ApplicationTools.h

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//
// File: ApplicationTools.h
// Authors:
//   Julien Dutheil
// Created: 2005-10-21 16:19:00
//
 
/*
  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.
*/
 
#ifndef BPP_APP_APPLICATIONTOOLS_H
#define BPP_APP_APPLICATIONTOOLS_H
 
 
#include "../Io/FileTools.h"
#include "../Io/OutputStream.h"
#include "../Numeric/Matrix/Matrix.h"
#include "../Text/NestedStringTokenizer.h"
#include "../Text/StringTokenizer.h"
#include "../Text/TextTools.h"
 
// From the STL:
#include <map>
#include <vector>
#include <iostream>
#include <ctime>
 
namespace bpp
{
class ApplicationTools
{
public:
  static std::shared_ptr<OutputStream> error;
  static std::shared_ptr<OutputStream> message;
  static std::shared_ptr<OutputStream> warning;
 
  static time_t startTime;
 
  static size_t terminalWidth;
 
  static float terminalSplit;
 
  static bool interactive;
 
  static int warningLevel;
 
public:
  ApplicationTools() {}
  virtual ~ApplicationTools() {}
 
public:
  static bool parameterExists(const std::string& parameterName, const std::map<std::string, std::string>& params)
  {
    std::map<std::string, std::string>::const_iterator it = params.find(parameterName);
 
    return it != params.end() && !TextTools::isEmpty(it->second);
  }
 
 
  static bool parameterExists(const std::string& parameterName, std::vector<std::string>& params)
  {
    for (size_t i = 0; i < params.size(); ++i)
    {
      if (params[i] == parameterName)
        return true;
    }
 
    return false;
  }
 
  static std::vector<std::string> matchingParameters(const std::string& pattern, const std::map<std::string, std::string>& params);
 
  static std::vector<std::string> matchingParameters(const std::string& pattern, std::vector<std::string>& params);
 
  static double getDoubleParameter(
    const std::string& parameterName,
    const std::map<std::string, std::string>& params,
    double defaultValue,
    const std::string& suffix = "",
    bool suffixIsOptional = true,
    int warn = 0);
 
  static int getIntParameter(
    const std::string& parameterName,
    const std::map<std::string, std::string>& params,
    int defaultValue,
    const std::string& suffix = "",
    bool suffixIsOptional = true,
    int warn = 0);
 
  static std::string getStringParameter(
    const std::string& parameterName,
    const std::map<std::string, std::string>& params,
    const std::string& defaultValue,
    const std::string& suffix = "",
    bool suffixIsOptional = true,
    int warn = 0)
  {
    std::string sParam = defaultValue;
    std::map<std::string, std::string>::const_iterator it1 = params.find(parameterName + suffix);
    if (it1 != params.end() && !TextTools::isEmpty(it1->second))
      sParam = it1->second;
    else
    {
      std::map<std::string, std::string>::const_iterator it2 = params.find(parameterName);
      if (suffixIsOptional && it2 != params.end() && !TextTools::isEmpty(it2->second))
        sParam = it2->second;
      else if (warn <= warningLevel)
      {
        displayWarning("Parameter " + parameterName + " not specified. Default used instead: " + defaultValue);
      }
    }
 
    return sParam;
  }
 
 
  static bool getBooleanParameter(
    const std::string& parameterName,
    const std::map<std::string, std::string>& params,
    bool defaultValue,
    const std::string& suffix = "",
    bool suffixIsOptional = true,
    int warn = 0);
 
  template<class T> static T getParameter(
    const std::string& parameterName,
    const std::map<std::string, std::string>& params,
    T defaultValue,
    const std::string& suffix = "",
    bool suffixIsOptional = true,
    int warn = 0)
  {
    T tParam = defaultValue;
    if (parameterExists(parameterName + suffix, params))
    {
      tParam = TextTools::to<T>(params.at(parameterName + suffix));
    }
    else if (suffixIsOptional && parameterExists(parameterName, params))
    {
      tParam = TextTools::to<T>(params.at(parameterName));
    }
    else if (warn <= warningLevel)
    {
      displayWarning("Parameter " + parameterName + suffix + " not specified. Default used instead: " + TextTools::toString(defaultValue));
    }
    return tParam;
  }
 
 
  static std::string getAFilePath(
    const std::string& parameter,
    const std::map<std::string, std::string>& params,
    bool isRequired = true,
    bool mustExist = true,
    const std::string& suffix = "",
    bool suffixIsOptional = false,
    const std::string& defaultPath = "none",
    int warn = 0);
 
  template<class T> static std::vector<T> getVectorParameter(
    const std::string& parameterName,
    const std::map<std::string, std::string>& params,
    char separator,
    const std::string& defaultValue,
    const std::string& suffix = "",
    bool suffixIsOptional = true,
    int warn = 0)
  {
    if (separator == ' ') throw Exception("ApplicationTools::getVectorParameter(). Separator cannot be a space character.");
    std::string s = getStringParameter(parameterName, params, defaultValue, suffix, suffixIsOptional, warn);
    if (TextTools::isEmpty(s)) return std::vector<T>(0);
    if (s[0] == '(' && s[s.size() - 1] == ')')
    {
      // This is a delimited vector:
      s = s.substr(1, s.size() - 2);
      if (TextTools::isEmpty(s)) return std::vector<T>(0);
    }
    NestedStringTokenizer st(s, "(", ")", TextTools::toString(separator));
    size_t n = st.numberOfRemainingTokens();
    std::vector<T> v(n);
    for (size_t i = 0; i < n; ++i)
    {
      v[i] = TextTools::fromString<T>(st.nextToken());
    }
    return v;
  }
 
  template<class T> static std::vector< std::vector<T> > getVectorOfVectorsParameter(
    const std::string& parameterName,
    const std::map<std::string, std::string>& params,
    char separator,
    const std::string& defaultValue,
    const std::string& suffix = "",
    bool suffixIsOptional = true,
    int warn = 0)
  {
    if (separator == ' ') throw Exception("ApplicationTools::getVectorOfVectorsParameter(). Separator cannot be a space character.");
    std::string s = getStringParameter(parameterName, params, defaultValue, suffix, suffixIsOptional, warn);
    if (TextTools::isEmpty(s)) return std::vector< std::vector<T> >(0);
    if (s[0] == '(' && s[s.size() - 1] == ')')
    {
      // This is a delimited vector:
      s = s.substr(1, s.size() - 2);
      if (TextTools::isEmpty(s)) return std::vector< std::vector<T> >(0);
    }
    NestedStringTokenizer st(s, "(", ")", TextTools::toString(separator));
    size_t n = st.numberOfRemainingTokens();
    std::string s2;
    std::vector< std::vector<T> > v(n);
    for (size_t i = 0; i < n; ++i)
    {
      s2 = st.nextToken();
      if (s2[0] == '(' && s2[s2.size() - 1] == ')')
      {
        // This is a delimited vector:
        s2 = s2.substr(1, s2.size() - 2);
      }
      if (!TextTools::isEmpty(s2))
      {
        NestedStringTokenizer st2(s2, "(", ")", TextTools::toString(separator));
        size_t n2 = st2.numberOfRemainingTokens();
        v[i].resize(n2);
        for (size_t j = 0; j < n2; ++j)
        {
          v[i][j] = TextTools::fromString<T>(st2.nextToken());
        }
      }
    }
    return v;
  }
 
  template<class T> static std::vector<T> getVectorParameter(
    const std::string& parameterName,
    const std::map<std::string, std::string>& params,
    char separator,
    char rangeOperator,
    const std::string& defaultValue,
    const std::string& suffix = "",
    bool suffixIsOptional = true,
    bool warn = true)
  {
    std::string s = getStringParameter(parameterName, params, defaultValue, suffix, suffixIsOptional, warn);
    if (s[0] == '(' && s[s.size() - 1] == ')')
    {
      // This is a delimited vector:
      s = s.substr(1, s.size() - 2);
      if (TextTools::isEmpty(s)) return std::vector<T>(0);
    }
    StringTokenizer st(s, TextTools::toString(separator));
    size_t n = st.numberOfRemainingTokens();
    std::vector<T> v;
    for (size_t i = 0; i < n; ++i)
    {
      std::string token = st.nextToken();
      std::string::size_type pos = token.find(rangeOperator);
      if (pos == std::string::npos)
        v.push_back(TextTools::fromString<T>(token));
      else
      {
        T d1 = TextTools::fromString<T>(token.substr(0, pos));
        T d2 = TextTools::fromString<T>(token.substr(pos + 1));
        for (T j = d1; j < d2; j++)
        {
          v.push_back(j);
        }
        v.push_back(d2);
      }
    }
    return v;
  }
 
  template<class T> static RowMatrix<T> getMatrixParameter(
    const std::string& parameterName,
    const std::map<std::string, std::string>& params,
    char separator,
    const std::string& defaultValue,
    const std::string& suffix = "",
    bool suffixIsOptional = true,
    bool warn = true)
  {
    RowMatrix<T> mat;
 
    std::string s = getStringParameter(parameterName, params, defaultValue, suffix, suffixIsOptional, warn);
    if (TextTools::isEmpty(s)) return RowMatrix<T>(0, 0);
    if (s[0] == '(' && s[s.size() - 1] == ')')
    {
      // This is a delimited vector:
      s = s.substr(1, s.size() - 2);
      if (TextTools::isEmpty(s)) return RowMatrix<T>(0, 0);
    }
 
    StringTokenizer st1(s, "()");
 
    while (st1.hasMoreToken())
    {
      std::string si = st1.nextToken();
      StringTokenizer st2(si, TextTools::toString(separator));
      size_t n = st2.numberOfRemainingTokens();
 
      std::vector<T> v(n);
      for (size_t i = 0; i < n; i++)
      {
        v[i] = TextTools::fromString<T>(st2.nextToken());
      }
 
      if (v.size() != 0)
        mat.addRow(v);
    }
    return mat;
  }
 
 
  static void displayMessage(const std::string& text);
 
  static void displayError(const std::string& text);
 
  static void displayWarning(const std::string& text);
 
  static void displayTask(const std::string& text, bool eof = false);
 
  static void displayTaskDone();
 
  template<class T>
  static void displayResult(const std::string& text, const T& result)
  {
    displayMessage(TextTools::resizeRight(text, static_cast<size_t>(static_cast<float>(terminalWidth) * terminalSplit - 1), '.') + ": " + TextTools::toString<T>(result));
  }
 
  static void displayBooleanResult(const std::string& text, bool result)
  {
    displayResult(text, result ? std::string("yes") : std::string("no"));
  }
 
  static void displayGauge(size_t iter, size_t total, char symbol = '>', const std::string& mes = "");
 
  static void displayUnlimitedGauge(size_t iter, const std::string& mes = "");
 
 
  static void startTimer()
  {
    time(&startTime);
  }
 
  static void displayTime(const std::string& msg);
 
  static double getTime();
};
} // end of namespace bpp.
#endif // BPP_APP_APPLICATIONTOOLS_H