Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FastaFile	37	62	30	0.00%	Show methods

Class FastaFile

Class FastaFile	Line # 37	Total Statements 62	Complexity 30	TOTAL Coverage 0.00%
FastaFile()   FastaFile()	4949	0.00	1.01	-1.0 -1.0 -
FastaFile(String,DataSourceType)   FastaFile(String,DataSourceType)	6464	1.01	1.01	0.0 0.00%
FastaFile(FileParse)   FastaFile(FileParse)	7070	1.01	1.01	0.0 0.00%
FastaFile(FileParse,boolean)   FastaFile(FileParse,boolean)	7575	1.01	1.01	0.0 0.00%
FastaFile(SequenceI[])   FastaFile(SequenceI[])	8080	1.01	1.01	0.0 0.00%
parse() : void   parse() : void	9191	28.028	12.012	0.0 0.00%
makeAnnotation(SequenceI,StringBuffer) : AlignmentAnnotation   makeAnnotation(SequenceI,StringBuffer) : AlignmentAnnotation	160160	8.08	3.03	0.0 0.00%
addAnnotations(Alignment) : void   addAnnotations(Alignment) : void	183183	5.05	2.02	0.0 0.00%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	194194	17.017	8.08	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 java.io.IOException;
24
25		import jalview.datamodel.Alignment;
26		import jalview.datamodel.AlignmentAnnotation;
27		import jalview.datamodel.Annotation;
28		import jalview.datamodel.Sequence;
29		import jalview.datamodel.SequenceI;
30
31		/**
32		* Parse and Write out FASTA
33		*
34		* @author $author$
35		* @version $Revision$
36		*/
		0% Uncovered Elements: 111 (111) Complexity: 30 Complexity Density: 0.48
37		public class FastaFile extends AlignFile
38		{
39		/**
40		* Length of a sequence line
41		*/
42		int len = 72;
43
44		StringBuffer out;
45
46		/**
47		* Creates a new FastaFile object.
48		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
49	0	public FastaFile()...
50		{
51		}
52
53		/**
54		* Creates a new FastaFile object.
55		*
56		* @param inFile
57		* DOCUMENT ME!
58		* @param sourceType
59		* DOCUMENT ME!
60		*
61		* @throws IOException
62		* DOCUMENT ME!
63		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
64	0	public FastaFile(String inFile, DataSourceType sourceType)...
65		throws IOException
66		{
67	0	super(inFile, sourceType);
68		}
69
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
70	0	public FastaFile(FileParse source) throws IOException...
71		{
72	0	this(source, true);
73		}
74
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
75	0	public FastaFile(FileParse source, boolean closeData) throws IOException...
76		{
77	0	super(true, source, closeData);
78		}
79
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
80	0	public FastaFile(SequenceI[] seqs)...
81		{
82	0	super(seqs);
83		}
84
85		/**
86		* DOCUMENT ME!
87		*
88		* @throws IOException
89		* DOCUMENT ME!
90		*/
		0% Uncovered Elements: 50 (50) Complexity: 12 Complexity Density: 0.43
91	0	@Override...
92		public void parse() throws IOException
93		{
94	0	StringBuffer sb = new StringBuffer();
95	0	boolean firstLine = true;
96
97	0	String line, uline;
98	0	Sequence seq = null;
99
100	0	boolean annotation = false;
101
102	0	while ((uline = nextLine()) != null)
103		{
104	0	line = uline.trim();
105	0	if (line.length() > 0)
106		{
107	0	if (line.charAt(0) == '>')
108		{
109	0	if (line.startsWith(">#_"))
110		{
111	0	if (annotation)
112		{
113	0	annotations.addElement(makeAnnotation(seq, sb));
114		}
115		}
116		else
117		{
118	0	annotation = false;
119		}
120
121	0	if (!firstLine)
122		{
123	0	seq.setSequence(sb.toString());
124
125	0	if (!annotation)
126		{
127	0	seqs.addElement(seq);
128		}
129		}
130
131	0	seq = parseId(line.substring(1));
132	0	firstLine = false;
133
134	0	sb = new StringBuffer();
135
136	0	if (line.startsWith(">#_"))
137		{
138	0	annotation = true;
139		}
140		}
141		else
142		{
143	0	sb.append(annotation ? uline : line);
144		}
145		}
146		}
147
148	0	if (annotation)
149		{
150	0	annotations.addElement(makeAnnotation(seq, sb));
151		}
152
153	0	else if (!firstLine)
154		{
155	0	seq.setSequence(sb.toString());
156	0	seqs.addElement(seq);
157		}
158		}
159
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
160	0	private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)...
161		{
162	0	Annotation[] anots = new Annotation[sb.length()];
163	0	char cb;
164	0	for (int i = 0; i < anots.length; i++)
165		{
166	0	char cn = sb.charAt(i);
167	0	if (cn != ' ')
168		{
169	0	anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
170		}
171		}
172	0	AlignmentAnnotation aa = new AlignmentAnnotation(
173		seq.getName().substring(2), seq.getDescription(), anots);
174	0	return aa;
175		}
176
177		/**
178		* called by AppletFormatAdapter to generate an annotated alignment, rather
179		* than bare sequences.
180		*
181		* @param al
182		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
183	0	public void addAnnotations(Alignment al)...
184		{
185	0	addProperties(al);
186	0	for (int i = 0; i < annotations.size(); i++)
187		{
188	0	AlignmentAnnotation aa = annotations.elementAt(i);
189	0	aa.setPadGaps(true, al.getGapCharacter());
190	0	al.addAnnotation(aa);
191		}
192		}
193
		0% Uncovered Elements: 29 (29) Complexity: 8 Complexity Density: 0.47
194	0	@Override...
195		public String print(SequenceI[] s, boolean jvsuffix)
196		{
197	0	out = new StringBuffer();
198	0	int i = 0;
199
200	0	while ((i < s.length) && (s[i] != null))
201		{
202	0	out.append(">" + printId(s[i], jvsuffix));
203	0	if (s[i].getDescription() != null)
204		{
205	0	out.append(" " + s[i].getDescription());
206		}
207
208	0	out.append(newline);
209
210	0	int nochunks = (s[i].getLength() / len)
211	0	+ (s[i].getLength() % len > 0 ? 1 : 0);
212
213	0	for (int j = 0; j < nochunks; j++)
214		{
215	0	int start = j * len;
216	0	int end = start + len;
217
218	0	if (end < s[i].getLength())
219		{
220	0	out.append(s[i].getSequenceAsString(start, end) + newline);
221		}
222	0	else if (start < s[i].getLength())
223		{
224	0	out.append(s[i].getSequenceAsString(start, s[i].getLength())
225		+ newline);
226		}
227		}
228
229	0	i++;
230		}
231
232	0	return out.toString();
233		}
234		}