Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ClustalFile	34	93	37	0.82119282.1%	Show methods

Class ClustalFile

Class ClustalFile	Line # 34	Total Statements 93	Complexity 37	TOTAL Coverage 0.82119282.1%
ClustalFile()   ClustalFile()	3737	0.00	1.01	-1.0 -1.0 -
ClustalFile(String,DataSourceType)   ClustalFile(String,DataSourceType)	4141	1.01	1.01	1.0 1.0100%
ClustalFile(FileParse)   ClustalFile(FileParse)	4747	1.01	1.01	1.0 1.0100%
initData() : void   initData() : void	5252	1.01	1.01	1.0 1.0100%
parse() : void   parse() : void	5858	60.060	21.021	0.7395833 0.739583374%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	201201	30.030	12.012	0.95652175 0.9565217595.7%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.7615894	jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip	1PASS
	0.5033113	jalview.io.ClustalFileTest.testParse_withNumberingjalview.io.ClustalFileTest.testParse_withNumbering	1PASS
	0.4834437	jalview.io.ClustalFileTest.testParse_noNumberingjalview.io.ClustalFileTest.testParse_noNumbering	1PASS
	0.29801324	jalview.analysis.AlignmentUtilsTests.testExpandContextjalview.analysis.AlignmentUtilsTests.testExpandContext	1PASS
	0.29139072	jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest	1PASS
	0.29139072	jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest	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.AlignmentAnnotation;
24		import jalview.datamodel.Sequence;
25		import jalview.datamodel.SequenceI;
26		import jalview.util.Format;
27
28		import java.io.IOException;
29		import java.util.HashMap;
30		import java.util.Map;
31		import java.util.StringTokenizer;
32		import java.util.Vector;
33
		82.1% Uncovered Elements: 27 (151) Complexity: 37 Complexity Density: 0.4
34		public class ClustalFile extends AlignFile
35		{
36
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
37	37	public ClustalFile()...
38		{
39		}
40
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
41	2	public ClustalFile(String inFile, DataSourceType sourceType)...
42		throws IOException
43		{
44	2	super(inFile, sourceType);
45		}
46
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
47	1	public ClustalFile(FileParse source) throws IOException...
48		{
49	1	super(source);
50		}
51
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
52	40	@Override...
53		public void initData()
54		{
55	40	super.initData();
56		}
57
		74% Uncovered Elements: 25 (96) Complexity: 21 Complexity Density: 0.35
58	5	@Override...
59		public void parse() throws IOException
60		{
61	5	int i = 0;
62	5	boolean flag = false;
63	5	boolean top = false;
64	5	StringBuffer pssecstr = new StringBuffer();
65	5	StringBuffer consstr = new StringBuffer();
66	5	Vector<String> headers = new Vector<>();
67	5	Map<String, StringBuffer> seqhash = new HashMap<>();
68	5	StringBuffer tempseq;
69	5	String line, id;
70	5	StringTokenizer str;
71
72	5	try
73		{
74	?	while ((line = nextLine()) != null)
75		{
76	78	if (line.length() == 0)
77		{
78	8	top = true;
79		}
80	78	boolean isConservation = line.startsWith(SPACE)
81		|| line.startsWith(TAB);
82	78	if (!isConservation)
83		{
84	76	str = new StringTokenizer(line);
85
86	76	if (str.hasMoreTokens())
87		{
88	68	id = str.nextToken();
89
90	68	if (id.equalsIgnoreCase("CLUSTAL"))
91		{
92	3	flag = true;
93		}
94		else
95		{
96	65	if (flag)
97		{
98	65	if (seqhash.containsKey(id))
99		{
100	40	tempseq = seqhash.get(id);
101		}
102		else
103		{
104	25	tempseq = new StringBuffer();
105	25	seqhash.put(id, tempseq);
106		}
107
108	65	if (!(headers.contains(id)))
109		{
110	25	headers.addElement(id);
111		}
112
113	65	if (str.hasMoreTokens())
114		{
115	65	tempseq.append(str.nextToken());
116		}
117	65	top = false;
118		}
119		}
120		}
121		else
122		{
123	8	flag = true;
124		}
125		}
126		else
127		{
128	2	if (line.matches("\\s+(-|\\.|\\(|\\[|\\]|\\))+"))
129		{
130	0	if (top)
131		{
132	0	pssecstr.append(line.trim());
133		}
134		else
135		{
136	0	consstr.append(line.trim());
137		}
138		}
139		}
140		}
141		} catch (IOException e)
142		{
143	2	jalview.bin.Console.errPrintln("Exception parsing clustal file " + e);
144	2	e.printStackTrace();
145		}
146
147	5	if (flag)
148		{
149	3	this.noSeqs = headers.size();
150
151		// Add sequences to the hash
152	28	for (i = 0; i < headers.size(); i++)
153		{
154	25	if (seqhash.get(headers.elementAt(i)) != null)
155		{
156	25	if (maxLength < seqhash.get(headers.elementAt(i)).toString()
157		.length())
158		{
159	3	maxLength = seqhash.get(headers.elementAt(i)).toString()
160		.length();
161		}
162
163	25	Sequence newSeq = parseId(headers.elementAt(i).toString());
164	25	newSeq.setSequence(
165		seqhash.get(headers.elementAt(i).toString()).toString());
166
167	25	seqs.addElement(newSeq);
168		}
169		else
170		{
171	0	jalview.bin.Console.errPrintln(
172		"Clustal File Reader: Can't find sequence for "
173		+ headers.elementAt(i));
174		}
175		}
176	3	AlignmentAnnotation lastssa = null;
177	3	if (pssecstr.length() == maxLength)
178		{
179	0	Vector<AlignmentAnnotation> ss = new Vector<>();
180	0	AlignmentAnnotation ssa = lastssa = StockholmFile
181		.parseAnnotationRow(ss, "secondary structure",
182		pssecstr.toString());
183	0	ssa.label = "Secondary Structure";
184	0	annotations.addElement(ssa);
185		}
186	3	if (consstr.length() == maxLength)
187		{
188	0	Vector<AlignmentAnnotation> ss = new Vector<>();
189	0	AlignmentAnnotation ssa = StockholmFile.parseAnnotationRow(ss,
190		"secondary structure", consstr.toString());
191	0	ssa.label = "Consensus Secondary Structure";
192	0	if (lastssa == null || !lastssa.getRNAStruc()
193		.equals(ssa.getRNAStruc().replace('-', '.')))
194		{
195	0	annotations.addElement(ssa);
196		}
197		}
198		}
199		}
200
		95.7% Uncovered Elements: 2 (46) Complexity: 12 Complexity Density: 0.4
201	37	@Override...
202		public String print(SequenceI[] s, boolean jvsuffix)
203		{
204	37	StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
205
206	37	int max = 0;
207	37	int maxid = 0;
208
209	37	int i = 0;
210
211	238	while ((i < s.length) && (s[i] != null))
212		{
213	201	String tmp = printId(s[i], jvsuffix);
214
215	201	max = Math.max(max, s[i].getLength());
216
217	201	if (tmp.length() > maxid)
218		{
219	53	maxid = tmp.length();
220		}
221
222	201	i++;
223		}
224
225	37	if (maxid < 15)
226		{
227	34	maxid = 15;
228		}
229
230	37	maxid++;
231
232	37	int len = 60;
233	37	int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
234
235	82	for (i = 0; i < nochunks; i++)
236		{
237	45	int j = 0;
238
239	366	while ((j < s.length) && (s[j] != null))
240		{
241	321	out.append(new Format("%-" + maxid + "s")
242		.form(printId(s[j], jvsuffix) + " "));
243
244	321	int chunkStart = i * len;
245	321	int chunkEnd = chunkStart + len;
246
247	321	int length = s[j].getLength();
248	321	if ((chunkEnd < length) && (chunkStart < length))
249		{
250	120	out.append(s[j].getSequenceAsString(chunkStart, chunkEnd));
251		}
252		else
253		{
254	201	if (chunkStart < length)
255		{
256	201	out.append(s[j].getSequenceAsString().substring(chunkStart));
257		}
258		}
259
260	321	out.append(newline);
261	321	j++;
262		}
263
264	45	out.append(newline);
265		}
266
267	37	return out.toString();
268		}
269		}