bio.bam.referenceinfo source code

1 /*
2     This file is part of BioD.
3     Copyright (C) 2012    Artem Tarasov <lomereiter@gmail.com>
4 
5     Permission is hereby granted, free of charge, to any person obtaining a
6     copy of this software and associated documentation files (the "Software"),
7     to deal in the Software without restriction, including without limitation
8     the rights to use, copy, modify, merge, publish, distribute, sublicense,
9     and/or sell copies of the Software, and to permit persons to whom the
10     Software is furnished to do so, subject to the following conditions:
11     
12     The above copyright notice and this permission notice shall be included in
13     all copies or substantial portions of the Software.
14     
15     THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16     IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17     FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18     AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19     LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
20     FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
21     DEALINGS IN THE SOFTWARE.
22 
23 */
24 module bio.bam.referenceinfo;
25 
26 import undead.stream;
27 import std.exception;
28 import std.array;
29 
30 /**
31   Stores basic information about reference sequence.
32  */
33 struct ReferenceSequenceInfo {
34     private {
35         string _name;
36         int _length;
37     }
38 
39     /// Reference sequence name
40     /// (null byte is guaranteed to follow the returned slice)
41     string name() @property const nothrow {
42         return _name[0 .. $ - 1];
43     }
44    
45     /// Reference sequence length
46     int length() @property const {
47         return _length;
48     }
49 
50     ///
51     this(string name, int length) {
52         _name = name ~ '\0';
53         _length = length;
54     }
55 
56     /// Constructs the structure from input stream
57     this(ref Stream stream) {
58         int l_name; // length of the reference name plus one
59         stream.read(l_name);
60         _name = cast(string)stream.readString(l_name); // keep '\0' at the end
61         stream.read(_length);
62     }
63 }