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Coverage Report

  1. Project Clover database Thu Nov 7 2024 10:11:34 GMT
  2. Package jalview.io

File PIRFile.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
29% of files have more coverage

Code metrics

34
69
5
1
202
143
24
0.35
13.8
5
4.8

Classes

Class Line # Actions
PIRFile 30 69 24
0.675925967.6%
 

Contributing tests

This file is covered by 1 test. .

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    import jalview.util.Comparison;
26   
27    import java.io.IOException;
28    import java.util.Vector;
29   
 
30    public class PIRFile extends AlignFile
31    {
32    public static boolean useModellerOutput = false;
33   
34    Vector words = new Vector(); // Stores the words in a line after splitting
35   
 
36  3 toggle public PIRFile()
37    {
38    }
39   
 
40  0 toggle public PIRFile(String inFile, DataSourceType sourceType)
41    throws IOException
42    {
43  0 super(inFile, sourceType);
44    }
45   
 
46  1 toggle public PIRFile(FileParse source) throws IOException
47    {
48  1 super(source);
49    }
50   
 
51  1 toggle @Override
52    public void parse() throws IOException
53    {
54  1 StringBuffer sequence;
55  1 String line = null;
56  1 ModellerDescription md;
57   
58  ? while ((line = nextLine()) != null)
59    {
60  15 if (line.length() == 0)
61    {
62    // jalview.bin.Console.outPrintln("blank line");
63  0 continue;
64    }
65  15 if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
66    {
67  0 continue;
68    }
69  15 Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
70   
71  15 sequence = new StringBuffer();
72   
73  15 newSeq.setDescription(nextLine()); // this is the title line
74   
75  15 boolean starFound = false;
76   
77  60 while (!starFound)
78    {
79  45 line = nextLine();
80  45 sequence.append(line);
81   
82  45 if (line == null)
83    {
84  0 break;
85    }
86   
87  45 if (line.indexOf("*") > -1)
88    {
89  15 starFound = true;
90    }
91    }
92   
93  15 if (sequence.length() > 0)
94    {
95  15 sequence.setLength(sequence.length() - 1);
96  15 newSeq.setSequence(sequence.toString());
97   
98  15 seqs.addElement(newSeq);
99   
100  15 md = new ModellerDescription(newSeq.getDescription());
101  15 md.updateSequenceI(newSeq);
102    }
103    }
104    }
105   
 
106  3 toggle @Override
107    public String print(SequenceI[] s, boolean jvsuffix)
108    {
109  3 boolean is_NA = Comparison.isNucleotide(s);
110  3 int len = 72;
111  3 StringBuffer out = new StringBuffer();
112  3 int i = 0;
113  3 ModellerDescription md;
114   
115  48 while ((i < s.length) && (s[i] != null))
116    {
117  45 String seq = s[i].getSequenceAsString();
118  45 seq = seq + "*";
119   
120  45 if (is_NA)
121    {
122    // modeller doesn't really do nucleotides, so we don't do anything fancy
123    // Official tags area as follows, for now we'll use P1 and DL
124    // Protein (complete) P1
125    // Protein (fragment) F1
126    // DNA (linear) Dl
127    // DNA (circular) DC
128    // RNA (linear) RL
129    // RNA (circular) RC
130    // tRNA N3
131    // other functional RNA N1
132   
133  0 out.append(">N1;" + s[i].getName());
134  0 out.append(newline);
135  0 if (s[i].getDescription() == null)
136    {
137  0 out.append(s[i].getName() + " "
138    + (s[i].getEnd() - s[i].getStart() + 1));
139  0 out.append(is_NA ? " bases" : " residues");
140  0 out.append(newline);
141    }
142    else
143    {
144  0 out.append(s[i].getDescription());
145  0 out.append(newline);
146    }
147    }
148    else
149    {
150   
151  45 if (useModellerOutput)
152    {
153  0 out.append(">P1;" + s[i].getName());
154  0 out.append(newline);
155  0 md = new ModellerDescription(s[i]);
156  0 out.append(md.getDescriptionLine());
157  0 out.append(newline);
158    }
159    else
160    {
161  45 out.append(">P1;" + printId(s[i], jvsuffix));
162  45 out.append(newline);
163  45 if (s[i].getDescription() != null)
164    {
165  45 out.append(s[i].getDescription());
166  45 out.append(newline);
167    }
168    else
169    {
170  0 out.append(s[i].getName() + " "
171    + (s[i].getEnd() - s[i].getStart() + 1) + " residues");
172  0 out.append(newline);
173    }
174    }
175    }
176  45 int nochunks = (seq.length() / len)
177  45 + (seq.length() % len > 0 ? 1 : 0);
178   
179  180 for (int j = 0; j < nochunks; j++)
180    {
181  135 int start = j * len;
182  135 int end = start + len;
183   
184  135 if (end < seq.length())
185    {
186  90 out.append(seq.substring(start, end));
187  90 out.append(newline);
188    }
189  45 else if (start < seq.length())
190    {
191  45 out.append(seq.substring(start));
192  45 out.append(newline);
193    }
194    }
195   
196  45 i++;
197    }
198   
199  3 return out.toString();
200    }
201   
202    }