Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RnamlFile	46	59	25	0.681818268.2%	Show methods

Class RnamlFile

Class RnamlFile	Line # 46	Total Statements 59	Complexity 25	TOTAL Coverage 0.681818268.2%
RnamlFile()   RnamlFile()	5252	1.01	1.01	0.0 0.00%
RnamlFile(String,DataSourceType)   RnamlFile(String,DataSourceType)	5858	1.01	1.01	1.0 1.0100%
RnamlFile(FileParse)   RnamlFile(FileParse)	6464	1.01	1.01	1.0 1.0100%
CreateReader() : BufferedReader   CreateReader() : BufferedReader	7070	4.04	1.01	0.0 0.00%
parse() : void   parse() : void	8484	13.013	7.07	0.26666668 0.2666666826.7%
_parse() : void   _parse() : void	132132	27.027	9.09	0.902439 0.90243990.2%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	202202	1.01	1.01	0.0 0.00%
getRNA() : List<RNA>   getRNA() : List<RNA>	208208	1.01	1.01	0.0 0.00%
safeName(String) : String   safeName(String) : String	225225	10.010	3.03	0.85714287 0.8571428785.7%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.64772725	jalview.io.RNAMLfileTest.testRnamlToStockholmIOjalview.io.RNAMLfileTest.testRnamlToStockholmIO	1PASS
	0.6363636	jalview.io.RNAMLfileTest.testRnamlSeqImportjalview.io.RNAMLfileTest.testRnamlSeqImport	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		import jalview.util.Platform;
30
31		import java.io.BufferedReader;
32		import java.io.FileNotFoundException;
33		import java.io.FileReader;
34		import java.io.IOException;
35		import java.util.ArrayList;
36		import java.util.List;
37
38		import com.stevesoft.pat.Regex;
39
40		import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
41		import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
42		import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
43		import fr.orsay.lri.varna.factories.RNAFactory;
44		import fr.orsay.lri.varna.models.rna.RNA;
45
		68.2% Uncovered Elements: 28 (88) Complexity: 25 Complexity Density: 0.42
46		public class RnamlFile extends AlignFile
47		{
48		public String id;
49
50		protected ArrayList<RNA> result;
51
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
52	0	public RnamlFile()...
53		{
54	0	super();
55
56		}
57
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
58	1	public RnamlFile(String inFile, DataSourceType type) throws IOException...
59		{
60	1	super(inFile, type);
61
62		}
63
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
64	1	public RnamlFile(FileParse source) throws IOException...
65		{
66	1	super(source);
67
68		}
69
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
70	0	public BufferedReader CreateReader() throws FileNotFoundException...
71		{
72	0	FileReader fr = null;
73	0	fr = new FileReader(inFile);
74
75	0	BufferedReader r = new BufferedReader(fr);
76	0	return r;
77		}
78
79		/*
80		* (non-Javadoc)
81		*
82		* @see jalview.io.AlignFile#parse()
83		*/
		26.7% Uncovered Elements: 11 (15) Complexity: 7 Complexity Density: 0.54
84	2	@Override...
85		public void parse() throws IOException
86		{
87	2	if (System.getProperty("java.version").indexOf("1.6") > -1
88		|| System.getProperty("java.version").indexOf("1.5") > -1)
89		{
90		// patch for 'This parser does not support specification "null" version
91		// "null"' error
92		// this hack ensures we get a properly updated SAXParserFactory on older
93		// JVMs
94		// thanks to Stefan Birkner over at https://coderwall.com/p/kqsrrw
95	0	System.setProperty("javax.xml.parsers.SAXParserFactory",
96		"com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
97		}
98		// rather than lose exception semantics whilst parsing RNAML with VARNA we
99		// wrap the routine and catch all exceptions before passing them up the
100		// chain as an IOException
101	2	try
102		{
103	2	_parse();
104		} catch (ExceptionPermissionDenied pdx)
105		{
106	0	errormessage = MessageManager.formatMessage(
107		"exception.rnaml_couldnt_access_datasource", new String[]
108		{ pdx.getMessage() });
109	0	throw new IOException(pdx);
110		} catch (ExceptionLoadingFailed lf)
111		{
112	0	errormessage = MessageManager.formatMessage(
113		"exception.ranml_couldnt_process_data", new String[]
114		{ lf.getMessage() });
115	0	throw new IOException(lf);
116		} catch (ExceptionFileFormatOrSyntax iff)
117		{
118	0	errormessage = MessageManager
119		.formatMessage("exception.ranml_invalid_file", new String[]
120		{ iff.getMessage() });
121	0	throw new IOException(iff);
122		} catch (Exception x)
123		{
124	0	error = true;
125	0	errormessage = MessageManager.formatMessage(
126		"exception.ranml_problem_parsing_data", new String[]
127		{ x.getMessage() });
128	0	throw new IOException(errormessage, x);
129		}
130		}
131
		90.2% Uncovered Elements: 4 (41) Complexity: 9 Complexity Density: 0.33
132	2	@SuppressWarnings("unchecked")...
133		public void _parse()
134		throws FileNotFoundException, ExceptionPermissionDenied,
135		ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
136		{
137
138	2	result = RNAFactory.loadSecStrRNAML(getReader());
139
140		// ArrayList<ArrayList> allarray = new ArrayList();
141		// ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
142		// ArrayList strucinarray = new ArrayList();
143	2	SequenceI[] sqs = new SequenceI[result.size()];
144
145	5	for (int i = 0; i < result.size(); i++)
146		{
147
148	3	RNA current = result.get(i);
149	3	String rna = current.getStructDBN(true);
150	3	String seq = current.getSeq();
151	3	int begin = 1;
152	3	int end = seq.length();
153
154	3	id = current.getName();
155	3	if (id == null || id.trim().length() == 0)
156		{
157	3	id = safeName(getDataName());
158	3	if (result.size() > 1)
159		{
160	2	id += "." + i;
161		}
162		}
163	3	sqs[i] = new Sequence(id, seq, begin, end);
164	3	if (seq.length() != (end - begin + 1))
165		{
166	0	sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
167		}
168	3	String[] annot = new String[rna.length()];
169	3	Annotation[] ann = new Annotation[rna.length()];
170
171	566	for (int j = 0; j < rna.length(); j++)
172		{
173	563	annot[j] = "" + rna.charAt(j);
174
175		}
176	566	for (int k = 0; k < rna.length(); k++)
177		{
178	563	ann[k] = new Annotation(annot[k], "",
179		Rna.getRNASecStrucState(annot[k]).charAt(0), 0f);
180		}
181
182	3	AlignmentAnnotation align = new AlignmentAnnotation(
183		"Secondary Structure",
184	3	current.getID().trim().length() > 0
185		? "Secondary Structure for " + current.getID()
186		: "",
187		ann);
188
189	3	sqs[i].addAlignmentAnnotation(align);
190	3	sqs[i].setRNA(result.get(i));
191
192		// allarray.add(strucinarray);
193
194	3	annotations.addElement(align);
195		// BP.add(align.bps);
196
197		}
198
199	2	setSeqs(sqs);
200		}
201
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
202	0	@Override...
203		public String print(SequenceI[] s, boolean jvSuffix)
204		{
205	0	return "not yet implemented";
206		}
207
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
208	0	public List<RNA> getRNA()...
209		{
210	0	return result;
211		}
212
213		// public static void main(String[] args) {
214		// Pattern p= Pattern.compile("(.+)[.][^.]+");
215		// Matcher m = p.matcher("toto.xml.zip");
216		// jalview.bin.Console.outPrintln(m.matches());
217		// jalview.bin.Console.outPrintln(m.group(1));
218		// }
219		/**
220		* make a friendly ID string.
221		*
222		* @param dataName
223		* @return truncated dataName to after last '/'
224		*/
		85.7% Uncovered Elements: 2 (14) Complexity: 3 Complexity Density: 0.3
225	3	private String safeName(String dataName)...
226		{
227	3	int b = 0;
228	?	if ((b = dataName.lastIndexOf(".")) > 0)
229		{
230	3	dataName = dataName.substring(0, b - 1);
231		}
232	3	b = 0;
233	3	Regex m = Platform.newRegex("[\\/]?([-A-Za-z0-9]+)\\.?");
234	3	String mm = dataName;
235	12	while (m.searchFrom(dataName, b))
236		{
237	9	mm = m.stringMatched();
238	9	b = m.matchedTo();
239		}
240	3	return mm;
241		}
242		}