Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
BSMLFile	56	71	18	0.684782668.5%	Show methods

Class BSMLFile

Class BSMLFile	Line # 56	Total Statements 71	Complexity 18	TOTAL Coverage 0.684782668.5%
BSMLFile()   BSMLFile()	5959	1.01	1.01	0.0 0.00%
BSMLFile(String,DataSourceType)   BSMLFile(String,DataSourceType)	6565	1.01	1.01	1.0 1.0100%
BSMLFile(FileParse)   BSMLFile(FileParse)	7171	1.01	1.01	0.0 0.00%
CreateReader() : BufferedReader   CreateReader() : BufferedReader	7777	4.04	1.01	0.0 0.00%
parse() : void   parse() : void	9191	11.011	5.05	0.18181819 0.1818181918.2%
_parse() : void   _parse() : void	125125	52.052	8.08	0.8636364 0.863636486.4%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	219219	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.6847826	jalview.io.BSMLFileTest.testParse_BSMLjalview.io.BSMLFileTest.testParse_BSML	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 jalview.datamodel.Sequence;
24		import jalview.datamodel.SequenceFeature;
25		import jalview.datamodel.SequenceI;
26		import jalview.util.MessageManager;
27
28		import java.io.BufferedReader;
29		import java.io.FileNotFoundException;
30		import java.io.FileReader;
31		import java.io.IOException;
32		import java.util.Hashtable;
33		import java.util.Map;
34
35		import javax.xml.parsers.DocumentBuilder;
36		import javax.xml.parsers.DocumentBuilderFactory;
37		import javax.xml.parsers.ParserConfigurationException;
38
39		import org.w3c.dom.Document;
40		import org.w3c.dom.Element;
41		import org.w3c.dom.NodeList;
42		import org.xml.sax.InputSource;
43		import org.xml.sax.SAXException;
44
45		import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
46		import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
47		import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
48
49		/**
50		* Preliminary reader for Bioinformatics Sequence Markup Language
51		* http://www.bsml.org
52		*
53		* @author hansonr
54		*
55		*/
		68.5% Uncovered Elements: 29 (92) Complexity: 18 Complexity Density: 0.25
56		public class BSMLFile extends AlignFile
57		{
58
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	public BSMLFile()...
60		{
61	0	super();
62
63		}
64
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
65	1	public BSMLFile(String inFile, DataSourceType type) throws IOException...
66		{
67	1	super(inFile, type);
68
69		}
70
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
71	0	public BSMLFile(FileParse source) throws IOException...
72		{
73	0	super(source);
74
75		}
76
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
77	0	public BufferedReader CreateReader() throws FileNotFoundException...
78		{
79	0	FileReader fr = null;
80	0	fr = new FileReader(inFile);
81
82	0	BufferedReader r = new BufferedReader(fr);
83	0	return r;
84		}
85
86		/*
87		* (non-Javadoc)
88		*
89		* @see jalview.io.AlignFile#parse()
90		*/
		18.2% Uncovered Elements: 9 (11) Complexity: 5 Complexity Density: 0.45
91	1	@Override...
92		public void parse() throws IOException
93		{
94	1	try
95		{
96	1	_parse();
97		} catch (ExceptionPermissionDenied pdx)
98		{
99	0	errormessage = MessageManager.formatMessage(
100		"exception.BSML_couldnt_access_datasource", new String[]
101		{ pdx.getMessage() });
102	0	throw new IOException(pdx);
103		} catch (ExceptionLoadingFailed lf)
104		{
105	0	errormessage = MessageManager.formatMessage(
106		"exception.BSML_couldnt_process_data", new String[]
107		{ lf.getMessage() });
108	0	throw new IOException(lf);
109		} catch (ExceptionFileFormatOrSyntax iff)
110		{
111	0	errormessage = MessageManager
112		.formatMessage("exception.BSML_invalid_file", new String[]
113		{ iff.getMessage() });
114	0	throw new IOException(iff);
115		} catch (Exception x)
116		{
117	0	error = true;
118	0	errormessage = MessageManager.formatMessage(
119		"exception.BSML_problem_parsing_data", new String[]
120		{ x.getMessage() });
121	0	throw new IOException(errormessage, x);
122		}
123		}
124
		86.4% Uncovered Elements: 9 (66) Complexity: 8 Complexity Density: 0.15
125	1	@SuppressWarnings("unchecked")...
126		public void _parse()
127		throws ExceptionPermissionDenied, ExceptionLoadingFailed,
128		ExceptionFileFormatOrSyntax, ParserConfigurationException,
129		SAXException, IOException
130		{
131
132	1	DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
133
134	1	dbf.setIgnoringElementContentWhitespace(true);
135	1	dbf.setIgnoringComments(true);
136	1	dbf.setValidating(true);
137	1	dbf.setCoalescing(true);
138	1	dbf.setNamespaceAware(true);
139	1	dbf.setFeature("http://xml.org/sax/features/namespaces", false);
140	1	dbf.setFeature("http://xml.org/sax/features/validation", false);
141	1	dbf.setFeature(
142		"http://apache.org/xml/features/nonvalidating/load-dtd-grammar",
143		false);
144	1	dbf.setFeature(
145		"http://apache.org/xml/features/nonvalidating/load-external-dtd",
146		false);
147
148	1	DocumentBuilder db = dbf.newDocumentBuilder();
149
150	1	Map<String, SequenceI> htSeq = new Hashtable<>();
151	1	InputSource is = new InputSource(getReader());
152	1	Document d = db.parse(is);
153	1	NodeList sequences = d.getElementsByTagName("Sequence-data");
154	1	int n = sequences.getLength();
155	1	SequenceI[] sqs = new SequenceI[n];
156	2	for (int i = 0; i < n; i++)
157		{
158	1	Element e = (Element) sequences.item(i);
159	1	String s = e.getTextContent();
160	1	String id = e.getAttribute("seq-name");
161	1	SequenceI seq = sqs[i] = new Sequence(id, s, 1, s.length());
162	1	htSeq.put(id, seq);
163		// ?? sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
164		}
165
166	1	sequences = d.getElementsByTagName("Sequence");
167	1	n = sequences.getLength();
168	2	for (int i = 0; i < n; i++)
169		{
170	1	Element e = (Element) sequences.item(i);
171	1	String mol = e.getAttribute("molecule"); // dna or rna
172	1	if (!"dna".equals(mol))
173		{
174	0	System.err.println("BSML molecule=rna not implemented");
175	0	continue;
176		}
177	1	String title = e.getAttribute("title");
178	1	SequenceI seq = htSeq.get(title);
179	1	if (seq == null)
180		{
181	0	continue;
182		}
183	1	NodeList features = e.getElementsByTagName("Feature");
184	1	int featureCount = features.getLength();
185	2	for (int f = 0; f < featureCount; f++)
186		{
187	1	Element feature = (Element) features.item(f);
188		// <Feature class="GENE" title="CPXV-GER_1980_EP4-211">
189		// <Interval-loc complement="0" endpos="217104" startpos="216643"/>
190		// <Resource id="GENE-ID:119705"/>
191		// </Feature>
192	1	Element iloc = (Element) feature
193		.getElementsByTagName("Interval-loc").item(0);
194	1	String complement = iloc.getAttribute("complement");
195	1	if (!"0".equals(complement))
196		{
197		// Jalview cannot handle complement genes (running backward on the
198		// complementary strand);
199	0	continue;
200		}
201	1	String fclass = feature.getAttribute("class");
202	1	if (!"GENE".equals(fclass))
203		{
204		// just processing GENE features for now;
205	0	continue;
206		}
207	1	String ftitle = feature.getAttribute("title");
208	1	int start = Integer.parseInt(iloc.getAttribute("startpos"));
209	1	int end = Integer.parseInt(iloc.getAttribute("endpos"));
210	1	SequenceFeature sf = new SequenceFeature("GENE", ftitle, start, end,
211		null);
212	1	seq.addSequenceFeature(sf);
213		}
214	1	setSeqs(sqs);
215		}
216
217		}
218
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
219	0	@Override...
220		public String print(SequenceI[] s, boolean jvSuffix)
221		{
222	0	return "not yet implemented";
223		}
224
225		}