File: adapt_ios.h

package info (click to toggle)
seqan2 2.4.0%2Bdfsg-11
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 223,504 kB
  • sloc: cpp: 256,886; ansic: 91,672; python: 8,339; sh: 995; xml: 570; makefile: 251; awk: 51
file content (402 lines) | stat: -rw-r--r-- 15,157 bytes parent folder | download | duplicates (6)
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
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
// ==========================================================================
//                 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: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
// ==========================================================================
// Adaptions for std::ios streams.
// ==========================================================================

#ifndef SEQAN_STREAM_ADAPT_IOS_H_
#define SEQAN_STREAM_ADAPT_IOS_H_

#define SEQAN_ASSERT_BADBIT(s) SEQAN_ASSERT_MSG(s.exceptions() | std::ios_base::badbit, \
        "The badbit exception is not set in the stream. Call either std::exceptions() or streamInit() on the stream.")

namespace seqan {

// ============================================================================
// Forwards
// ============================================================================
// TODO(esiragusa): remove this when chunking goes into basic.

template <typename TObject> struct Chunk;

// ============================================================================
// Metafunctions
// ============================================================================

// ----------------------------------------------------------------------------
// Metafunction Position
// ----------------------------------------------------------------------------

template <typename TValue, typename TTraits>
struct Position<std::istreambuf_iterator<TValue, TTraits> >
{
    typedef typename std::istreambuf_iterator<TValue, TTraits>::difference_type Type;
};

template <typename TValue, typename TTraits>
struct Position<std::basic_istream<TValue, TTraits> >
{
    typedef typename std::basic_istream<TValue, TTraits>::pos_type Type;
};

template <typename TValue, typename TTraits>
struct Position<std::basic_ostream<TValue, TTraits> >
{
    typedef typename std::basic_ostream<TValue, TTraits>::pos_type Type;
};

template <typename TValue, typename TTraits>
struct Position<std::basic_iostream<TValue, TTraits> >
{
    typedef typename std::basic_iostream<TValue, TTraits>::pos_type Type;
};

template <typename TValue, typename TTraits>
struct Position<std::basic_fstream<TValue, TTraits> > :
    Position<std::basic_iostream<TValue, TTraits> > {};

template <typename TValue, typename TTraits>
struct Position<std::basic_stringstream<TValue, TTraits> > :
    Position<std::basic_iostream<TValue, TTraits> > {};


template <typename TValue, typename TTraits>
struct Position<std::basic_ifstream<TValue, TTraits> > :
    Position<std::basic_istream<TValue, TTraits> > {};

template <typename TValue, typename TTraits>
struct Position<std::basic_istringstream<TValue, TTraits> > :
    Position<std::basic_istream<TValue, TTraits> > {};


template <typename TValue, typename TTraits>
struct Position<std::basic_ofstream<TValue, TTraits> > :
    Position<std::basic_ostream<TValue, TTraits> > {};

template <typename TValue, typename TTraits>
struct Position<std::basic_ostringstream<TValue, TTraits> > :
    Position<std::basic_ostream<TValue, TTraits> > {};

// ----------------------------------------------------------------------------
// Metafunction Value
// ----------------------------------------------------------------------------

template <typename TValue, typename TTraits>
struct Value<std::istreambuf_iterator<TValue, TTraits> >
{
    typedef typename std::istreambuf_iterator<TValue, TTraits>::char_type Type;
};

template <typename TValue, typename TTraits>
struct Value<std::basic_istream<TValue, TTraits> >
{
    typedef typename std::basic_istream<TValue, TTraits>::char_type Type;
};

template <typename TValue, typename TTraits>
struct Value<std::basic_ostream<TValue, TTraits> >
{
    typedef typename std::basic_ostream<TValue, TTraits>::char_type Type;
};

template <typename TValue, typename TTraits>
struct Value<std::basic_iostream<TValue, TTraits> >
{
    typedef typename std::basic_iostream<TValue, TTraits>::char_type Type;
};

template <typename TValue, typename TTraits>
struct Value<std::basic_fstream<TValue, TTraits> > :
    Value<std::basic_iostream<TValue, TTraits> > {};

template <typename TValue, typename TTraits>
struct Value<std::basic_stringstream<TValue, TTraits> > :
    Value<std::basic_iostream<TValue, TTraits> > {};


template <typename TValue, typename TTraits>
struct Value<std::basic_ifstream<TValue, TTraits> > :
    Value<std::basic_istream<TValue, TTraits> > {};

template <typename TValue, typename TTraits>
struct Value<std::basic_istringstream<TValue, TTraits> > :
    Value<std::basic_istream<TValue, TTraits> > {};


template <typename TValue, typename TTraits>
struct Value<std::basic_ofstream<TValue, TTraits> > :
    Value<std::basic_ostream<TValue, TTraits> > {};

template <typename TValue, typename TTraits>
struct Value<std::basic_ostringstream<TValue, TTraits> > :
    Value<std::basic_ostream<TValue, TTraits> > {};

// ----------------------------------------------------------------------------
// Metafunction Reference
// ----------------------------------------------------------------------------

template <typename TValue, typename TTraits>
struct Reference<std::istreambuf_iterator<TValue, TTraits> >
{
    typedef typename std::istreambuf_iterator<TValue, TTraits>::char_type Type;
//    typedef typename std::istreambuf_iterator<TValue, TTraits>::reference Type;
};

// ----------------------------------------------------------------------------
// Metafunction Chunk
// ----------------------------------------------------------------------------

template <typename TValue, typename TTraits>
struct Chunk<std::basic_streambuf<TValue, TTraits> >
{
    typedef Range<TValue*> Type;
};

//template <typename TValue, typename TTraits>
//struct Chunk<std::istreambuf_iterator<TValue, TTraits> >:
//    Chunk<std::basic_streambuf<TValue, TTraits> > {};
//
//template <typename TValue, typename TTraits>
//struct Chunk<std::ostreambuf_iterator<TValue, TTraits> >:
//    Chunk<std::basic_streambuf<TValue, TTraits> > {};

// ----------------------------------------------------------------------------
// Metafunction DefaultOpenMode<std::>
// ----------------------------------------------------------------------------

template <typename TValue, typename TTraits, typename TDummy>
struct DefaultOpenMode<std::basic_fstream<TValue, TTraits>, TDummy>
{
    enum { VALUE = OPEN_RDWR | OPEN_CREATE | OPEN_APPEND };
};

template <typename TValue, typename TTraits, typename TDummy>
struct DefaultOpenMode<std::basic_ifstream<TValue, TTraits>, TDummy>
{
    enum { VALUE = OPEN_RDONLY };
};

template <typename TValue, typename TTraits, typename TDummy>
struct DefaultOpenMode<std::basic_ofstream<TValue, TTraits>, TDummy>
{
    enum { VALUE = OPEN_WRONLY | OPEN_CREATE };
};

// ============================================================================
// Concepts
// ============================================================================

template <typename TValue, typename TTraits>
SEQAN_CONCEPT_IMPL((std::basic_istream<TValue, TTraits>), (InputStreamConcept));
template <typename TValue, typename TTraits>
SEQAN_CONCEPT_IMPL((std::basic_ifstream<TValue, TTraits>), (InputStreamConcept));
template <typename TValue, typename TTraits>
SEQAN_CONCEPT_IMPL((std::basic_istringstream<TValue, TTraits>), (InputStreamConcept));

template <typename TValue, typename TTraits>
SEQAN_CONCEPT_IMPL((std::basic_ostream<TValue, TTraits>), (OutputStreamConcept));
template <typename TValue, typename TTraits>
SEQAN_CONCEPT_IMPL((std::basic_ofstream<TValue, TTraits>), (OutputStreamConcept));
template <typename TValue, typename TTraits>
SEQAN_CONCEPT_IMPL((std::basic_ostringstream<TValue, TTraits>), (OutputStreamConcept));

template <typename TValue, typename TTraits>
SEQAN_CONCEPT_IMPL((std::basic_iostream<TValue, TTraits>), (BidirectionalStreamConcept));
template <typename TValue, typename TTraits>
SEQAN_CONCEPT_IMPL((std::basic_fstream<TValue, TTraits>), (BidirectionalStreamConcept));
template <typename TValue, typename TTraits>
SEQAN_CONCEPT_IMPL((std::basic_stringstream<TValue, TTraits>), (BidirectionalStreamConcept));

// ============================================================================
// Functions
// ============================================================================

// ----------------------------------------------------------------------------
// Function _getSTLStyleOrigin()
// ----------------------------------------------------------------------------

template <typename TPos>
inline std::ios_base::seekdir
_getSTLStyleOrigin(TPos origin)
{
    switch (origin)
    {
    case SEEK_CUR:
        return std::ios_base::cur;
    case SEEK_END:
        return std::ios_base::end;
    case SEEK_SET:
    default:
        return std::ios_base::beg;
    }
}

// ----------------------------------------------------------------------------
// Function _getSTLStyleOpenMode()
// ----------------------------------------------------------------------------

inline std::ios_base::openmode
_getSTLStyleOpenMode(int openMode)
{
    std::ios_base::openmode flags = std::ios_base::binary;

    if (openMode & OPEN_RDONLY)
        flags |= std::ios_base::in;
    if (openMode & OPEN_WRONLY)
    {
        flags |= std::ios_base::out;
        if (!(openMode & OPEN_APPEND))
            flags |= std::ios_base::trunc;
    }

    return flags;
}

// ----------------------------------------------------------------------------
// Function getChunk()
// ----------------------------------------------------------------------------

//template <typename TValue, typename TTraits, typename TDirection>
//inline typename Chunk<std::basic_streambuf<TValue, TTraits> >::Type
//getChunk(std::basic_streambuf<TValue, TTraits> const &buf, Tag<TDirection>)
//{
//    return getChunk(static_cast<StreamBuffer<TValue, TTraits> &>(buf), Tag<TDirection>());
//}

// ----------------------------------------------------------------------------
// Function writeValue()
// ----------------------------------------------------------------------------

template <typename TValue, typename TTraits, typename TValue2>
inline void writeValue(std::ostreambuf_iterator<TValue, TTraits> &iter, TValue2 val)
{
    *iter = val;
    ++iter;
}

template <typename TValue, typename TTraits, typename TValue2>
inline void writeValue(std::basic_ostream<TValue, TTraits> &ostream, TValue2 val)
{
    ostream.put(val);
}

// ----------------------------------------------------------------------------
// Function atEnd()
// ----------------------------------------------------------------------------

template <typename TValue, typename TTraits>
inline bool atEnd(std::istreambuf_iterator<TValue, TTraits> const &it)
{
    return it == std::istreambuf_iterator<TValue, TTraits>();
}

template <typename TValue, typename TTraits>
inline bool atEnd(std::ostreambuf_iterator<TValue, TTraits> const &it)
{
    return it == std::ostreambuf_iterator<TValue, TTraits>();
}

// ----------------------------------------------------------------------------
// Function open()
// ----------------------------------------------------------------------------

template <typename TValue, typename TTraits>
inline bool open(std::basic_fstream<TValue, TTraits> & stream, const char *fileName, int openMode)
{
    stream.exceptions(std::ios_base::badbit);
    stream.open(fileName, _getSTLStyleOpenMode(openMode));
    return stream.is_open();
}

template <typename TValue, typename TTraits>
inline bool open(std::basic_ifstream<TValue, TTraits> & stream, const char *fileName, int openMode)
{
    stream.exceptions(std::ios_base::badbit);
    stream.open(fileName, _getSTLStyleOpenMode(openMode));
    return stream.is_open();
}

template <typename TValue, typename TTraits>
inline bool open(std::basic_ofstream<TValue, TTraits> & stream, const char *fileName, int openMode)
{
    stream.exceptions(std::ios_base::badbit);
    stream.open(fileName, _getSTLStyleOpenMode(openMode));
    return stream.is_open();
}

template <typename TValue, typename TTraits>
inline bool open(std::basic_fstream<TValue, TTraits> & stream, const char *fileName)
{
    return open(stream, fileName, DefaultOpenMode<std::basic_fstream<TValue, TTraits> >::VALUE);
}

template <typename TValue, typename TTraits>
inline bool open(std::basic_ifstream<TValue, TTraits> & stream, const char *fileName)
{
    return open(stream, fileName, DefaultOpenMode<std::basic_ifstream<TValue, TTraits> >::VALUE);
}

template <typename TValue, typename TTraits>
inline bool open(std::basic_ofstream<TValue, TTraits> & stream, const char *fileName)
{
    return open(stream, fileName, DefaultOpenMode<std::basic_ofstream<TValue, TTraits> >::VALUE);
}

// ----------------------------------------------------------------------------
// Function close()
// ----------------------------------------------------------------------------

template <typename TValue, typename TTraits>
inline bool close(std::basic_fstream<TValue, TTraits> & stream)
{
    stream.close();
    return !stream.is_open();
}

template <typename TValue, typename TTraits>
inline bool close(std::basic_ifstream<TValue, TTraits> & stream)
{
    stream.close();
    return !stream.is_open();
}

template <typename TValue, typename TTraits>
inline bool close(std::basic_ofstream<TValue, TTraits> & stream)
{
    stream.close();
    return !stream.is_open();
}

}  // namespace seqan

#endif  // #ifndef SEQAN_STREAM_ADAPT_IOS_H_