| 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 | |||
| 38 | |||
| 39 | /////////////////////// Local includes | ||
| 40 | #include "CrossLinkerSpec.hpp" | ||
| 41 | |||
| 42 | |||
| 43 | namespace MsXpS | ||
| 44 | { | ||
| 45 | |||
| 46 | namespace libXpertMass | ||
| 47 | { | ||
| 48 | |||
| 49 | |||
| 50 | /*! | ||
| 51 | \class MsXpS::libXpertMass::CrossLinkerSpec | ||
| 52 | \inmodule libXpertMass | ||
| 53 | \ingroup PolChemDefBuildingdBlocks | ||
| 54 | \inheaderfile CrossLinkerSpec.hpp | ||
| 55 | |||
| 56 | \brief The CrossLinkerSpec class provides the specification about how \l | ||
| 57 | CrossLinker objects are represented. | ||
| 58 | |||
| 59 | The CrossLinkerSpec class specifies how a \l CrossLinker object is represented | ||
| 60 | graphically, mainly by connecting its name to a graphics SVG file that | ||
| 61 | is located in the Polymer chemistry definition directory. That connection is | ||
| 62 | performed in the "cross_linker_dictionary" dictionary file itself also located | ||
| 63 | in the polymer chemistry definition directory. Its contents look like this: | ||
| 64 | |||
| 65 | \code | ||
| 66 | DisulfideBond%disulfidebond-cross-link.svg | ||
| 67 | CFP-chromophore%cfp-chromophore.svg | ||
| 68 | \endcode | ||
| 69 | |||
| 70 | The \c{DisulfideBond%disulfidebond-cross-link.svg} line indicates that, when a | ||
| 71 | CrossLinker object by name "DisulfideBond" is | ||
| 72 | to be rendered graphically, the corresponding vignette to be used is in the | ||
| 73 | file named "disulfidebond-cross-link.svg" in the polymer chemistry definition | ||
| 74 | directory. | ||
| 75 | */ | ||
| 76 | |||
| 77 | |||
| 78 | /*! | ||
| 79 | \variable int MsXpS::libXpertMass::CrossLinkerSpec::m_name | ||
| 80 | |||
| 81 | \brief The name of the cross-linker. | ||
| 82 | */ | ||
| 83 | |||
| 84 | /*! | ||
| 85 | \variable int MsXpS::libXpertMass::CrossLinkerSpec::m_vector | ||
| 86 | |||
| 87 | \brief The filename of the vector representation of the cross-linker. | ||
| 88 | */ | ||
| 89 | |||
| 90 | /*! | ||
| 91 | \variable int MsXpS::libXpertMass::CrossLinkerSpec::m_sound | ||
| 92 | |||
| 93 | \brief The file name of the sound for the cross-linker. | ||
| 94 | */ | ||
| 95 | |||
| 96 | |||
| 97 | /*! | ||
| 98 | \brief Constructs a CrossLinkerSpec instance. | ||
| 99 | */ | ||
| 100 | ✗ | CrossLinkerSpec::CrossLinkerSpec() | |
| 101 | { | ||
| 102 | ✗ | } | |
| 103 | |||
| 104 | /*! | ||
| 105 | \brief Destructs this CrossLinkerSpec instance. | ||
| 106 | */ | ||
| 107 | ✗ | CrossLinkerSpec::~CrossLinkerSpec() | |
| 108 | { | ||
| 109 | ✗ | } | |
| 110 | |||
| 111 | /*! | ||
| 112 | \brief Sets the cross-linker \a name. | ||
| 113 | */ | ||
| 114 | void | ||
| 115 | ✗ | CrossLinkerSpec::setName(const QString &name) | |
| 116 | { | ||
| 117 | ✗ | m_name = name; | |
| 118 | ✗ | } | |
| 119 | |||
| 120 | /* | ||
| 121 | \brief Gets the cross-linker name. | ||
| 122 | */ | ||
| 123 | const QString & | ||
| 124 | ✗ | CrossLinkerSpec::name() | |
| 125 | { | ||
| 126 | ✗ | return m_name; | |
| 127 | } | ||
| 128 | |||
| 129 | |||
| 130 | /*! | ||
| 131 | \brief Sets the vector image file name to \a vector. | ||
| 132 | */void | ||
| 133 | ✗ | CrossLinkerSpec::setVector(const QString &vector) | |
| 134 | { | ||
| 135 | ✗ | m_vector = vector; | |
| 136 | ✗ | } | |
| 137 | |||
| 138 | |||
| 139 | /*! | ||
| 140 | \brief Returns the vector image file name. | ||
| 141 | */ | ||
| 142 | const QString & | ||
| 143 | ✗ | CrossLinkerSpec::vector() | |
| 144 | { | ||
| 145 | ✗ | return m_vector; | |
| 146 | } | ||
| 147 | |||
| 148 | |||
| 149 | /*! | ||
| 150 | \brief Sets the file name of the CrossLinkerSpec's \a sound file. | ||
| 151 | */ | ||
| 152 | void | ||
| 153 | ✗ | CrossLinkerSpec::setSound(const QString &sound) | |
| 154 | { | ||
| 155 | ✗ | m_sound = sound; | |
| 156 | ✗ | } | |
| 157 | |||
| 158 | |||
| 159 | /*! | ||
| 160 | \brief Returns the file name of the CrossLinkerSpec's sound file. | ||
| 161 | */ | ||
| 162 | const QString & | ||
| 163 | ✗ | CrossLinkerSpec::sound() | |
| 164 | { | ||
| 165 | ✗ | return m_sound; | |
| 166 | } | ||
| 167 | |||
| 168 | |||
| 169 | /*! | ||
| 170 | \brief Parses the \a file_path dictionary containing the \l CrossLinker | ||
| 171 | specifications. | ||
| 172 | |||
| 173 | At the moment the file has this format: | ||
| 174 | |||
| 175 | \code | ||
| 176 | DisulfideBond%disulfidebond-cross-link.svg | ||
| 177 | CFP-chromophore%cfp-chromophore.svg | ||
| 178 | \endcode | ||
| 179 | |||
| 180 | Upon parsing, the \a cross_linker_spec_list of CrossLinkerSpec instances will | ||
| 181 | be filled with | ||
| 182 | instances created on the basis of each parsed line in the file. | ||
| 183 | |||
| 184 | Returns true if the parsing was successful, false otherwise. | ||
| 185 | */ | ||
| 186 | bool | ||
| 187 | ✗ | CrossLinkerSpec::parseFile(QString &file_path, | |
| 188 | QList<CrossLinkerSpec *> *cross_linker_spec_list) | ||
| 189 | { | ||
| 190 | ✗ | CrossLinkerSpec *crossLinkerSpec = 0; | |
| 191 | |||
| 192 | qint64 lineLength; | ||
| 193 | |||
| 194 | ✗ | QString line; | |
| 195 | ✗ | QString temp; | |
| 196 | |||
| 197 | char buffer[1024]; | ||
| 198 | |||
| 199 | ✗ | int percentSignIdx = 0; | |
| 200 | |||
| 201 | ✗ | Q_ASSERT(cross_linker_spec_list != 0); | |
| 202 | |||
| 203 | ✗ | if(file_path.isEmpty()) | |
| 204 | ✗ | return false; | |
| 205 | |||
| 206 | ✗ | QFile file(file_path); | |
| 207 | |||
| 208 | ✗ | if(!file.open(QFile::ReadOnly)) | |
| 209 | ✗ | return false; | |
| 210 | |||
| 211 | // The lines we have to parse are of the following type: | ||
| 212 | // DisulfideBon%disulfidebond.svg | ||
| 213 | // Any line starting with ' ' or '#' are not parsed. | ||
| 214 | |||
| 215 | // Get the first line of the file. Next we enter in to a | ||
| 216 | // while loop. | ||
| 217 | |||
| 218 | ✗ | lineLength = file.readLine(buffer, sizeof(buffer)); | |
| 219 | |||
| 220 | ✗ | while(lineLength != -1) | |
| 221 | { | ||
| 222 | // The line is now in buffer, and we want to convert | ||
| 223 | // it to Unicode by setting it in a QString. | ||
| 224 | ✗ | line = buffer; | |
| 225 | |||
| 226 | // The line that is in line should contain something like: | ||
| 227 | // DisulfideBon%disulfidebond.svg | ||
| 228 | // | ||
| 229 | // Note, however that lines beginning with either '\n'(newline) | ||
| 230 | // or '#' are comments. | ||
| 231 | |||
| 232 | // Remove all the spaces from the borders: Whitespace means any | ||
| 233 | // character for which QChar::isSpace() returns true. This | ||
| 234 | // includes the ASCII characters '\t', '\n', '\v', '\f', '\r', | ||
| 235 | // and ' '. | ||
| 236 | |||
| 237 | ✗ | line = line.trimmed(); | |
| 238 | |||
| 239 | ✗ | if(line.isEmpty() || line.startsWith('#', Qt::CaseInsensitive)) | |
| 240 | { | ||
| 241 | ✗ | lineLength = file.readLine(buffer, sizeof(buffer)); | |
| 242 | ✗ | continue; | |
| 243 | } | ||
| 244 | |||
| 245 | // Now some other checks. Remember the format of the line: | ||
| 246 | // DisulfideBon%disulfidebond.svg | ||
| 247 | |||
| 248 | ✗ | percentSignIdx = line.indexOf('%', 0, Qt::CaseInsensitive); | |
| 249 | |||
| 250 | ✗ | if(percentSignIdx == -1 || line.count('%', Qt::CaseInsensitive) > 2) | |
| 251 | ✗ | return false; | |
| 252 | |||
| 253 | // OK, we finally can allocate a new CrossLinkerSpec *. | ||
| 254 | ✗ | crossLinkerSpec = new CrossLinkerSpec(); | |
| 255 | |||
| 256 | ✗ | crossLinkerSpec->m_name = line.left(percentSignIdx); | |
| 257 | |||
| 258 | // Remove from the line the "DisulfideBond%" substring, as we | ||
| 259 | // do not need it anymore. | ||
| 260 | ✗ | line.remove(0, percentSignIdx + 1); | |
| 261 | |||
| 262 | // Now we can go on with the graphics files stuff. At this point | ||
| 263 | // all that remains up to the end of the line is the filename | ||
| 264 | // with extension .svg. | ||
| 265 | |||
| 266 | ✗ | if(!line.endsWith(".svg", Qt::CaseSensitive)) | |
| 267 | { | ||
| 268 | ✗ | delete crossLinkerSpec; | |
| 269 | ✗ | return false; | |
| 270 | } | ||
| 271 | |||
| 272 | // Ok that's done, we can get the vector graphics filename: | ||
| 273 | |||
| 274 | ✗ | crossLinkerSpec->m_vector = line; | |
| 275 | |||
| 276 | ✗ | cross_linker_spec_list->append(crossLinkerSpec); | |
| 277 | |||
| 278 | // Continue to next line to further parse the file. | ||
| 279 | ✗ | lineLength = file.readLine(buffer, sizeof(buffer)); | |
| 280 | } | ||
| 281 | |||
| 282 | ✗ | return true; | |
| 283 | ✗ | } | |
| 284 | |||
| 285 | } // namespace libXpertMass | ||
| 286 | |||
| 287 | } // namespace MsXpS | ||
| 288 |