ApplicationTools.cpp

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//
// File: ApplicationTools.cpp
// Authors:
//   Julien Dutheil
// Created: 2005-10-21 16:19:00
//
 
/*
  Copyright or © or Copr. Bio++ Development Team, (November 16, 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.
*/
 
 
#include "ApplicationTools.h"
 
using namespace bpp;
 
// From the STL:
#include <cmath>
 
using namespace std;
 
/******************************************************************************/
 
std::shared_ptr<OutputStream> ApplicationTools::error(new StdErr());
std::shared_ptr<OutputStream> ApplicationTools::message(new StdOut());
std::shared_ptr<OutputStream> ApplicationTools::warning(new StdOut());
time_t ApplicationTools::startTime;
size_t ApplicationTools::terminalWidth = 80;
float ApplicationTools::terminalSplit = 0.5;
bool ApplicationTools::interactive = true;
int ApplicationTools::warningLevel = 0;
 
 
/******************************************************************************/
 
vector<string> ApplicationTools::matchingParameters(const string& pattern, const map<string, string>& params)
{
  vector<string> retv;
 
  for (const auto& it : params)
  {
    StringTokenizer stj(pattern, "*", true, false);
    size_t pos1, pos2;
    string parn = it.first;
    bool flag(true);
    string g = stj.nextToken();
    pos1 = parn.find(g);
    if (pos1 != 0)
      flag = false;
    pos1 += g.length();
    while (flag && stj.hasMoreToken())
    {
      g = stj.nextToken();
      pos2 = parn.find(g, pos1);
      if (pos2 == string::npos)
      {
        flag = false;
        break;
      }
      pos1 = pos2 + g.length();
    }
    if (flag &&
        ((g.length() == 0) || (pos1 == parn.length()) || (parn.rfind(g) == parn.length() - g.length())))
      retv.push_back(parn);
  }
 
  return retv;
}
 
vector<string> ApplicationTools::matchingParameters(const string& pattern, vector<string>& params)
{
  vector<string> retv;
 
  for (size_t i = 0; i < params.size(); i++)
  {
    StringTokenizer stj(pattern, "*", true, false);
    size_t pos1, pos2;
    string parn = params.at(i);
    bool flag(true);
    string g = stj.nextToken();
    pos1 = parn.find(g);
    if (pos1 != 0)
      flag = false;
    pos1 += g.length();
    while (flag && stj.hasMoreToken())
    {
      g = stj.nextToken();
      pos2 = parn.find(g, pos1);
      if (pos2 == string::npos)
      {
        flag = false;
        break;
      }
      pos1 = pos2 + g.length();
    }
    if (flag &&
        ((g.length() == 0) || (pos1 == parn.length()) || (parn.rfind(g) == parn.length() - g.length())))
      retv.push_back(parn);
  }
 
  return retv;
}
 
/******************************************************************************/
 
string ApplicationTools::getAFilePath(
  const string& parameter,
  const map<string, string>& params,
  bool isRequired,
  bool mustExist,
  const string& suffix,
  bool suffixIsOptional,
  const string& defaultPath,
  int warn)
{
  string filePath = getStringParameter(parameter, params, defaultPath, suffix, suffixIsOptional, warn);
  if (filePath == "")
    filePath = "none";
  if (filePath == "none" && isRequired)
  {
    throw Exception("You must specify a file for this parameter: " + parameter + (suffixIsOptional ? "" : suffix));
  }
  if (filePath == "none")
    return filePath;
  if (mustExist && !FileTools::fileExists(filePath))
  {
    throw Exception("File does not exists: " + filePath);
  }
  return filePath;
}
 
/******************************************************************************/
 
double ApplicationTools::getDoubleParameter(
  const string& parameterName,
  const map<string, string>& params,
  double defaultValue,
  const string& suffix,
  bool suffixIsOptional,
  int warn)
{
  double dParam = defaultValue;
  if (parameterExists(parameterName + suffix, params))
  {
    dParam = TextTools::toDouble(params.at(parameterName + suffix));
  }
  else if (suffixIsOptional && parameterExists(parameterName, params))
  {
    dParam = TextTools::toDouble(params.at(parameterName));
  }
  else if (warn <= warningLevel)
  {
    displayWarning("Parameter " + parameterName + suffix + " not specified. Default used instead: " + TextTools::toString(defaultValue));
  }
  return dParam;
}
 
/******************************************************************************/
 
int ApplicationTools::getIntParameter(
  const string& parameterName,
  const map<string, string>& params,
  int defaultValue,
  const string& suffix,
  bool suffixIsOptional,
  int warn)
{
  int iParam = defaultValue;
  if (parameterExists(parameterName + suffix, params))
  {
    iParam = TextTools::toInt(params.at(parameterName + suffix));
  }
  else if (suffixIsOptional && parameterExists(parameterName, params))
  {
    iParam = TextTools::toInt(params.at(parameterName));
  }
  else if (warn <= warningLevel)
  {
    displayWarning("Parameter " + parameterName + suffix + " not specified. Default used instead: " + TextTools::toString(defaultValue));
  }
  return iParam;
}
 
/******************************************************************************/
 
 
bool ApplicationTools::getBooleanParameter(
  const string& parameterName,
  const map<string, string>& params,
  bool defaultValue,
  const string& suffix,
  bool suffixIsOptional,
  int warn)
{
  string sParam;
  bool bParam = defaultValue;
  if (parameterExists(parameterName + suffix, params))
  {
    sParam = params.at(parameterName + suffix);
  }
  else if (suffixIsOptional && parameterExists(parameterName, params))
  {
    sParam = params.at(parameterName);
  }
  else
  {
    if (warn <= warningLevel)
    {
      displayWarning("Parameter " + parameterName + " not specified. Default used instead: " + TextTools::toString(defaultValue));
    }
    return bParam;
  }
  if ((sParam == "true")
      || (sParam == "TRUE")
      || (sParam == "t")
      || (sParam == "T")
      || (sParam == "yes")
      || (sParam == "YES")
      || (sParam == "y")
      || (sParam == "Y")
      || (sParam == "1"))
    bParam = true;
  else if ((sParam == "false")
           || (sParam == "FALSE")
           || (sParam == "f")
           || (sParam == "F")
           || (sParam == "no")
           || (sParam == "NO")
           || (sParam == "n")
           || (sParam == "N")
           || (sParam == "0"))
    bParam = false;
  else
    throw Exception("ApplicationTools::getBooleanParameter. Wrong description:" + sParam);
 
  return bParam;
}
 
/******************************************************************************/
 
void ApplicationTools::displayMessage(const string& text)
{
  if (message)
    (*message << text).endLine();
}
 
void ApplicationTools::displayError(const string& text)
{
  if (error)
    (*error << "ERROR!!! " << text).endLine();
}
 
void ApplicationTools::displayWarning(const string& text)
{
  if (warning)
    (*warning << "WARNING!!! " << text).endLine();
}
 
void ApplicationTools::displayTask(const string& text, bool eof)
{
  if (message)
  {
    *message << TextTools::resizeRight(text, static_cast<size_t>(static_cast<float>(terminalWidth) * terminalSplit - 1), '.') << ": ";
    if (eof)
      message->endLine();
    else
      message->flush();
  }
}
 
void ApplicationTools::displayTaskDone()
{
  if (message)
    (*message << "Done.").endLine();
}
 
/******************************************************************************/
 
void ApplicationTools::displayGauge(size_t iter, size_t total, char symbol, const string& mes)
{
  if (!message)
    return;
  if (total == 0)
    return; // We do not display anything in that case.
  size_t width = static_cast<size_t>(static_cast<float>(terminalWidth) * terminalSplit - 2);
  string gauge = string(static_cast<size_t>((1. * static_cast<double>(iter) / static_cast<double>(total)) * static_cast<double>(width)), symbol);
  string info = mes;
  size_t step = static_cast<size_t>(ceil(1. * static_cast<double>(total) / static_cast<double>(width)));
  size_t x = iter % step;
  if (interactive)
  {
    string fill = string(width - gauge.length(), ' ');
    gauge = "[" + gauge + fill + "] " + TextTools::resizeLeft(TextTools::toString(100 * iter / total), 3) + "%";
    if (mes.size() > terminalWidth - gauge.size())
      info = TextTools::resizeRight(mes, terminalWidth - gauge.size());
    if (x == 0 || iter == total)
    {
      *message << '\r' + info + gauge; message->flush();
    }
  }
  else
  {
    if (iter == 0)
    {
      *message << "[";
      message->flush();
      return;
    }
    if (iter >= total)
    {
      size_t fill = static_cast<size_t>(static_cast<float>(terminalWidth) * terminalSplit) - (total - 1) / step - 1;
      *message << TextTools::resizeLeft("]", fill, symbol);
      message->flush();
      return;
    }
    if (x == 0)
    {
      *message << symbol; message->flush();
    }
  }
}
 
/******************************************************************************/
 
void ApplicationTools::displayUnlimitedGauge(size_t iter, const string& mes)
{
  if (!message)
    return;
  string chars = "-/-\\";
  string info = mes;
  if (interactive)
  {
    unsigned int i = iter % 4;
    *message << '\r' << info << chars[i] << " " << TextTools::toString(iter);
    message->flush();
  }
  else
  {
    if (iter == 0)
      *message << info;
    *message << "*";
    message->flush();
    return;
  }
}
 
/******************************************************************************/
 
void ApplicationTools::displayTime(const string& msg)
{
  time_t endTime;
  time(&endTime);
  if (message)
  {
    double nsec = difftime(endTime, startTime);
    double nmin = floor(nsec / 60.);
    double nhou = floor(nmin / 60.);
    double nday = floor(nhou / 24.);
    nhou = nhou - nday * 24;
    nmin = nmin - (nday * 24 + nhou) * 60;
    nsec = nsec - ((nday * 24 + nhou) * 60 + nmin) * 60;
    *message << msg << " ";
    *message << nday << "d, ";
    *message << nhou << "h, ";
    *message << nmin << "m, ";
    *message << nsec << "s.";
    message->endLine();
  }
}
 
/******************************************************************************/
 
double ApplicationTools::getTime()
{
  time_t endTime;
  time(&endTime);
  return difftime(endTime, startTime);
}
 
/******************************************************************************/