Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
BLCFile	35	81	34	0.755725275.6%	Show methods

Class BLCFile

Class BLCFile	Line # 35	Total Statements 81	Complexity 34	TOTAL Coverage 0.755725275.6%
BLCFile()   BLCFile()	4242	0.00	1.01	-1.0 -1.0 -
BLCFile(String,DataSourceType)   BLCFile(String,DataSourceType)	5757	1.01	1.01	0.0 0.00%
BLCFile(FileParse)   BLCFile(FileParse)	6363	1.01	1.01	1.0 1.0100%
initData() : void   initData() : void	7171	2.02	1.01	1.0 1.0100%
parse() : void   parse() : void	9494	54.054	22.022	0.6931818 0.693181869.3%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	226226	23.023	8.08	0.90909094 0.9090909490.9%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.7557252	jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip	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.SequenceI;
25
26		import java.io.IOException;
27		import java.util.Vector;
28
29		/**
30		* DOCUMENT ME!
31		*
32		* @author $author$
33		* @version $Revision$
34		*/
		75.6% Uncovered Elements: 32 (131) Complexity: 34 Complexity Density: 0.42
35		public class BLCFile extends AlignFile
36		{
37		Vector titles;
38
39		/**
40		* Creates a new BLCFile object.
41		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
42	6	public BLCFile()...
43		{
44		}
45
46		/**
47		* Creates a new BLCFile object.
48		*
49		* @param inFile
50		* DOCUMENT ME!
51		* @param sourceType
52		* DOCUMENT ME!
53		*
54		* @throws IOException
55		* DOCUMENT ME!
56		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
57	0	public BLCFile(String inFile, DataSourceType sourceType)...
58		throws IOException
59		{
60	0	super(inFile, sourceType);
61		}
62
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
63	1	public BLCFile(FileParse source) throws IOException...
64		{
65	1	super(source);
66		}
67
68		/**
69		* DOCUMENT ME!
70		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
71	7	@Override...
72		public void initData()
73		{
74	7	super.initData();
75	7	titles = new Vector();
76		}
77
78		/**
79		* Control the number of block iterations to skip before returning. set to 0
80		* to read first block file entry only set to -1 to read last block file entry
81		* only set to greater than zero to skip at most that many entries before
82		* parsing
83		*/
84		int iterationSkips = 0;
85
86		/**
87		* The iteration number for the alignment actually parsed from the blc file
88		*/
89		int iterationCount = 0;
90
91		/**
92		* DOCUMENT ME!
93		*/
		69.3% Uncovered Elements: 27 (88) Complexity: 22 Complexity Density: 0.41
94	1	@Override...
95		public void parse() throws IOException
96		{
97	1	StringBuffer headerLines = new StringBuffer();
98	1	int numHeaderLines = 0; // number of lines appended.
99	1	StringBuffer[] seqstrings = null;
100	1	if (suffix != null)
101		{
102	0	try
103		{
104	0	iterationSkips = Integer.parseInt(suffix);
105		} catch (NumberFormatException e)
106		{
107	0	iterationSkips = 0; // first
108		}
109		}
110
111	1	String line = null;
112
113	1	do
114		{
115	1	boolean idsFound = false;
116	1	boolean newids = false;
117		// search for ID header.
118	1	do
119		{
120	16	line = nextLine();
121	16	if (line == null)
122		{
123	0	break;
124		}
125		// seek end of ids
126	16	if (line.indexOf("*") > -1)
127		{
128	1	idsFound = true;
129
130	1	break;
131		}
132
133	15	int abracket = line.indexOf(">");
134
135	15	if (abracket > -1)
136		{
137
138	15	if (iterationCount > 0 && !newids)
139		{
140		// we have a new set of IDs to record.
141	0	newids = true;
142	0	seqs.removeAllElements();
143		}
144
145	15	line = line.substring(abracket + 1);
146
147	15	Sequence seq = parseId(line);
148	15	seqs.addElement(seq);
149		}
150		else
151		{
152		// header lines - keep them for the alignment comments.
153	0	headerLines.append(line);
154	0	headerLines.append(newline);
155	0	numHeaderLines++;
156		}
157	15	} while (!idsFound);
158	1	if (line == null)
159		{
160	0	break; // end of file.
161		}
162	1	int starCol = line.indexOf("*");
163	1	seqstrings = new StringBuffer[seqs.size()];
164
165	16	for (int i = 0; i < seqs.size(); i++)
166		{
167	15	if (seqstrings[i] == null)
168		{
169	15	seqstrings[i] = new StringBuffer();
170		}
171		}
172
173	1	try
174		{
175	1	line = nextLine();
176	158	while (line != null && line.indexOf("*") == -1)
177		{
178	2512	for (int i = 0; i < seqs.size(); i++)
179		{
180	2355	if (line.length() > (i + starCol))
181		{
182	2355	seqstrings[i].append(line.charAt(i + starCol));
183		}
184		}
185	157	line = nextLine();
186		}
187		} catch (IOException e)
188		{
189	0	if (iterationCount == 0)
190		{
191	0	throw (e); // otherwise we've just run out of iterations.
192		}
193		else
194		{
195	0	iterationSkips = 0;
196		}
197		}
198	1	iterationCount++;
199	1	} while (--iterationSkips != -1);
200
201	16	for (int i = 0; i < seqs.size(); i++)
202		{
203	15	Sequence newSeq = (Sequence) seqs.elementAt(i);
204
205	15	newSeq.setSequence(seqstrings[i].toString());
206		}
207	1	if (seqs.size() > 0)
208		{
209	1	if (headerLines.length() > 1 + numHeaderLines)
210		{
211		// just whitespace or not.
212	0	setAlignmentProperty("Comments", headerLines.toString());
213		}
214	1	setAlignmentProperty("iteration", "" + iterationCount);
215		}
216		}
217
218		/**
219		* DOCUMENT ME!
220		*
221		* @param s
222		* DOCUMENT ME!
223		*
224		* @return DOCUMENT ME!
225		*/
		90.9% Uncovered Elements: 3 (33) Complexity: 8 Complexity Density: 0.35
226	6	@Override...
227		public String print(SequenceI[] s, boolean jvsuffix)
228		{
229	6	StringBuffer out = new StringBuffer();
230		/**
231		* A general parser for ids. Will look for dbrefs in Uniprot format
232		* source|id And also Jalview /start-end
233		*
234		* @String id Id to be parsed
235		*/
236	6	int i = 0;
237	6	int max = -1;
238
239	96	while ((i < s.length) && (s[i] != null))
240		{
241	90	out.append(">" + printId(s[i], jvsuffix));
242	90	if (s[i].getDescription() != null)
243		{
244	90	out.append(" " + s[i].getDescription());
245		}
246
247	90	out.append(newline);
248
249	90	max = Math.max(max, s[i].getLength());
250
251	90	i++;
252		}
253
254	6	out.append("* iteration 1");
255	6	out.append(newline);
256
257	948	for (int j = 0; j < max; j++)
258		{
259	942	i = 0;
260
261	15072	while ((i < s.length) && (s[i] != null))
262		{
263	14130	if (s[i].getSequence().length > j)
264		{
265	14130	out.append(s[i].getSequenceAsString(j, j + 1));
266		}
267		else
268		{
269	0	out.append("-");
270		}
271
272	14130	i++;
273		}
274
275	942	out.append(newline);
276		}
277
278	6	out.append("*");
279	6	out.append(newline);
280
281	6	return out.toString();
282		}
283		}