Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RnamlFile	45	59	25	0.00%	Show methods

Class RnamlFile

Class RnamlFile	Line # 45	Total Statements 59	Complexity 25	TOTAL Coverage 0.00%
RnamlFile()   RnamlFile()	5151	1.01	1.01	0.0 0.00%
RnamlFile(String,DataSourceType)   RnamlFile(String,DataSourceType)	5757	1.01	1.01	0.0 0.00%
RnamlFile(FileParse)   RnamlFile(FileParse)	6363	1.01	1.01	0.0 0.00%
CreateReader() : BufferedReader   CreateReader() : BufferedReader	6969	4.04	1.01	0.0 0.00%
parse() : void   parse() : void	8383	13.013	7.07	0.0 0.00%
_parse() : void   _parse() : void	131131	27.027	9.09	0.0 0.00%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	201201	1.01	1.01	0.0 0.00%
getRNA() : List<RNA>   getRNA() : List<RNA>	207207	1.01	1.01	0.0 0.00%
safeName(String) : String   safeName(String) : String	224224	10.010	3.03	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 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
		0% Uncovered Elements: 88 (88) Complexity: 25 Complexity Density: 0.42
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
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
63	0	public RnamlFile(FileParse source) throws IOException...
64		{
65	0	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		*/
		0% Uncovered Elements: 15 (15) Complexity: 7 Complexity Density: 0.54
83	0	@Override...
84		public void parse() throws IOException
85		{
86	0	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	0	try
101		{
102	0	_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
		0% Uncovered Elements: 41 (41) Complexity: 9 Complexity Density: 0.33
131	0	@SuppressWarnings("unchecked")...
132		public void _parse()
133		throws FileNotFoundException, ExceptionPermissionDenied,
134		ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
135		{
136
137	0	result = RNAFactory.loadSecStrRNAML(getReader());
138
139		// ArrayList<ArrayList> allarray = new ArrayList();
140		// ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
141		// ArrayList strucinarray = new ArrayList();
142	0	SequenceI[] sqs = new SequenceI[result.size()];
143
144	0	for (int i = 0; i < result.size(); i++)
145		{
146
147	0	RNA current = result.get(i);
148	0	String rna = current.getStructDBN(true);
149	0	String seq = current.getSeq();
150	0	int begin = 1;
151	0	int end = seq.length();
152
153	0	id = current.getName();
154	0	if (id == null || id.trim().length() == 0)
155		{
156	0	id = safeName(getDataName());
157	0	if (result.size() > 1)
158		{
159	0	id += "." + i;
160		}
161		}
162	0	sqs[i] = new Sequence(id, seq, begin, end);
163	0	if (seq.length() != (end - begin + 1))
164		{
165	0	sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
166		}
167	0	String[] annot = new String[rna.length()];
168	0	Annotation[] ann = new Annotation[rna.length()];
169
170	0	for (int j = 0; j < rna.length(); j++)
171		{
172	0	annot[j] = "" + rna.charAt(j);
173
174		}
175	0	for (int k = 0; k < rna.length(); k++)
176		{
177	0	ann[k] = new Annotation(annot[k], "",
178		Rna.getRNASecStrucState(annot[k]).charAt(0), 0f);
179		}
180
181	0	AlignmentAnnotation align = new AlignmentAnnotation(
182		"Secondary Structure",
183	0	current.getID().trim().length() > 0
184		? "Secondary Structure for " + current.getID()
185		: "",
186		ann);
187
188	0	sqs[i].addAlignmentAnnotation(align);
189	0	sqs[i].setRNA(result.get(i));
190
191		// allarray.add(strucinarray);
192
193	0	annotations.addElement(align);
194		// BP.add(align.bps);
195
196		}
197
198	0	setSeqs(sqs);
199		}
200
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
201	0	@Override...
202		public String print(SequenceI[] s, boolean jvSuffix)
203		{
204	0	return "not yet implemented";
205		}
206
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
207	0	public List<RNA> getRNA()...
208		{
209	0	return result;
210		}
211
212		// public static void main(String[] args) {
213		// Pattern p= Pattern.compile("(.+)[.][^.]+");
214		// Matcher m = p.matcher("toto.xml.zip");
215		// jalview.bin.Console.outPrintln(m.matches());
216		// jalview.bin.Console.outPrintln(m.group(1));
217		// }
218		/**
219		* make a friendly ID string.
220		*
221		* @param dataName
222		* @return truncated dataName to after last '/'
223		*/
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
224	0	private String safeName(String dataName)...
225		{
226	0	int b = 0;
227	0	if ((b = dataName.lastIndexOf(".")) > 0)
228		{
229	0	dataName = dataName.substring(0, b - 1);
230		}
231	0	b = 0;
232	0	Regex m = new Regex("[\\/]?([-A-Za-z0-9]+)\\.?");
233	0	String mm = dataName;
234	0	while (m.searchFrom(dataName, b))
235		{
236	0	mm = m.stringMatched();
237	0	b = m.matchedTo();
238		}
239	0	return mm;
240		}
241		}