AttributesTools.cpp

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//
// File: AttributesTools.cpp
// Authors:
//   Julien Dutheil
// Created: 2003-10-07 00:00:00
//
 
/*
  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.
*/
 
 
 
// From the STL:
#include <cstdlib>
#include <string>
#include <iostream>
#include <fstream>
#include <algorithm>
 
 
using namespace std;
 
#include "AttributesTools.h"
#include "../App/ApplicationTools.h"
#include "../Text/TextTools.h"
#include "../Io/FileTools.h"
 
using namespace bpp;
 
std::vector<std::string> AttributesTools::vParam_;
 
/******************************************************************************/
 
std::vector<std::string> AttributesTools::getVector(int argc, char* argv[])
{
  size_t n = static_cast<size_t>(argc);
  vector<string> result(n);
  for (size_t i = 1; i < n; ++i)
  {
    result[i] = string(argv[i]);
  }
  // Ignore first argc which is the program name!
  return result;
}
 
/******************************************************************************/
 
std::map<std::string, std::string> AttributesTools::getAttributesMap(
  const std::vector<std::string>& argv,
  const std::string& delimiter)
{
  map<string, string> am;
  getAttributesMap(argv, am, delimiter);
  return am;
}
 
/******************************************************************************/
 
void AttributesTools::getAttributesMap(
  const std::vector<std::string>& argv,
  std::map<std::string, std::string>& am,
  const std::string& delimiter)
{
  vector<string> argv2(argv.size());
  // First make a few cleaning:
  for (size_t i = 0; i < argv.size(); i++)
  {
    // Make a few corrections first:
    string arg = removeComments(argv[i], string("#"), string("\n")); // remove shell comments.
    arg = removeComments(arg, string("//"), string("\n")); // remove C simple comments.
    arg = removeComments(arg, string("/*"), string("*/")); // remove C multiple comments.
    arg = TextTools::removeWhiteSpaces(arg);
    argv2[i] = arg;
  }
  // Now parse arguments:
  for (size_t i = 0; i < argv.size(); i++)
  {
    string arg = argv2[i];
    if (arg == "")
      continue;                   // Skipping void line.
    while (arg[arg.size() - 1] == '\\')
    {
      // Splitted line
      i++;
      arg = arg.substr(0, arg.length() - 1) + argv2[i];
    }
    // Parsing:
    string::size_type limit = arg.find(delimiter, 0);
    if (limit == string::npos)
    {
      // Invalid parameter
      (*ApplicationTools::warning << "WARNING!!! Parameter '" << arg << "' has been ignored.").endLine();
    }
    else
    {
      string name  = string(arg.begin(), arg.begin() + static_cast<ptrdiff_t>(limit));
      string value = string(arg.begin() + static_cast<ptrdiff_t>(limit + delimiter.size()), arg.end());
      // if ((name == "param") || (name == "params"))
      // {
      //   if (std::find(vParam_.begin(),vParam_.end(),value)!=vParam_.end())
      //     throw Exception("Param name " + value + " already seen.");
 
      //   //Recursive inclusion:
      //   getAttributesMapFromFile(value, am, delimiter);
      //   vParam_.push_back(value);
      // }
      // else
      am[name] = value;
    }
  }
}
 
/******************************************************************************/
 
void AttributesTools::getAttributesMapFromFile(
  const std::string& file,
  std::map<std::string, std::string>& params,
  const std::string& delimiter)
{
  cout << "Parsing file " << file << " for options." << endl;
  ifstream input(file.c_str(), ios::in);
  vector<string> lines = FileTools::putStreamIntoVectorOfStrings(input);
  getAttributesMap(lines, params, delimiter);
}
 
/******************************************************************************/
 
std::map<std::string, std::string> AttributesTools::getAttributesMapFromFile(
  const std::string& file,
  const std::string& delimiter)
{
  map<string, string> params;
  getAttributesMapFromFile(file, params, delimiter);
  return params;
}
 
/******************************************************************************/
 
void AttributesTools::actualizeAttributesMap(
  std::map<std::string, std::string>& attMap,
  const std::map<std::string, std::string>& atts)
{
  for (map<string, string>::const_iterator i = atts.begin(); i != atts.end(); i++)
  {
    attMap[i->first] = i->second;
  }
}
 
/******************************************************************************/
 
void AttributesTools::resolveVariables(
  std::map<std::string, std::string>& am,
  char varCode,
  char varBeg,
  char varEnd)
{
  // Now resolve any variable:
  for (map<string, string>::iterator it = am.begin(); it != am.end(); it++)
  {
    string value = it->second;
    string::size_type index1 = value.find(TextTools::toString(varCode) + TextTools::toString(varBeg));
    while (index1 != string::npos)
    {
      string::size_type index2 = value.find(TextTools::toString(varEnd), index1);
      if (index2 != string::npos)
      {
        string varName  = value.substr(index1 + 2, index2 - index1 - 2);
        map<string, string>::iterator varIt = am.find(varName);
        string varValue = "";
        if (varIt == am.end())
        {
          if (ApplicationTools::error)
            (*ApplicationTools::error << "Variable '" << varName << "' is undefined and was ignored.").endLine();
        }
        else
        {
          varValue = varIt->second;
        }
        // Modify original field:
        string newValue = value.substr(0, index1) + varValue + value.substr(index2 + 1);
        it->second = newValue;
      }
      else
        throw Exception("Syntax error, variable name is not closed.");
      value = it->second;
      index1 = value.find(TextTools::toString(varCode) + TextTools::toString(varBeg));
    }
  }
}
 
/******************************************************************************/
 
std::string AttributesTools::removeComments(
  const std::string& s,
  const std::string& begin,
  const std::string& end)
{
  string r = s;
  string::size_type last = 0;
  do
  {
    string::size_type first = r.find(begin, last);
    if (first == string::npos)
      return r;                   // No shell comment.
    // else:
    last = r.find(end, first);
    if (last == string::npos)
    {
      r.erase(r.begin() + static_cast<ptrdiff_t>(first), r.end());
    }
    else
    {
      r.erase(r.begin() + static_cast<ptrdiff_t>(first), r.begin() + static_cast<ptrdiff_t>(last));
    }
  }
  while (last != string::npos);
  return r;
}
 
/******************************************************************************/
 
std::map<std::string, std::string> AttributesTools::parseOptions(int args, char** argv)
{
  // Get the parameters from command line:
  map<string, string> cmdParams = AttributesTools::getAttributesMap(
    AttributesTools::getVector(args, argv), "=");
 
 
  // Look for a specified file with parameters:
  resolveVariables(cmdParams);
  map<string, string> params;
 
  while (cmdParams.find("param") != cmdParams.end() || cmdParams.find("params") != cmdParams.end())
  {
    string file = (cmdParams.find("param") != cmdParams.end()) ? cmdParams["param"] : cmdParams["params"];
 
    if (std::find(vParam_.begin(), vParam_.end(), file) != vParam_.end())
      throw Exception("Param name " + file + " already seen.");
 
    if (!FileTools::fileExists(file))
      throw Exception("AttributesTools::parseOptions(). Parameter file not found.: " + file);
 
    params = getAttributesMapFromFile(file, "=");
    // Actualize attributes with ones passed to command line:
    if (cmdParams.find("param") != cmdParams.end())
      cmdParams.erase("param");
    else
      cmdParams.erase("params");
 
    actualizeAttributesMap(params, cmdParams);
 
    cmdParams = params;
    resolveVariables(cmdParams);
 
    vParam_.push_back(file);
  }
 
  return cmdParams;
}
 
/******************************************************************************/