/usr/include/Bpp/Seq/Sequence.h is in libbpp-seq-dev 2.2.0-1+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 | //
// File: Sequence.h
// Created by: Guillaume Deuchst
// Julien Dutheil
// Created on: Tue Aug 21 2003
//
/*
Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide classes
for sequences analysis.
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited
liability.
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
#ifndef _SEQUENCE_H_
#define _SEQUENCE_H_
#include "SymbolList.h"
#include "SequenceExceptions.h"
// From the STL:
#include <string>
#include <vector>
namespace bpp
{
/**
* @brief Declaration of Comments type.
*
* Comments are defined as a std::vector of std::strings to allow the later creation of a
* full Comments class.
*/
typedef std::vector<std::string> Comments;
/**
* @brief The sequence interface.
*
* This is a general purpose container, containing an ordered list of states.
* The states that allowed to be present in the sequence are defined
* by an alphabet object.
*
* Sequence objets also contain a name attribute and potentially several comment lines.
* A sequence object is also event-driven, allowing easy extension.
*
* @see Alphabet
*/
class Sequence:
public virtual SymbolList
{
public:
virtual ~Sequence() {}
public:
#ifndef NO_VIRTUAL_COV
Sequence* clone() const = 0;
#endif
/**
* @name Setting/getting the name of the sequence.
*
* @{
*/
/**
* @brief Get the name of this sequence.
*
* @return This sequence name.
*/
virtual const std::string& getName() const = 0;
/**
* @brief Set the name of this sequence.
*
* @param name The new name of the sequence.
*/
virtual void setName(const std::string& name) = 0;
/** @} */
/**
* @name Setting/getting the comments associated to the sequence.
*
* @{
*/
/**
* @brief Get the comments associated to this sequence.
*
* @return The comments of the sequence.
*/
virtual const Comments& getComments() const = 0;
/**
* @brief Set the comments associated to this sequence.
*
* @param comments The new comments of the sequence.
*/
virtual void setComments(const Comments& comments) = 0;
/** @} */
/**
* @name Adjusting the size of the sequence.
*
* @{
*/
/**
* @brief Set the whole content of the sequence.
*
* @param sequence The new content of the sequence.
* @see The Sequence constructor for information about the way sequences are internaly stored.
*/
virtual void setContent(const std::string& sequence) throw (BadCharException) = 0;
virtual void setContent(const std::vector<int>& list) throw (BadIntException) = 0;
virtual void setContent(const std::vector<std::string>& list) throw (BadCharException) = 0;
/**
* @brief Set up the size of a sequence from the right side.
*
* All new characters are filled with gaps.
* If the specified size is < to the sequence size, the sequence will be truncated.
*
* @param newSize The new size of the sequence.
*/
virtual void setToSizeR(size_t newSize) = 0;
/**
* @brief Set up the size of a sequence from the left side.
*
* All new characters are filled with gaps.
* If the specified size is < to the sequence size, the sequence will be truncated.
*
* @param newSize The new size of the sequence.
*/
virtual void setToSizeL(size_t newSize) = 0;
/**
* @brief Append the specified content to the sequence.
*
* @param content The content to append to the sequence.
* @throw BadIntException If the content does not match the current alphabet.
*/
virtual void append(const std::vector<int>& content) throw (BadIntException) = 0;
/**
* @brief Append the specified content to the sequence.
*
* @param content The content to append to the sequence.
* @throw BadCharException If the content does not match the current alphabet.
*/
virtual void append(const std::vector<std::string>& content) throw (BadCharException) = 0;
/**
* @brief Append the specified content to the sequence.
*
* @param content The content to append to the sequence.
* @throw BadCharException If the content does not match the current alphabet.
*/
virtual void append(const std::string& content) throw (BadCharException) = 0;
/** @} */
};
/**
* @brief A basic implementation of the Sequence interface.
*
* This is a general purpose container, containing an ordered list of states.
* The states that allowed to be present in the sequence are defined
* by an alphabet object, which is passed to the sequence constructor by a pointer.
*
* For programming convenience, the states are stored as integers, but the translation toward
* and from a char description is easily performed with the Alphabet classes.
*
* Sequence objets also contain a name attribute and potentially several comment lines.
*
* @see Alphabet
*/
class BasicSequence :
public Sequence,
public BasicSymbolList
{
private:
/**
* @brief The sequence name.
*/
std::string name_;
/**
* @brief The sequence comments.
*/
Comments comments_;
public:
/**
* @brief Empty constructor: build a void Sequence with just an Alphabet
*
* You can use it safely for all type of Alphabet in order to build an
* empty Sequence i.e. without name nor sequence data.
*
* @param alpha A pointer toward the Alphabet to be used with this Sequence.
*/
BasicSequence(const Alphabet* alpha);
/**
* @brief Direct constructor: build a Sequence object from a std::string
* You can use it safely for RNA, DNA and protein sequences.
*
* It can be used with codon sequences too, the std::string will be cut into
* parts of size 3. But for more complicated alphabets, you should use one
* complete constructors.
*
* @param name The sequence name.
* @param sequence The whole sequence to be parsed as a std::string.
* @param alpha A pointer toward the alphabet to be used with this sequence.
*/
BasicSequence(const std::string& name, const std::string& sequence, const Alphabet* alpha) throw (BadCharException);
/**
* @brief Direct constructor: build a Sequence object from a std::string.
*
* You can use it safely for RNA, DNA and protein sequences.
*
* It can be used with codon sequences too, the std::string will be cut into
* tokens of size 3. But for more complicated alphabets, you should use one
* complete constructors.
*
* @param name The sequence name.
* @param sequence The whole sequence to be parsed as a std::string.
* @param comments Comments to add to the sequence.
* @param alpha A pointer toward the alphabet to be used with this sequence.
*/
BasicSequence(const std::string& name, const std::string& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
/**
* @brief General purpose constructor, can be used with any alphabet.
*
* You should note that the sequence is stored as a std::vector of int.
* Hence each std::string in the std::vector will be translated using the alphabet object.
*
* @param name The sequence name.
* @param sequence The sequence content.
* @param alpha A pointer toward the alphabet to be used with this sequence.
*/
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Alphabet* alpha) throw (BadCharException);
/**
* @brief General purpose constructor, can be used with any alphabet.
*
* You should note that the sequence is stored as a std::vector of int.
* Hence each std::string in the std::vector will be translated using the alphabet object.
*
* @param name The sequence name.
* @param sequence The sequence content.
* @param comments Comments to add to the sequence.
* @param alpha A pointer toward the alphabet to be used with this sequence.
*/
BasicSequence(const std::string& name, const std::vector<std::string>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadCharException);
/**
* @brief General purpose constructor, can be used with any alphabet.
*
* @param name The sequence name.
* @param sequence The sequence content.
* @param alpha A pointer toward the alphabet to be used with this sequence.
*/
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Alphabet* alpha) throw (BadIntException);
/**
* @brief General purpose constructor, can be used with any alphabet.
*
* @param name The sequence name.
* @param sequence The sequence content.
* @param comments Comments to add to the sequence.
* @param alpha A pointer toward the alphabet to be used with this sequence.
*/
BasicSequence(const std::string& name, const std::vector<int>& sequence, const Comments& comments, const Alphabet* alpha) throw (BadIntException);
/**
* @brief The Sequence generic copy constructor. This does not perform a hard copy of the alphabet object.
*/
BasicSequence(const Sequence& s);
/**
* @brief The Sequence copy constructor. This does not perform a hard copy of the alphabet object.
*/
BasicSequence(const BasicSequence& s);
/**
* @brief The Sequence generic assignment operator. This does not perform a hard copy of the alphabet object.
*
* @return A ref toward the assigned Sequence.
*/
BasicSequence& operator=(const Sequence& s);
/**
* @brief The Sequence assignment operator. This does not perform a hard copy of the alphabet object.
*
* @return A ref toward the assigned Sequence.
*/
BasicSequence& operator=(const BasicSequence& s);
virtual ~BasicSequence() {}
public:
/**
* @name The Clonable interface
*
* @{
*/
BasicSequence* clone() const { return new BasicSequence(*this); }
/** @} */
/**
* @name Setting/getting the name of the sequence.
*
* @{
*/
/**
* @brief Get the name of this sequence.
*
* @return This sequence name.
*/
const std::string& getName() const { return name_; }
/**
* @brief Set the name of this sequence.
*
* @param name The new name of the sequence.
*/
void setName(const std::string& name) { name_ = name; }
/** @} */
/**
* @name Setting/getting the comments associated to the sequence.
*
* @{
*/
/**
* @brief Get the comments associated to this sequence.
*
* @return The comments of the sequence.
*/
const Comments& getComments() const { return comments_; }
/**
* @brief Set the comments associated to this sequence.
*
* @param comments The new comments of the sequence.
*/
void setComments(const Comments& comments) { comments_ = comments; }
/** @} */
/**
* @name Adjusting the size of the sequence.
*
* @{
*/
/**
* @brief Set the whole content of the sequence.
*
* @param sequence The new content of the sequence.
* @see The Sequence constructor for information about the way sequences are internaly stored.
*/
virtual void setContent(const std::string& sequence) throw (BadCharException);
void setContent(const std::vector<int>& list) throw (BadIntException)
{
BasicSymbolList::setContent(list);
}
void setContent(const std::vector<std::string>& list) throw (BadCharException)
{
BasicSymbolList::setContent(list);
}
/**
* @brief Set up the size of a sequence from the right side.
*
* All new characters are filled with gaps.
* If the specified size is < to the sequence size, the sequence will be truncated.
*
* @param newSize The new size of the sequence.
*/
virtual void setToSizeR(size_t newSize);
/**
* @brief Set up the size of a sequence from the left side.
*
* All new characters are filled with gaps.
* If the specified size is < to the sequence size, the sequence will be truncated.
*
* @param newSize The new size of the sequence.
*/
virtual void setToSizeL(size_t newSize);
/**
* @brief Append the specified content to the sequence.
*
* @param content The content to append to the sequence.
* @throw BadIntException If the content does not match the current alphabet.
*/
virtual void append(const std::vector<int>& content) throw (BadIntException);
/**
* @brief Append the specified content to the sequence.
*
* @param content The content to append to the sequence.
* @throw BadCharException If the content does not match the current alphabet.
*/
virtual void append(const std::vector<std::string>& content) throw (BadCharException);
/**
* @brief Append the specified content to the sequence.
*
* @param content The content to append to the sequence.
* @throw BadCharException If the content does not match the current alphabet.
*/
virtual void append(const std::string& content) throw (BadCharException);
/** @} */
};
} //end of namespace bpp.
#endif // _SEQUENCE_H_
|