/**
77		* @param errors
78		* the errors to set
79		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
80	0	public void setErrors(Vector<EmblError> errors)...
81		{
82	0	this.errors = errors;
83		}
84
85		/**
86		* Parse an EmblXML file into an EmblFile object
87		*
88		* @param file
89		* @return parsed EmblXML or null if exceptions were raised
90		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.43
91	0	public static EmblFile getEmblFile(File file)...
92		{
93	0	if (file == null)
94		{
95	0	return null;
96		}
97	0	try
98		{
99	0	return EmblFile.getEmblFile(new FileReader(file));
100		} catch (Exception e)
101		{
102	0	System.err.println("Exception whilst reading EMBLfile from " + file);
103	0	e.printStackTrace(System.err);
104		}
105	0	return null;
106		}
107
		85% Uncovered Elements: 3 (20) Complexity: 4 Complexity Density: 0.22
108	2	public static EmblFile getEmblFile(Reader file)...
109		{
110	2	EmblFile record = new EmblFile();
111	2	try
112		{
113		// 1. Load the mapping information from the file
114	2	Mapping map = new Mapping(record.getClass().getClassLoader());
115
116	2	java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
117	2	map.loadMapping(url);
118
119		// 2. Unmarshal the data
120	2	Unmarshaller unmar = new Unmarshaller(record);
121	2	try
122		{
123		// uncomment to DEBUG EMBLFile reading
124	2	if (jalview.bin.Cache
125		.getDefault(jalview.bin.Cache.CASTORLOGLEVEL, "debug")
126		.equalsIgnoreCase("DEBUG"))
127		{
128	2	unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
129		}
130		} catch (Exception e)
131		{
132		}
133	2	unmar.setIgnoreExtraElements(true);
134	2	unmar.setIgnoreExtraAttributes(true);
135	2	unmar.setMapping(map);
136	2	unmar.setLogWriter(new PrintWriter(System.out));
137	2	record = (EmblFile) unmar.unmarshal(file);
138
139	2	canonicaliseDbRefs(record);
140		} catch (Exception e)
141		{
142	0	e.printStackTrace(System.err);
143	0	record = null;
144		}
145
146	2	return record;
147		}
148
149		/**
150		* Change blank version to "0" in any DBRefEntry, to ensure consistent
151		* comparison with other DBRefEntry in Jalview
152		*
153		* @param record
154		* @see Uniprot#getDbVersion
155		*/
		84% Uncovered Elements: 4 (25) Complexity: 7 Complexity Density: 0.54
156	2	static void canonicaliseDbRefs(EmblFile record)...
157		{
158	2	if (record.getEntries() == null)
159		{
160	0	return;
161		}
162	2	for (EmblEntry entry : record.getEntries())
163		{
164	2	if (entry.getDbRefs() != null)
165		{
166	2	for (DBRefEntry dbref : entry.getDbRefs())
167		{
168	4	if ("".equals(dbref.getVersion()))
169		{
170	2	dbref.setVersion("0");
171		}
172		}
173		}
174
175	2	if (entry.getFeatures() != null)
176		{
177	2	for (EmblFeature feature : entry.getFeatures())
178		{
179	6	if (feature.getDbRefs() != null)
180		{
181	4	for (DBRefEntry dbref : feature.getDbRefs())
182		{
183	6	if ("".equals(dbref.getVersion()))
184		{
185	4	dbref.setVersion("0");
186		}
187		}
188		}
189		}
190		}
191		}
192		}
193
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
194	2	public String getText()...
195		{
196	2	return text;
197		}
198
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
199	0	public void setText(String text)...
200		{
201	0	this.text = text;
202		}
203		}