1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
|
// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
// Facade header for the stream module.
// ==========================================================================
#ifndef SEQAN_STREAM_H_
#define SEQAN_STREAM_H_
// ===========================================================================
// Prerequisites.
// ===========================================================================
#include <iostream>
#include <fstream>
#include <sstream>
#include <sys/types.h>
#include <sys/stat.h>
#ifdef _WIN32
#ifndef ZLIB_WINAPI
//#define ZLIB_WINAPI
#endif
#else
#include <unistd.h>
#endif
#include <seqan/basic.h>
#include <seqan/file.h>
#include <seqan/sequence.h>
// ===========================================================================
// Basic Definitions.
// ===========================================================================
#include <seqan/stream/stream_base.h>
// ===========================================================================
// File Format and Type Guessing.
// ===========================================================================
#include <seqan/stream/guess_format.h>
// ===========================================================================
// Stream Iterators.
// ===========================================================================
#include <seqan/stream/iter_stream.h>
// ===========================================================================
// Stream Implementations and Adaptions.
// ===========================================================================
#include <seqan/stream/adapt_ios.h>
#include <seqan/stream/file_stream.h>
#include <seqan/stream/stream_compressor.h>
#include <seqan/stream/buffered_stream.h>
#if SEQAN_HAS_BZIP2 && !SEQAN_HAS_ZLIB
#error "-DSEQAN_HAS_BZIP2 is defined, but -DSEQAN_HAS_ZLIB not. \
Since BZip2 depends on ZLIB, this would cause hard-to-track compiler errors. \
Either disable -DSEQAN_HAS_BZIP2 or define -DSEQAN_HAS_ZLIB"
#endif
#if SEQAN_HAS_ZLIB
#include <zlib.h>
#include <seqan/stream/iostream_zutil.h>
#include <seqan/stream/iostream_zip.h>
#include <seqan/stream/iostream_zip_impl.h>
#include <seqan/stream/iostream_bgzf.h>
#endif
#if SEQAN_HAS_BZIP2
#include <seqan/stream/iostream_bzip2.h>
#endif
#include <seqan/stream/virtual_stream.h>
#include <seqan/stream/formatted_file.h>
// ===========================================================================
// Tokenization and Lexical Cast.
// ===========================================================================
// TODO(esiragusa): move these files into basic - they are not unique to streams.
#include <seqan/stream/tokenization.h>
#include <seqan/stream/lexical_cast.h>
#endif // SEQAN_STREAM_H_
|
