Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
RnamlFile	45	58	24	29	0.6588235565.9%	Show methods

Class RnamlFile

Class RnamlFile	Line # 45	Total Statements 58	Complexity 24	Uncovered Elements 29	TOTAL Coverage 0.6588235565.9%
RnamlFile()   RnamlFile()	5151	1.01	1.01	1.01	0.0 0.00%
RnamlFile(String,DataSourceType)   RnamlFile(String,DataSourceType)	5757	1.01	1.01	1.01	0.0 0.00%
RnamlFile(FileParse)   RnamlFile(FileParse)	6363	1.01	1.01	0.00	1.0 1.0100%
CreateReader() : BufferedReader   CreateReader() : BufferedReader	6969	4.04	1.01	4.04	0.0 0.00%
parse() : void   parse() : void	8383	13.013	7.07	11.011	0.26666668 0.2666666826.7%
_parse() : void   _parse() : void	131131	26.026	8.08	3.03	0.92105263 0.9210526392.1%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	199199	1.01	1.01	1.01	0.0 0.00%
getRNA() : List<RNA>   getRNA() : List<RNA>	205205	1.01	1.01	1.01	0.0 0.00%
safeName(String) : String   safeName(String) : String	222222	10.010	3.03	2.02	0.85714287 0.8571428785.7%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.65882355	jalview.io.RNAMLfileTest.testRnamlToStockholmIOjalview.io.RNAMLfileTest.testRnamlToStockholmIO	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.analysis.Rna;
24		import jalview.datamodel.AlignmentAnnotation;
25		import jalview.datamodel.Annotation;
26		import jalview.datamodel.Sequence;
27		import jalview.datamodel.SequenceI;
28		import jalview.util.MessageManager;
29
30		import java.io.BufferedReader;
31		import java.io.FileNotFoundException;
32		import java.io.FileReader;
33		import java.io.IOException;
34		import java.util.ArrayList;
35		import java.util.List;
36
37		import com.stevesoft.pat.Regex;
38
39		import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
40		import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
41		import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
42		import fr.orsay.lri.varna.factories.RNAFactory;
43		import fr.orsay.lri.varna.models.rna.RNA;
44
		65.9% Uncovered Elements: 29 (85) Complexity: 24 Complexity Density: 0.41
45		public class RnamlFile extends AlignFile
46		{
47		public String id;
48
49		protected ArrayList<RNA> result;
50
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
51	0	public RnamlFile()...
52		{
53	0	super();
54
55		}
56
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
57	0	public RnamlFile(String inFile, DataSourceType type) throws IOException...
58		{
59	0	super(inFile, type);
60
61		}
62
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
63	1	public RnamlFile(FileParse source) throws IOException...
64		{
65	1	super(source);
66
67		}
68
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
69	0	public BufferedReader CreateReader() throws FileNotFoundException...
70		{
71	0	FileReader fr = null;
72	0	fr = new FileReader(inFile);
73
74	0	BufferedReader r = new BufferedReader(fr);
75	0	return r;
76		}
77
78		/*
79		* (non-Javadoc)
80		*
81		* @see jalview.io.AlignFile#parse()
82		*/
		26.7% Uncovered Elements: 11 (15) Complexity: 7 Complexity Density: 0.54
83	1	@Override...
84		public void parse() throws IOException
85		{
86	1	if (System.getProperty("java.version").indexOf("1.6") > -1
87		|| System.getProperty("java.version").indexOf("1.5") > -1)
88		{
89		// patch for 'This parser does not support specification "null" version
90		// "null"' error
91		// this hack ensures we get a properly updated SAXParserFactory on older
92		// JVMs
93		// thanks to Stefan Birkner over at https://coderwall.com/p/kqsrrw
94	0	System.setProperty("javax.xml.parsers.SAXParserFactory",
95		"com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
96		}
97		// rather than lose exception semantics whilst parsing RNAML with VARNA we
98		// wrap the routine and catch all exceptions before passing them up the
99		// chain as an IOException
100	1	try
101		{
102	1	_parse();
103		} catch (ExceptionPermissionDenied pdx)
104		{
105	0	errormessage = MessageManager.formatMessage(
106		"exception.rnaml_couldnt_access_datasource", new String[]
107		{ pdx.getMessage() });
108	0	throw new IOException(pdx);
109		} catch (ExceptionLoadingFailed lf)
110		{
111	0	errormessage = MessageManager.formatMessage(
112		"exception.ranml_couldnt_process_data", new String[]
113		{ lf.getMessage() });
114	0	throw new IOException(lf);
115		} catch (ExceptionFileFormatOrSyntax iff)
116		{
117	0	errormessage = MessageManager
118		.formatMessage("exception.ranml_invalid_file", new String[]
119		{ iff.getMessage() });
120	0	throw new IOException(iff);
121		} catch (Exception x)
122		{
123	0	error = true;
124	0	errormessage = MessageManager.formatMessage(
125		"exception.ranml_problem_parsing_data", new String[]
126		{ x.getMessage() });
127	0	throw new IOException(errormessage, x);
128		}
129		}
130
		92.1% Uncovered Elements: 3 (38) Complexity: 8 Complexity Density: 0.31
131	1	@SuppressWarnings("unchecked")...
132		public void _parse()
133		throws FileNotFoundException, ExceptionPermissionDenied,
134		ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
135		{
136
137	1	result = RNAFactory.loadSecStrRNAML(getReader());
138
139		// ArrayList<ArrayList> allarray = new ArrayList();
140		// ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
141		// ArrayList strucinarray = new ArrayList();
142	1	SequenceI[] sqs = new SequenceI[result.size()];
143
144	3	for (int i = 0; i < result.size(); i++)
145		{
146
147	2	RNA current = result.get(i);
148	2	String rna = current.getStructDBN(true);
149	2	String seq = current.getSeq();
150	2	int begin = 1;
151	2	int end = seq.length();
152
153	2	id = current.getName();
154	2	if (id == null || id.trim().length() == 0)
155		{
156	2	id = safeName(getDataName());
157	2	if (result.size() > 1)
158		{
159	2	id += "." + i;
160		}
161		}
162	2	sqs[i] = new Sequence(id, seq, begin, end);
163
164	2	sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
165	2	String[] annot = new String[rna.length()];
166	2	Annotation[] ann = new Annotation[rna.length()];
167
168	545	for (int j = 0; j < rna.length(); j++)
169		{
170	543	annot[j] = "" + rna.charAt(j);
171
172		}
173	545	for (int k = 0; k < rna.length(); k++)
174		{
175	543	ann[k] = new Annotation(annot[k], "",
176		Rna.getRNASecStrucState(annot[k]).charAt(0), 0f);
177		}
178
179	2	AlignmentAnnotation align = new AlignmentAnnotation(
180		"Secondary Structure",
181	2	current.getID().trim().length() > 0
182		? "Secondary Structure for " + current.getID()
183		: "",
184		ann);
185
186	2	sqs[i].addAlignmentAnnotation(align);
187	2	sqs[i].setRNA(result.get(i));
188
189		// allarray.add(strucinarray);
190
191	2	annotations.addElement(align);
192		// BP.add(align.bps);
193
194		}
195
196	1	setSeqs(sqs);
197		}
198
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
199	0	@Override...
200		public String print(SequenceI[] s, boolean jvSuffix)
201		{
202	0	return "not yet implemented";
203		}
204
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
205	0	public List<RNA> getRNA()...
206		{
207	0	return result;
208		}
209
210		// public static void main(String[] args) {
211		// Pattern p= Pattern.compile("(.+)[.][^.]+");
212		// Matcher m = p.matcher("toto.xml.zip");
213		// System.out.println(m.matches());
214		// System.out.println(m.group(1));
215		// }
216		/**
217		* make a friendly ID string.
218		*
219		* @param dataName
220		* @return truncated dataName to after last '/'
221		*/
		85.7% Uncovered Elements: 2 (14) Complexity: 3 Complexity Density: 0.3
222	2	private String safeName(String dataName)...
223		{
224	2	int b = 0;
225	?	if ((b = dataName.lastIndexOf(".")) > 0)
226		{
227	2	dataName = dataName.substring(0, b - 1);
228		}
229	2	b = 0;
230	2	Regex m = new Regex("[\\/]?([-A-Za-z0-9]+)\\.?");
231	2	String mm = dataName;
232	8	while (m.searchFrom(dataName, b))
233		{
234	6	mm = m.stringMatched();
235	6	b = m.matchedTo();
236		}
237	2	return mm;
238		}
239		}