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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.io

File FastaFile.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
28% of files have more coverage

Code metrics

40
61
8
1
229
145
29
0.48
7.62
8
3.62

Classes

Class Line # Actions
FastaFile 37 61 29 42
0.614678961.5%
 

Contributing tests

This file is covered by 98 tests. .

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.Alignment;
24    import jalview.datamodel.AlignmentAnnotation;
25    import jalview.datamodel.Annotation;
26    import jalview.datamodel.Sequence;
27    import jalview.datamodel.SequenceI;
28   
29    import java.io.IOException;
30   
31    /**
32    * DOCUMENT ME!
33    *
34    * @author $author$
35    * @version $Revision$
36    */
 
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    */
 
49  36 toggle 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    */
 
64  0 toggle public FastaFile(String inFile, DataSourceType sourceType)
65    throws IOException
66    {
67  0 super(inFile, sourceType);
68    }
69   
 
70  154 toggle public FastaFile(FileParse source) throws IOException
71    {
72  154 super(source);
73    }
74   
 
75  0 toggle public FastaFile(SequenceI[] seqs)
76    {
77  0 super(seqs);
78    }
79   
80    /**
81    * DOCUMENT ME!
82    *
83    * @throws IOException
84    * DOCUMENT ME!
85    */
 
86  154 toggle @Override
87    public void parse() throws IOException
88    {
89  154 StringBuffer sb = new StringBuffer();
90  154 boolean firstLine = true;
91   
92  154 String line, uline;
93  154 Sequence seq = null;
94   
95  154 boolean annotation = false;
96   
97  ? while ((uline = nextLine()) != null)
98    {
99  4111 line = uline.trim();
100  4111 if (line.length() > 0)
101    {
102  4111 if (line.charAt(0) == '>')
103    {
104  1132 if (line.startsWith(">#_"))
105    {
106  0 if (annotation)
107    {
108  0 annotations.addElement(makeAnnotation(seq, sb));
109    }
110    }
111    else
112    {
113  1132 annotation = false;
114    }
115   
116  1132 if (!firstLine)
117    {
118  978 seq.setSequence(sb.toString());
119   
120  978 if (!annotation)
121    {
122  978 seqs.addElement(seq);
123    }
124    }
125   
126  1132 seq = parseId(line.substring(1));
127  1132 firstLine = false;
128   
129  1132 sb = new StringBuffer();
130   
131  1132 if (line.startsWith(">#_"))
132    {
133  0 annotation = true;
134    }
135    }
136    else
137    {
138  2979 sb.append(annotation ? uline : line);
139    }
140    }
141    }
142   
143  154 if (annotation)
144    {
145  0 annotations.addElement(makeAnnotation(seq, sb));
146    }
147   
148  154 else if (!firstLine)
149    {
150  154 seq.setSequence(sb.toString());
151  154 seqs.addElement(seq);
152    }
153    }
154   
 
155  0 toggle private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
156    {
157  0 Annotation[] anots = new Annotation[sb.length()];
158  0 char cb;
159  0 for (int i = 0; i < anots.length; i++)
160    {
161  0 char cn = sb.charAt(i);
162  0 if (cn != ' ')
163    {
164  0 anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
165    }
166    }
167  0 AlignmentAnnotation aa = new AlignmentAnnotation(
168    seq.getName().substring(2), seq.getDescription(), anots);
169  0 return aa;
170    }
171   
172    /**
173    * called by AppletFormatAdapter to generate an annotated alignment, rather
174    * than bare sequences.
175    *
176    * @param al
177    */
 
178  0 toggle public void addAnnotations(Alignment al)
179    {
180  0 addProperties(al);
181  0 for (int i = 0; i < annotations.size(); i++)
182    {
183  0 AlignmentAnnotation aa = annotations.elementAt(i);
184  0 aa.setPadGaps(true, al.getGapCharacter());
185  0 al.addAnnotation(aa);
186    }
187    }
188   
 
189  36 toggle @Override
190    public String print(SequenceI[] s, boolean jvsuffix)
191    {
192  36 out = new StringBuffer();
193  36 int i = 0;
194   
195  1727 while ((i < s.length) && (s[i] != null))
196    {
197  1691 out.append(">" + printId(s[i], jvsuffix));
198  1691 if (s[i].getDescription() != null)
199    {
200  32 out.append(" " + s[i].getDescription());
201    }
202   
203  1691 out.append(newline);
204   
205  1691 int nochunks = (s[i].getLength() / len)
206  1691 + (s[i].getLength() % len > 0 ? 1 : 0);
207   
208  5734 for (int j = 0; j < nochunks; j++)
209    {
210  4043 int start = j * len;
211  4043 int end = start + len;
212   
213  4043 if (end < s[i].getLength())
214    {
215  2352 out.append(s[i].getSequenceAsString(start, end) + newline);
216    }
217  1691 else if (start < s[i].getLength())
218    {
219  1691 out.append(s[i].getSequenceAsString(start, s[i].getLength())
220    + newline);
221    }
222    }
223   
224  1691 i++;
225    }
226   
227  36 return out.toString();
228    }
229    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.