| Line | Branch | Exec | Source |
|---|---|---|---|
| 1 | /* BEGIN software license | ||
| 2 | * | ||
| 3 | * MsXpertSuite - mass spectrometry software suite | ||
| 4 | * ----------------------------------------------- | ||
| 5 | * Copyright(C) 2009,...,2018 Filippo Rusconi | ||
| 6 | * | ||
| 7 | * http://www.msxpertsuite.org | ||
| 8 | * | ||
| 9 | * This file is part of the MsXpertSuite project. | ||
| 10 | * | ||
| 11 | * The MsXpertSuite project is the successor of the massXpert project. This | ||
| 12 | * project now includes various independent modules: | ||
| 13 | * | ||
| 14 | * - massXpert, model polymer chemistries and simulate mass spectrometric data; | ||
| 15 | * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner; | ||
| 16 | * | ||
| 17 | * This program is free software: you can redistribute it and/or modify | ||
| 18 | * it under the terms of the GNU General Public License as published by | ||
| 19 | * the Free Software Foundation, either version 3 of the License, or | ||
| 20 | * (at your option) any later version. | ||
| 21 | * | ||
| 22 | * This program is distributed in the hope that it will be useful, | ||
| 23 | * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| 24 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| 25 | * GNU General Public License for more details. | ||
| 26 | * | ||
| 27 | * You should have received a copy of the GNU General Public License | ||
| 28 | * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| 29 | * | ||
| 30 | * END software license | ||
| 31 | */ | ||
| 32 | |||
| 33 | |||
| 34 | /////////////////////// Qt includes | ||
| 35 | #include <QFile> | ||
| 36 | #include <QDebug> | ||
| 37 | #include <QRegularExpression> | ||
| 38 | #include <QRegularExpressionMatch> | ||
| 39 | |||
| 40 | /////////////////////// Local includes | ||
| 41 | #include "MonomerSpec.hpp" | ||
| 42 | |||
| 43 | |||
| 44 | namespace MsXpS | ||
| 45 | { | ||
| 46 | |||
| 47 | namespace libXpertMass | ||
| 48 | { | ||
| 49 | |||
| 50 | /*! | ||
| 51 | \class MsXpS::libXpertMass::MonomerSpec | ||
| 52 | \inmodule libXpertMass | ||
| 53 | \ingroup PolChemDefBuildingdBlocks | ||
| 54 | \inheaderfile MonomerSpec.hpp | ||
| 55 | |||
| 56 | \brief The MonomerSpec class provides the specification about how \l Monomer | ||
| 57 | objects are represented. | ||
| 58 | |||
| 59 | The MonomerSpec class specifies how a \l Monomer object is represented | ||
| 60 | graphically, mainly by connecting its monomer code to a graphics SVG file that | ||
| 61 | is located in the Polymer chemistry definition directory. That connection is | ||
| 62 | performed in the "monomer_dictionary" dictionary file itself also located in | ||
| 63 | the polymer chemistry definition directory. Its contents look like this: | ||
| 64 | |||
| 65 | \code | ||
| 66 | A%alanine.svg | ||
| 67 | C%cysteine.svg | ||
| 68 | D%aspartate.svg | ||
| 69 | E%glutamate.svg | ||
| 70 | F%phenylalanine.svg | ||
| 71 | G%glycine.svg | ||
| 72 | H%histidine.svg" | ||
| 73 | \endcode | ||
| 74 | |||
| 75 | The \c{A%alanine.svg} line indicates that, when a Monomer object by code 'A' is | ||
| 76 | to be rendered graphically, the corresponding vignette to be used is in the | ||
| 77 | file named "alanine.svg" in the polymer chemistry definition directory. | ||
| 78 | */ | ||
| 79 | |||
| 80 | /*! | ||
| 81 | \variable int MsXpS::libXpertMass::MonomerSpec::m_name | ||
| 82 | |||
| 83 | \brief The name of the monomer. | ||
| 84 | */ | ||
| 85 | |||
| 86 | /*! | ||
| 87 | \variable int MsXpS::libXpertMass::MonomerSpec::m_code | ||
| 88 | |||
| 89 | \brief The code of the monomer. | ||
| 90 | */ | ||
| 91 | |||
| 92 | /*! | ||
| 93 | \variable int MsXpS::libXpertMass::MonomerSpec::m_raster | ||
| 94 | |||
| 95 | \brief The file name of the raster representation of the monomer. | ||
| 96 | */ | ||
| 97 | |||
| 98 | /*! | ||
| 99 | \variable int MsXpS::libXpertMass::MonomerSpec::m_vector | ||
| 100 | |||
| 101 | \brief The filename of the vector representation of the monomer. | ||
| 102 | */ | ||
| 103 | |||
| 104 | /*! | ||
| 105 | \variable int MsXpS::libXpertMass::MonomerSpec::m_nameSound | ||
| 106 | |||
| 107 | \brief The file name of the sound for the name of the monomer. | ||
| 108 | */ | ||
| 109 | |||
| 110 | /*! | ||
| 111 | \variable int MsXpS::libXpertMass::MonomerSpec::m_codeSound | ||
| 112 | |||
| 113 | \brief The file name of the sound for the code of the monomer. | ||
| 114 | */ | ||
| 115 | |||
| 116 | /*! | ||
| 117 | \brief Constructs a MonomerSpec instance. | ||
| 118 | */ | ||
| 119 | ✗ | MonomerSpec::MonomerSpec() | |
| 120 | { | ||
| 121 | ✗ | } | |
| 122 | |||
| 123 | /*! | ||
| 124 | \brief Destructs this MonomerSpec instance. | ||
| 125 | */ | ||
| 126 | ✗ | MonomerSpec::~MonomerSpec() | |
| 127 | { | ||
| 128 | ✗ | } | |
| 129 | |||
| 130 | /*! | ||
| 131 | \brief Sets the monomer \a name. | ||
| 132 | */ | ||
| 133 | void | ||
| 134 | ✗ | MonomerSpec::setName(const QString &name) | |
| 135 | { | ||
| 136 | ✗ | m_name = name; | |
| 137 | ✗ | } | |
| 138 | |||
| 139 | /*! | ||
| 140 | \brief Returns the monomer name. | ||
| 141 | */ | ||
| 142 | const QString & | ||
| 143 | ✗ | MonomerSpec::name() | |
| 144 | { | ||
| 145 | ✗ | return m_name; | |
| 146 | } | ||
| 147 | |||
| 148 | |||
| 149 | /*! | ||
| 150 | \brief Sets the monomer \a code. | ||
| 151 | */ | ||
| 152 | void | ||
| 153 | ✗ | MonomerSpec::setCode(const QString &code) | |
| 154 | { | ||
| 155 | ✗ | m_code = code; | |
| 156 | ✗ | } | |
| 157 | |||
| 158 | |||
| 159 | /*! | ||
| 160 | \brief Returns the monomer code. | ||
| 161 | */ | ||
| 162 | const QString & | ||
| 163 | ✗ | MonomerSpec::code() | |
| 164 | { | ||
| 165 | ✗ | return m_code; | |
| 166 | } | ||
| 167 | |||
| 168 | /*! | ||
| 169 | \brief Sets the raster image file name to \a raster. | ||
| 170 | */ | ||
| 171 | void | ||
| 172 | ✗ | MonomerSpec::setRaster(const QString &raster) | |
| 173 | { | ||
| 174 | ✗ | m_raster = raster; | |
| 175 | ✗ | } | |
| 176 | |||
| 177 | /*! | ||
| 178 | \brief Returns the raster image file name. | ||
| 179 | */ | ||
| 180 | const QString & | ||
| 181 | ✗ | MonomerSpec::raster() | |
| 182 | { | ||
| 183 | ✗ | return m_raster; | |
| 184 | } | ||
| 185 | |||
| 186 | /*! | ||
| 187 | \brief Sets the vector image file name to \a vector. | ||
| 188 | */ | ||
| 189 | void | ||
| 190 | ✗ | MonomerSpec::setVector(const QString &vector) | |
| 191 | { | ||
| 192 | ✗ | m_vector = vector; | |
| 193 | ✗ | } | |
| 194 | |||
| 195 | /*! | ||
| 196 | \brief Returns the vector image file name. | ||
| 197 | */ | ||
| 198 | const QString & | ||
| 199 | ✗ | MonomerSpec::vector() | |
| 200 | { | ||
| 201 | ✗ | return m_vector; | |
| 202 | } | ||
| 203 | |||
| 204 | |||
| 205 | /*! | ||
| 206 | \brief Sets the file name of the Monomer's name \a sound file. | ||
| 207 | */ | ||
| 208 | void | ||
| 209 | ✗ | MonomerSpec::setNameSound(const QString &sound) | |
| 210 | { | ||
| 211 | ✗ | m_nameSound = sound; | |
| 212 | ✗ | } | |
| 213 | |||
| 214 | |||
| 215 | /*! | ||
| 216 | \brief Returns the file name of the Monomer's name sound file. | ||
| 217 | */ | ||
| 218 | const QString & | ||
| 219 | ✗ | MonomerSpec::nameSound() | |
| 220 | { | ||
| 221 | ✗ | return m_nameSound; | |
| 222 | } | ||
| 223 | |||
| 224 | |||
| 225 | /*! | ||
| 226 | \brief Sets the file name of the Monomer's code \a sound file. | ||
| 227 | */ | ||
| 228 | void | ||
| 229 | ✗ | MonomerSpec::setCodeSound(const QString &sound) | |
| 230 | { | ||
| 231 | ✗ | m_codeSound = sound; | |
| 232 | ✗ | } | |
| 233 | |||
| 234 | |||
| 235 | /*! | ||
| 236 | \brief Returns the file name of the Monomer's code sound file. | ||
| 237 | */ | ||
| 238 | const QString & | ||
| 239 | ✗ | MonomerSpec::codeSound() | |
| 240 | { | ||
| 241 | ✗ | return m_codeSound; | |
| 242 | } | ||
| 243 | |||
| 244 | |||
| 245 | /*! | ||
| 246 | \brief Parses the \a file_path dictionary containing the Monomer | ||
| 247 | specifications. | ||
| 248 | |||
| 249 | At the moment the file has this format: | ||
| 250 | |||
| 251 | \code | ||
| 252 | A%alanine.svg | ||
| 253 | C%cysteine.svg | ||
| 254 | D%aspartate.svg | ||
| 255 | E%glutamate.svg | ||
| 256 | \endcode | ||
| 257 | |||
| 258 | Upon parsing, the \a monomer_spec_list of MonomerSpec instances will | ||
| 259 | be filled with instances created on the basis of each parsed line in the file. | ||
| 260 | |||
| 261 | Returns true if the parsing was successful, false otherwise. | ||
| 262 | */ | ||
| 263 | bool | ||
| 264 | ✗ | MonomerSpec::parseFile(QString &file_path, QList<MonomerSpec *> | |
| 265 | *monomer_spec_list) | ||
| 266 | { | ||
| 267 | ✗ | MonomerSpec *monomerSpec = 0; | |
| 268 | |||
| 269 | qint64 lineLength; | ||
| 270 | |||
| 271 | ✗ | QString line; | |
| 272 | ✗ | QString temp; | |
| 273 | |||
| 274 | char buffer[1024]; | ||
| 275 | |||
| 276 | ✗ | Q_ASSERT(monomer_spec_list != 0); | |
| 277 | |||
| 278 | ✗ | if(file_path.isEmpty()) | |
| 279 | ✗ | return false; | |
| 280 | |||
| 281 | ✗ | QFile file(file_path); | |
| 282 | |||
| 283 | ✗ | if(!file.open(QFile::ReadOnly)) | |
| 284 | ✗ | return false; | |
| 285 | |||
| 286 | // The lines we have to parse are of the following type: | ||
| 287 | // A%alanine.svg|alanine.png | ||
| 288 | // Any line starting with '#' are not parsed. | ||
| 289 | |||
| 290 | // Get the first line of the file. Next we enter in to a | ||
| 291 | // while loop. | ||
| 292 | |||
| 293 | ✗ | lineLength = file.readLine(buffer, sizeof(buffer)); | |
| 294 | |||
| 295 | ✗ | while(lineLength != -1) | |
| 296 | { | ||
| 297 | // The line is now in buffer, and we want to convert | ||
| 298 | // it to Unicode by setting it in a QString. | ||
| 299 | ✗ | line = buffer; | |
| 300 | |||
| 301 | // The line that is in line should contain something like: | ||
| 302 | // A%alanine.svg | ||
| 303 | |||
| 304 | // Remove all the spaces from the borders: whitespace means any | ||
| 305 | // character for which QChar::isSpace() returns true. This | ||
| 306 | // includes the ASCII characters '\t', '\n', '\v', '\f', '\r', | ||
| 307 | // and ' '. | ||
| 308 | |||
| 309 | ✗ | line = line.trimmed(); | |
| 310 | |||
| 311 | ✗ | if(line.isEmpty() || line.startsWith('#', Qt::CaseInsensitive)) | |
| 312 | { | ||
| 313 | ✗ | lineLength = file.readLine(buffer, sizeof(buffer)); | |
| 314 | ✗ | continue; | |
| 315 | } | ||
| 316 | |||
| 317 | // Now some other checks. Remember the format of the line: | ||
| 318 | // A%alanine.svg | ||
| 319 | ✗ | QString code; | |
| 320 | ✗ | QString file_name; | |
| 321 | ✗ | QRegularExpression reg_exp(QString("^([A-Z][a-z]*)%(.*)$")); | |
| 322 | |||
| 323 | ✗ | QRegularExpressionMatch match = reg_exp.match(line); | |
| 324 | |||
| 325 | ✗ | if(match.hasMatch()) | |
| 326 | { | ||
| 327 | ✗ | code = match.captured(1); | |
| 328 | ✗ | file_name = match.captured(2); | |
| 329 | } | ||
| 330 | |||
| 331 | // qDebug() << "code:" << code << "file_name:" << file_name; | ||
| 332 | |||
| 333 | // OK, we finally can allocate a new MonomerSpec *. | ||
| 334 | ✗ | monomerSpec = new MonomerSpec(); | |
| 335 | |||
| 336 | ✗ | monomerSpec->m_code = code; | |
| 337 | ✗ | monomerSpec->m_vector = file_name; | |
| 338 | |||
| 339 | ✗ | monomer_spec_list->append(monomerSpec); | |
| 340 | ✗ | lineLength = file.readLine(buffer, sizeof(buffer)); | |
| 341 | ✗ | } | |
| 342 | |||
| 343 | ✗ | return true; | |
| 344 | ✗ | } | |
| 345 | |||
| 346 | } // namespace libXpertMass | ||
| 347 | |||
| 348 | } // namespace MsXpS | ||
| 349 |