/usr/include/Bpp/App/ApplicationTools.h is in libbpp-core-dev 2.1.0-1ubuntu1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 | //
// File: ApplicationTools.h
// Created by: Julien Dutheil
// Created on: Fri Oct 21 16:19 2005
// From old file created on: Sun Dec 14 09:36:26 2003
//
/*
Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide basal and
utilitary classes. This file belongs to the Bio++ Project.
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 _APPLICATIONTOOLS_H_
#define _APPLICATIONTOOLS_H_
#include "../Io/FileTools.h"
#include "../Io/OutputStream.h"
#include "../Text/TextTools.h"
#include "../Text/StringTokenizer.h"
#include "../Text/NestedStringTokenizer.h"
// From the STL:
#include <map>
#include <vector>
#include <iostream>
#include <ctime>
namespace bpp
{
/**
* @brief This class provides some common tools for developping applications.
*
* These functions are designed for helping to parse an option file.
*
* The option files are supposed to follow this simple format:<br>
* @code
* parameterName = parameterContent
* @endcode
* with one parameter per line.
*
* In files, shell comments:
* @code
* # my comment line here
* @endcode
* C comments:
* @code
* / * my comment block here * /
* @endcode
* and C++ comments:
* @code
* // my comment line here
* @endcode
* are allowed, and ignored while parsing.
*
* Some methods for displaying information (messages, errors, warnings...) are also provided.
*
* Methods dealing with parameters takes as argument a map<string, string> object
* containing the parameters (names are the keys of the map, and values are... the values of the map!).
* These map objects may be obtained from the AttributesTools utilitary class.
*/
class ApplicationTools
{
public:
/**
* @brief The output stream where errors have to be displayed.
*/
static OutputStream* error;
/**
* @brief The output stream where messages have to be displayed.
*/
static OutputStream* message;
/**
* @brief The output stream where warnings have to be displayed.
*/
static OutputStream* warning;
/**
* @brief Timer variable.
*/
static time_t startTime;
/**
* @brief The width of the output terminal (in character).
*/
static size_t terminalWidth;
/**
* @brief The fraction of terminal width dedicated to messages.
*/
static float terminalSplit;
/**
* @brief Tell if the program is interactive (typically run in foreground). Default to yes.
*/
static bool interactive;
public:
ApplicationTools() {}
virtual ~ApplicationTools() {}
public:
/**
* @brief Tells if a parameter have been specified.
*
* @param parameterName The name of the parameter.
* @param params The parameter list.
* @return True is the parameter of specified name is in the list.
*/
static bool parameterExists(const std::string& parameterName, std::map<std::string, std::string>& params);
/**
* @brief Get a double parameter.
*
* @param parameterName The name of the corresponding parameter.
* @param params The attribute map where options may be found.
* @param defaultValue The default value to use if the parameter is not found.
* @param suffix A suffix to be applied to the parameter name.
* @param suffixIsOptional Tell if the suffix is absolutely required.
* @param warn Tell if a warning must be sent in case the parameter is not found.
* @return The corresponding value.
*/
static double getDoubleParameter(
const std::string& parameterName,
std::map<std::string, std::string>& params,
double defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
bool warn = true);
/**
* @brief Get an integer parameter.
*
* @param parameterName The name of the corresponding parameter.
* @param params The attribute map where options may be found.
* @param defaultValue The default value to use if the parameter is not found.
* @param suffix A suffix to be applied to the parameter name.
* @param suffixIsOptional Tell if the suffix is absolutely required.
* @param warn Tell if a warning must be sent in case the parameter is not found.
* @return The corresponding value.
*/
static int getIntParameter(
const std::string& parameterName,
std::map<std::string, std::string>& params,
int defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
bool warn = true);
/**
* @brief Get a string parameter.
*
* @param parameterName The name of the corresponding parameter.
* @param params The attribute map where options may be found.
* @param defaultValue The default value to use if the parameter is not found.
* @param suffix A suffix to be applied to the parameter name.
* @param suffixIsOptional Tell if the suffix is absolutely required.
* @param warn Tell if a warning must be sent in case the parameter is not found.
* @return The corresponding value.
*/
static std::string getStringParameter(
const std::string& parameterName,
std::map<std::string, std::string>& params,
const std::string& defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
bool warn = true);
/**
* @brief Get a boolean parameter.
*
* @param parameterName The name of the corresponding parameter.
* @param params The attribute map where options may be found.
* @param defaultValue The default value to use if the parameter is not found.
* @param suffix A suffix to be applied to the parameter name.
* @param suffixIsOptional Tell if the suffix is absolutely required.
* @param warn Tell if a warning must be sent in case the parameter is not found.
* @return The corresponding value.
*/
static bool getBooleanParameter(
const std::string& parameterName,
std::map<std::string, std::string>& params,
bool defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
bool warn = true);
/**
* @brief Get a parameter.
*
* @param parameterName The name of the corresponding parameter.
* @param params The attribute map where options may be found.
* @param defaultValue The default value to use if the parameter is not found.
* @param suffix A suffix to be applied to the parameter name.
* @param suffixIsOptional Tell if the suffix is absolutely required.
* @param warn Tell if a warning must be sent in case the parameter is not found.
* @return The corresponding value.
*/
template<class T> static T getParameter(
const std::string& parameterName,
std::map<std::string, std::string>& params,
T defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
bool warn = true)
{
T tParam = defaultValue;
if(parameterExists(parameterName + suffix, params))
{
tParam = TextTools::to<T>(params[parameterName + suffix]);
}
else if(suffixIsOptional && parameterExists(parameterName, params))
{
tParam = TextTools::to<T>(params[parameterName]);
} else if(warn)
{
displayWarning("Parameter " + parameterName + suffix + " not specified. Default used instead: " + TextTools::toString(defaultValue));
}
return tParam;
}
/**
* @brief Get a file path.
*
* @param parameter The name of the corresponding parameter.
* @param params The attribute map where options may be found.
* @param isRequired Tell if this path is strictly required or is optional
* (in the first case, if the parameter is not found, the programm will
* send an error and exit).
* @param mustExist Tell if the corresponding file must already exist.
* @param suffix A suffix to be applied to the parameter name.
* @param suffixIsOptional Tell if the suffix is absolutely required.
* @throw Exception If no file path is specified and isRequired is
* true, or the file does not exist and mustExist
* is set to true.
*/
static std::string getAFilePath(
const std::string& parameter,
std::map<std::string, std::string>& params,
bool isRequired = true,
bool mustExist = true,
const std::string& suffix = "",
bool suffixIsOptional = false) throw (Exception);
/**
* @brief Get a vector.
*
* @param parameterName The name of the corresponding parameter.
* @param params The attribute map where options may be found.
* @param separator The character used to delimit values.
* @param defaultValue The default value to use if the parameter is not found.
* @param suffix A suffix to be applied to the parameter name.
* @param suffixIsOptional Tell if the suffix is absolutely required.
* @param warn Tell if a warning must be sent in case the parameter is not found.
* @return The corresponding value.
*/
template<class T> static std::vector<T> getVectorParameter(
const std::string& parameterName,
std::map<std::string, std::string>& params,
char separator,
const std::string& defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
bool warn = true)
{
std::string s = getStringParameter(parameterName, params, defaultValue, suffix, suffixIsOptional, warn);
if (TextTools::isEmpty(s)) return std::vector<T>(0);
if (s[0] == '(' && s[s.size() - 1] == ')') {
//This is a delimited vector:
s = s.substr(1, s.size() - 2);
if (TextTools::isEmpty(s)) return std::vector<T>(0);
}
NestedStringTokenizer st(s, "(", ")", TextTools::toString(separator));
size_t n = st.numberOfRemainingTokens();
std::vector<T> v(n);
for (size_t i = 0; i < n; i++)
{
v[i] = TextTools::fromString<T>(st.nextToken());
}
return v;
}
/**
* @brief Get a vector.
*
* Similar to getVectorParameter, but dedicated to numerical values.
* It allows the possibility to set range of values, which will be incremented by 1 (like the : operator in R).
*
* @param parameterName The name of the corresponding parameter.
* @param params The attribute map where options may be found.
* @param separator The character used to delimit values.
* @param rangeOperator The character used to delimit ranges (the + 1 operator must be available for T).
* @param defaultValue The default value to use if the parameter is not found.
* @param suffix A suffix to be applied to the parameter name.
* @param suffixIsOptional Tell if the suffix is absolutely required.
* @param warn Tell if a warning must be sent in case the parameter is not found.
* @return The corresponding value.
*/
template<class T> static std::vector<T> getVectorParameter(
const std::string& parameterName,
std::map<std::string, std::string>& params,
char separator,
char rangeOperator,
const std::string& defaultValue,
const std::string& suffix = "",
bool suffixIsOptional = true,
bool warn = true)
{
std::string s = getStringParameter(parameterName, params, defaultValue, suffix, suffixIsOptional, warn);
StringTokenizer st(s, TextTools::toString(separator));
size_t n = st.numberOfRemainingTokens();
std::vector<T> v;
for (size_t i = 0; i < n; i++)
{
std::string token = st.nextToken();
std::string::size_type pos = token.find(rangeOperator);
if (pos == std::string::npos)
v.push_back(TextTools::fromString<T>(token));
else
{
T d1 = TextTools::fromString<T>(token.substr(0, pos));
T d2 = TextTools::fromString<T>(token.substr(pos + 1));
for (T j = d1; j < d2; j++)
{
v.push_back(j);
}
v.push_back(d2);
}
}
return v;
}
/**
* @name Output methods.
*
* @{
*/
/**
* @brief Print a message.
*
* @param text The text of the message.
*/
static void displayMessage(const std::string& text);
/**
* @brief Print an error message.
*
* @param text The text of the message.
*/
static void displayError(const std::string& text);
/**
* @brief Print a warning message.
*
* @param text The text of the message.
*/
static void displayWarning(const std::string& text);
/**
* @brief Print a task message.
*
* Display the message and flush the buffer, but do not end the current line.
*
* @param text The text of the message.
* @param eof Insert a carriage return after displaying the message.
*/
static void displayTask(const std::string& text, bool eof = false);
/**
* @brief Print a task ended message.
*
* Print "Done." and go to next line.
*/
static void displayTaskDone();
/**
* @brief Print a result message.
*
* Result will be aligned to 30 character from the begining of the message.
* ex: text = "Here is what you get:" and result = "THAT" gives
* "Here is what you get: THAT".
*
* @param text The text of the message.
* @param result The result.
*/
template<class T>
static void displayResult(const std::string& text, const T& result)
{
displayMessage(TextTools::resizeRight(text, static_cast<size_t>(static_cast<float>(terminalWidth) * terminalSplit - 1), '.') + ": " + TextTools::toString<T>(result));
}
/**
* @brief Print a boolean result message ("yes" or "no").
*
* Result will be aligned to 30 character from the begining of the message.
* @param text The text of the message.
* @param result The result.
*/
static void displayBooleanResult(const std::string& text, bool result)
{
displayResult(text, result ? std::string("yes") : std::string("no"));
}
/**
* @brief Display a gauge.
*
* Show progress status.
* @code
* for(size_t i = 0; i < 1000; i++)
* {
* ApplicationTools::displayGauge(i, 999, '*');
* //Perform time consuming task...
* }
* @endcode
* will result in something like:
* @verbatim
* [************************************]
* @endverbatim
*
* @param iter The current iteration number.
* @param total The total number of iteration.
* @param symbol The character to display in the gauge.
* @param mes A message to print before the gauge.
*/
static void displayGauge(size_t iter, size_t total, char symbol='>', const std::string& mes="");
/**
* @brief Display a gauge for unefined amount of iterations.
*
* Show progress status.
* @code
* for(size_t i = 0; i < 1000; i++)
* {
* ApplicationTools::displayUnlimitedGauge(i);
* //Perform time consuming task...
* }
* @endcode
* will result in something like:
* @verbatim
* - 1
* / 2
* - 3
* \ 4
* - 5
* etc
* @endverbatim
*
* @param iter The current iteration number.
* @param mes A message to print before the gauge.
*/
static void displayUnlimitedGauge(size_t iter, const std::string& mes="");
/** @} */
/**
* @brief Starts the timer.
*/
static void startTimer()
{
time(&startTime);
}
/**
* @brief Display the current timer value to the 'message' stream.
*
* @param msg Message to display before time.
*/
static void displayTime(const std::string& msg);
/**
* @brief Get the current timer value.
*
* @return The number of seconds from when timer was started.
*/
static double getTime();
};
} //end of namespace bpp.
#endif //_APPLICATIONTOOLS_H_
|