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
|
// ==========================================================================
// 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: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
// Defines basic tags and flags for file access.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_FILE_INTERFACE_H_
#define SEQAN_INCLUDE_SEQAN_FILE_INTERFACE_H_
namespace seqan {
/*!
* @class SyncFile
* @extends File
* @headerfile <seqan/file.h>
* @brief File structure supporting synchronous input/output access.
*
* @signature template <[typename TSpec]>
* class File<Sync<TSpec> >;
*
* @tparam TSpec Further specializing type. Default: <tt>void</tt>.
*
* This class supports pseudo-asynchronous access methods, i.e. the method to initiate an I/O request blocks until the
* request completion.
*/
template <typename TSpec = void>
struct Sync;
/*!
* @class AsyncFile
* @extends File
* @headerfile <seqan/file.h>
* @brief File structure supporting asynchronous input/output access.
*
* @signature template <[typename TSpec]>
* class File<Async<TSpec> >;
*
* @tparam TSpec Further specializing type. Default: <tt>void</tt>.
*/
#if SEQAN_ASYNC_IO
template <typename TSpec = void>
struct Async;
#else
// define async as sync
template <typename TSpec = void>
using Async = Sync<TSpec>;
#endif
/*!
* @class File
* @headerfile <seqan/file.h>
* @brief Represents a file.
*
* @signature template <[typename TSpec]>
* class File<TSpec>;
*
* @tparam TSpec Specializing type. Default: <tt>Async<></tt>.
*/
template <typename TSpec = Async<> >
class File;
/*!
* @enum FileOpenMode
* @headerfile <seqan/file.h>
* @brief Flags to select the open mode of a @link File @endlink or external string.
*
* These flags can be combined via the <tt>|</tt> operator (bitwise OR). The defualt open mode is <tt>OPEN_RDWR |
* OPEN_CREATE | OPEN_APPEND</tt>.
*
* If you omit the <tt>OPEN_APPEND</tt> flag in write mode, the file will be truncated to size 0 when opened.
*
* @section Examples
*
* Code example to test for read-only mode:
*
* @code{.cpp}
* if (openMode & OPEN_MASK == OPEN_READ)
* // do something if opened in read-only mode
* @endcode
*
* @val FileOpenMode OPEN_RDONLY
* @brief Open in read-only mode.
*
* @val FileOpenMode OPEN_WRONLY
* @brief Open in write-only mode.
*
* @val FileOpenMode OPEN_RDWR
* @brief Open for reading and writing.
*
* @val FileOpenMode OPEN_CREATE
* @brief Create the file if it does not yet exists.
*
* @val FileOpenMode OPEN_APPEND
* @brief Keep the existing data. If this flag is not given then the file is cleared in write mode.
*
* @val FileOpenMode OPEN_QUIET
* @brief Don't print any warning message if the file could not be opened.
*
* @val FileOpenMode OPEN_MASK
* @brief (Internal) Bitmask to extract the read/write open mode.
*
* @val FileOpenMode OPEN_ASYNC
* @brief (Internal) Open the file for asynchronous file access. For asynchronous file access, use the @link AsyncFile
* @endlink.
*
* @val FileOpenMode OPEN_TEMPORARY
* @brief (Internal) Open automatically delete the file after close. Use the <tt>openTemp</tt> methods to open
* temporary files.
*/
// --------------------------------------------------------------------------
// Enum FileOpenMode
// --------------------------------------------------------------------------
enum FileOpenMode {
OPEN_RDONLY = 1,
OPEN_WRONLY = 2,
OPEN_RDWR = 3,
OPEN_MASK = 3,
OPEN_CREATE = 4,
OPEN_APPEND = 8,
OPEN_ASYNC = 16,
OPEN_TEMPORARY = 32,
OPEN_QUIET = 128
}; //IOREV is it intended that two labels share the same value? What is OPEN_MASK anyway?
// --------------------------------------------------------------------------
// Direction Tags
// --------------------------------------------------------------------------
struct Input_;
typedef Tag<Input_> Input;
struct Output_;
typedef Tag<Output_> Output;
struct Bidirectional_;
typedef Tag<Bidirectional_> Bidirectional;
// --------------------------------------------------------------------------
// Metafunction DefaultOpenMode
// --------------------------------------------------------------------------
// helper metafunction to avoid ambiguous partial specializations of the 1st/2nd argument
template <typename TDirection>
struct DefaultFileOpenMode_
{
enum { VALUE = OPEN_RDWR | OPEN_CREATE | OPEN_APPEND };
};
template <>
struct DefaultFileOpenMode_<Input>
{
enum { VALUE = OPEN_RDONLY };
};
template <>
struct DefaultFileOpenMode_<Output>
{
enum { VALUE = OPEN_WRONLY | OPEN_CREATE };
};
template <typename T, typename TDirection = Bidirectional>
struct DefaultOpenMode:
DefaultFileOpenMode_<TDirection> {};
// --------------------------------------------------------------------------
// Metafunction DefaultOpenTempMode
// --------------------------------------------------------------------------
template <typename T>
struct DefaultOpenTempMode
{
enum { VALUE = OPEN_RDWR | OPEN_CREATE };
};
enum FileSeekMode {
SEEK_BEGIN = 0,
SEEK_CURRENT = 1
#ifndef SEEK_END
, SEEK_END = 2
#endif
}; //IOREV why not use constants SEEK_SET, SEEK_CUR, SEEK_END from cstdio?
//////////////////////////////////////////////////////////////////////////////
// result type of asynch. functions
// you have to call release(AsyncRequest<T>) after a finished *event based* transfer
struct AsyncDummyRequest
{
AsyncDummyRequest()
{}
AsyncDummyRequest(AsyncDummyRequest &, Move)
{}
AsyncDummyRequest(AsyncDummyRequest &&)
{}
private:
AsyncDummyRequest(AsyncDummyRequest const &)
{}
};
template <>
struct HasMoveConstructor<AsyncDummyRequest> : True {};
/*!
* @class AsyncRequest
* @headerfile <seqan/file.h>
* @brief Associated with an asynchronous I/O request.
*
* @signature template <typenam TFile>
* struct AsyncRequest;
*
* @tparam TFile The file type.
*
* This structure is used to identify asynchronous requests after their initiation.
*/
template < typename T >
struct AsyncRequest
{
//IOREV _stub_ this seems not to be implemented at all, most functions are commented
typedef AsyncDummyRequest Type;
};
// ============================================================================
// Exceptions
// ============================================================================
// ----------------------------------------------------------------------------
// Exception IOError
// ----------------------------------------------------------------------------
/*!
* @class IOError
* @headerfile <seqan/basic.h>
* @brief Input/Output error exception.
*
* @signature typedef std::ios_base::failure IOError;
*
*
* @fn IOError::IOError
* @brief Constructor
*
* @signature IOError::IOError(msg, errorCode);
*
* @param[in] msg Message as <tt>std::string</tt>.
* @param[in] errorCode The error code as an <tt>int</tt>.
*/
typedef std::ios_base::failure IOError;
// ----------------------------------------------------------------------------
// Exception FileOpenError
// ----------------------------------------------------------------------------
struct FileOpenError : IOError
{
public:
FileOpenError(const char *fileName):
IOError((std::string)"Could not open file " + fileName)
{}
protected:
FileOpenError(std::string const &msg):
IOError(msg)
{}
};
// ----------------------------------------------------------------------------
// Exception UnknownFileFormat
// ----------------------------------------------------------------------------
struct UnknownFileFormat : FileOpenError
{
UnknownFileFormat():
FileOpenError(std::string("Could not detect file format"))
{}
UnknownFileFormat(const char *fileName):
FileOpenError(std::string("Could not detect file format of ") + fileName)
{}
};
// ----------------------------------------------------------------------------
// Exception UnknownExtensionError
// ----------------------------------------------------------------------------
struct UnknownExtensionError : FileOpenError
{
UnknownExtensionError(const char *fileName):
FileOpenError(std::string("Unknown file extension of ") + fileName)
{}
};
} // namespace seqan;
#endif // #ifndef SEQAN_INCLUDE_SEQAN_FILE_INTERFACE_H_
|