xref: /dports/science/massxpert/massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f/lib/polChemDefCatParser.cpp

/* massXpert - the true massist's program.
   --------------------------------------
   Copyright(C) 2006,2007 Filippo Rusconi

   http://www.massxpert.org/massXpert

   This file is part of the massXpert project.

   The massxpert project is the successor to the "GNU polyxmass"
   project that is an official GNU project package(see
   www.gnu.org). The massXpert project is not endorsed by the GNU
   project, although it is released ---in its entirety--- under the
   GNU General Public License. A huge part of the code in massXpert
   is actually a C++ rewrite of code in GNU polyxmass. As such
   massXpert was started at the Centre National de la Recherche
   Scientifique(FRANCE), that granted me the formal authorization to
   publish it under this Free Software License.

   This software is free software; you can redistribute it and/or
   modify it under the terms of the GNU  General Public
   License version 3, as published by the Free Software Foundation.


   This software is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
   General Public License for more details.

   You should have received a copy of the GNU General Public License
   along with this software; if not, write to the

   Free Software Foundation, Inc.,

   51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
*/


/////////////////////// Qt includes
#include<QFile>
#include<QDir>
#include<QDebug>


/////////////////////// Local includes
#include "polChemDefCatParser.hpp"
#include "configSettings.hpp"


namespace massXpert
{

  PolChemDefCatParser::PolChemDefCatParser()
  {
    mp_configSettings = 0;
    m_pendingMode = 0;
    m_configSysUser = 0;

    return ;
  }


  PolChemDefCatParser::~PolChemDefCatParser()
  {
    return;
  }


  void
  PolChemDefCatParser::setFilePath(const QString &filePath)
  {
    m_filePath = filePath;
  }


  const QString &
  PolChemDefCatParser::getFilePath()
  {
    return m_filePath;
  }


  void
  PolChemDefCatParser::setPendingMode(int pendingMode)
  {
    m_pendingMode = pendingMode;
  }


  int
  PolChemDefCatParser::getPendingMode()
  {
    return m_pendingMode;
  }


  void
  PolChemDefCatParser::setConfigSysUser(int configSysUser)
  {
    m_configSysUser = configSysUser;
  }


  int
  PolChemDefCatParser::getConfigSysUser()
  {
    return m_configSysUser;
  }


  int
  PolChemDefCatParser::parseFiles(const ConfigSettings &configSettings,
				   QList<PolChemDefSpec *>
				   *polChemDefSpecList)
  {
    mp_configSettings = &configSettings;

    QDir dir;

    int count = 0;
    int totCount = 0;

    // Polymer chemistry definition catalogue files are located in
    // pol-chem-defs directories that are located in turn in either
    // system-wide configuration places, like
    // /etc/massxpert/pol-chem-defs, for example on UNIX-like systems,
    // and/or in private user locations, like
    // $HOME/.massxpert/pol-chem-defs.

    Q_ASSERT(polChemDefSpecList);

    // Depending on m_configSysUser, we are going to get all the files
    // that are polymer chemistry def catalogues in the different
    // locations and parse these files one after the other.

    if (m_configSysUser & POLCHEMDEF_CAT_PARSE_SYSTEM_CONFIG)
      {
	// We have to parse all the catalogue files in the system
	// configuration directory.

	dir.setPath(configSettings.systemPolChemDefCatDir());

	if(dir.exists())
	  {
	    // All the polchem definition catalogues must have the
	    // "pol-chem-defs-cat" filename suffix. So we filter the list of
	    // files in the directory according to that wildcard expression.

	    QStringList filters;
	    filters << "*pol-chem-defs-cat";
	    dir.setNameFilters(filters);

	    dir.setFilter(QDir::Files | QDir::NoSymLinks);

	    QFileInfoList list = dir.entryInfoList();

	    for (int iter = 0; iter < list.size(); ++iter)
	      {
		QFileInfo fileInfo = list.at(iter);

		m_filePath = fileInfo.absoluteFilePath();
		count = parse(polChemDefSpecList,
			       POLCHEMDEF_CAT_PARSE_SYSTEM_CONFIG);

		if(count == -1)
		  return -1;
		else
		  totCount += count;
	      }
	  }
      }

    if (m_configSysUser & POLCHEMDEF_CAT_PARSE_USER_CONFIG)
      {
	// We have to parse all the catalogue files in the user
	// configuration directory.

	dir.setPath(configSettings.userPolChemDefCatDir());

	if(dir.exists())
	  {
	    // All the atom definition catalogues must have the
	    // "atom-defs-cat" filename suffix. So we filter the list of
	    // files in the directory according to that wildcard expression.

	    QStringList filters;
	    filters << "*pol-chem-defs-cat";
	    dir.setNameFilters(filters);

	    dir.setFilter(QDir::Files | QDir::NoSymLinks);

	    QFileInfoList list = dir.entryInfoList();

	    for (int iter = 0; iter < list.size(); ++iter)
	      {
		QFileInfo fileInfo = list.at(iter);

		m_filePath = fileInfo.absoluteFilePath();
		count = parse(polChemDefSpecList,
			       POLCHEMDEF_CAT_PARSE_USER_CONFIG);

		if(count == -1)
		  return -1;
		else
		  totCount += count;
	      }
	  }
      }

    return totCount;
  }


  int
  PolChemDefCatParser::parse(QList<PolChemDefSpec *>
			      *polChemDefSpecList,
			      int forSystemOrUser)
  {
    qint64 lineLength;

    QString line;

    char buffer [1024];

    int equalSignIdx = 0;
    int count = 0;

    PolChemDefSpec *polChemDefSpec = 0;

    // We are given a QList in which to store all the
    // PolChemDefSpec* instances that we create by parsing the
    // catalogue files.
    //
    // Each line in the catalogue(s) that we may have to parse gives the
    // name of a polymer chemistry definition, like "protein", and the
    // full pathname of the file in which that definition is stored and
    // the full pathname to the directory where all its corresponding
    // stuff is stored.  Example:
    // protein=/some/dir/protein/protein.xml
    //
    // All we have to do is parse each line and for each valid one
    // create a PolChemDefSpec item that we append/prepend to the
    // QList passed as parameter.

    Q_ASSERT(polChemDefSpecList);

    QFile file(m_filePath);

    if (! file.open(QFile::ReadOnly))
      return -1;

    //qDebug() << "Begin file:" << m_filePath.toAscii();


    // Get the first line of the file. Next we enter in to a
    // while loop.

    lineLength = file.readLine(buffer, sizeof(buffer));

    while(lineLength != -1)
      {
	// The line is now in buffer, and we want to convert
	// it to Unicode by setting it in a QString.
	line = buffer;

	// Remove all the spaces from the borders: Whitespace means any
	// character for which QChar::isSpace() returns true. This
	// includes the ASCII characters '\t', '\n', '\v', '\f', '\r',
	// and ' '.

	line = line.trimmed();

	// The line that is in line should contain something like:

	// protein=protein/protein.xml(relative path)

	// or:

	// protein=/some/dir/protein/protein.xml(absolute path)
	//
	// Note, however that lines beginning with either ' '(space) or
	// '\n'(newline) or '#' are comments.

	if(line.isEmpty() || line.startsWith('#', Qt::CaseInsensitive))
	  {
	    lineLength = file.readLine(buffer, sizeof(buffer));
	    continue;
	  }

	// Now some other checks.
	equalSignIdx = line.indexOf('=', 0, Qt::CaseInsensitive);

	if(equalSignIdx == -1 || line.count('=', Qt::CaseInsensitive) > 1)
	  return -1;

	// Ok at this point, we might have a nicely parseable line, it
	// makes sens to allocate a new AtomDefSpec object.
	polChemDefSpec = new(PolChemDefSpec);

	polChemDefSpec->setName(line.left(equalSignIdx));

	// Of course we have to make sure that we are getting
	// a file path corresponding to something we actually
	// can use.

	QString polChemDefFile = line.right(line.length()
					     - equalSignIdx - 1);

	QFileInfo fileInfo(polChemDefFile);

	if(fileInfo.isRelative())
	  {
	    // The polymer chemistry definition file is not an
	    // absolute filePath. We have to change it into an
	    // absolute filePath by prepending the directory path
	    // where it is located.

	    if (forSystemOrUser == POLCHEMDEF_CAT_PARSE_SYSTEM_CONFIG)
	      {
		QFile file(mp_configSettings->systemPolChemDefCatDir() +
			    QDir::separator() + polChemDefFile);

		if(!file.exists())
		  {
		    delete polChemDefSpec;
		    return -1;
		  }

		polChemDefSpec->setFilePath(file.fileName());
	      }
	    else if (forSystemOrUser == POLCHEMDEF_CAT_PARSE_USER_CONFIG)
	      {
		QFile file(mp_configSettings->userPolChemDefCatDir() +
			    QDir::separator() + polChemDefFile);

		if(!file.exists())
		  {
		    delete polChemDefSpec;
		    return -1;
		  }

		polChemDefSpec->setFilePath(file.fileName());
	      }
	    else
	      qFatal("%s@%d: Failed to parse polymer chemistry definition "
		      "catalogues.", __FILE__, __LINE__);
	  }
	else
	  {
	    if (!fileInfo.exists())
	      {
		delete polChemDefSpec;
		return -1;
	      }

	    polChemDefSpec->setFilePath(polChemDefFile);
	  }


	// OK, the file exists, and thus we can set the newly allocated
	// polChemDefSpec object to the QList passed as parameter.

	if(m_pendingMode == POLCHEMDEF_CAT_PARSE_APPEND_CONFIG)
	  polChemDefSpecList->append(polChemDefSpec);
	else
	  polChemDefSpecList->prepend(polChemDefSpec);

	++count;

	//qDebug() << "Parsed line: " << line.toAscii();

	lineLength = file.readLine(buffer, sizeof(buffer));
      }
    // while(lineLength != -1)

    file.close();

    //qDebug() << "Endfile:" << m_filePath.toAscii();

    return count;
  }

} // namespace massXpert