text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry               
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2013.
  // 
  // This software is released under a three-clause BSD license:
  //  * Redistributions of source code must retain the above copyright
  //    notice, this list of conditions and the following disclaimer.
  //  * Redistributions in binary form must reproduce the above copyright
  //    notice, this list of conditions and the following disclaimer in the
  //    documentation and/or other materials provided with the distribution.
  //  * Neither the name of any author or any participating institution 
  //    may be used to endorse or promote products derived from this software 
  //    without specific prior written permission.
  // For a full list of authors, refer to the file AUTHORS. 
  // --------------------------------------------------------------------------
  // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
  // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING 
  // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 
  // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 
  // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; 
  // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
  // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR 
  // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF 
  // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  // 
  // --------------------------------------------------------------------------
  // $Maintainer: Stephan Aiche $
  // $Authors: Stephan Aiche $
  // --------------------------------------------------------------------------
  
  #include <OpenMS/CONCEPT/ClassTest.h>
  #include <OpenMS/test_config.h>
  
  ///////////////////////////
  #include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabet.h>
  #include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabetTextParser.h>
  ///////////////////////////
  
  using namespace OpenMS;
  using namespace ims;
  using namespace std;
  
  class IMSAlphabetParserImpl
      : public IMSAlphabetParser<>
  {
  private:
    ContainerType elements_;
  public:
    virtual ContainerType& getElements()
    {
      return elements_;
    }
  
    virtual void parse(std::istream& )
    {
      // ignore istream, just enter something into the map
      elements_.insert(std::make_pair("hydrogen", 1.0));
      elements_.insert(std::make_pair("oxygen", 16.0));
    }
  };
  
  
  START_TEST(IMSAlphabet, "$Id$")
  
  /////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////
  
  IMSElement hydrogen("hydrogen", 1.0);
  IMSElement oxygen("oxygen", 16.0);
  IMSElement nitrogen("nitrogen", 14.0);
  
  vector<IMSElement> elements;
  elements.push_back(hydrogen);
  elements.push_back(oxygen);
  elements.push_back(nitrogen);
  
  DoubleReal carbon_mass = 12.0;
  IMSElement carbon("carbon", carbon_mass);
  
  IMSAlphabet* ptr = 0;
  IMSAlphabet* null_ptr = 0;
  START_SECTION(IMSAlphabet())
  {
    ptr = new IMSAlphabet();
    TEST_NOT_EQUAL(ptr, null_ptr)
  }
  END_SECTION
  
  START_SECTION(~IMSAlphabet())
  {
    delete ptr;
  }
  END_SECTION
  
  START_SECTION((IMSAlphabet(const container &elements)))
  {
    ptr = new IMSAlphabet(elements);
    TEST_NOT_EQUAL(ptr, null_ptr)
  
    TEST_EQUAL(ptr->size(), 3)
    TEST_EQUAL(ptr->getName(0), "hydrogen")
  
    delete ptr;
  }
  END_SECTION
  
  // test instance for the following tests
  IMSAlphabet alphabet(elements);
  
  START_SECTION((IMSAlphabet(const IMSAlphabet &alphabet)))
  {
    IMSAlphabet alphabet_copy(alphabet);
  
    TEST_EQUAL(alphabet_copy.size(), 3)
    TEST_EQUAL(alphabet_copy.getName(0), "hydrogen")
  }
  END_SECTION
  
  START_SECTION((const element_type& getElement(const name_type &name) const ))
  {
    TEST_EQUAL(alphabet.getElement("hydrogen"), hydrogen)
    TEST_EQUAL(alphabet.getElement("oxygen"), oxygen)
    TEST_EQUAL(alphabet.getElement("nitrogen"), nitrogen)
  }
  END_SECTION
  
  START_SECTION((const element_type& getElement(size_type index) const ))
  {
    TEST_EQUAL(alphabet.getElement(0), hydrogen)
    TEST_EQUAL(alphabet.getElement(1), oxygen)
    TEST_EQUAL(alphabet.getElement(2), nitrogen)
  
    TEST_EXCEPTION(Exception::InvalidValue, alphabet.getElement("nitrogen2"))
  }
  END_SECTION
  
  START_SECTION((void setElement(const name_type &name, mass_type mass, bool forced=false)))
  {
    IMSAlphabet alphabet_copy(alphabet);
  
    alphabet_copy.setElement("hydrogen", 2.0, false);
    TEST_EQUAL(alphabet_copy.size(), 3)
    TEST_EQUAL(alphabet_copy.getMass("hydrogen"), 2.0)
  
    // this should not change the alphabet, since there is no
    // element named carbon
    alphabet_copy.setElement("carbon", carbon_mass, false);
    TEST_EQUAL(alphabet_copy.size(), 3)
  
    alphabet_copy.setElement("carbon", carbon_mass, true);
    TEST_EQUAL(alphabet_copy.size(), 4)
    TEST_EQUAL(alphabet_copy.getMass("carbon"), 12)
  }
  END_SECTION
  
  START_SECTION((const name_type& getName(size_type index) const ))
  {
    TEST_STRING_EQUAL(alphabet.getName(0),"hydrogen")
    TEST_STRING_EQUAL(alphabet.getName(1),"oxygen")
    TEST_STRING_EQUAL(alphabet.getName(2),"nitrogen")
  }
  END_SECTION
  
  START_SECTION((mass_type getMass(const name_type &name) const ))
  {
    TEST_EQUAL(alphabet.getMass("hydrogen"), hydrogen.getMass())
    TEST_EQUAL(alphabet.getMass("oxygen"), oxygen.getMass())
    TEST_EQUAL(alphabet.getMass("nitrogen"), nitrogen.getMass())
  
    TEST_EXCEPTION(Exception::InvalidValue, alphabet.getMass("nitrogen2"))
  }
  END_SECTION
  
  START_SECTION((mass_type getMass(size_type index) const ))
  {
    TEST_EQUAL(alphabet.getMass(0), hydrogen.getMass())
    TEST_EQUAL(alphabet.getMass(1), oxygen.getMass())
    TEST_EQUAL(alphabet.getMass(2), nitrogen.getMass())
  }
  END_SECTION
  
  START_SECTION((masses_type getMasses(size_type isotope_index=0) const ))
  {
    IMSAlphabet::masses_type masses = alphabet.getMasses();
    TEST_EQUAL(masses.size(), 3)
    ABORT_IF(masses.size() != 3)
  
    TEST_EQUAL(masses[0], hydrogen.getMass())
    TEST_EQUAL(masses[1], oxygen.getMass())
    TEST_EQUAL(masses[2], nitrogen.getMass())
  }
  END_SECTION
  
  START_SECTION((masses_type getAverageMasses() const ))
  {
    IMSAlphabet::masses_type average_masses = alphabet.getAverageMasses();
  
    TEST_EQUAL(average_masses.size(), 3)
    ABORT_IF(average_masses.size() != 3)
  
    TEST_EQUAL(average_masses[0], hydrogen.getAverageMass())
    TEST_EQUAL(average_masses[1], oxygen.getAverageMass())
    TEST_EQUAL(average_masses[2], nitrogen.getAverageMass())
  }
  END_SECTION
  
  START_SECTION((bool hasName(const name_type &name) const ))
  {
    TEST_EQUAL(alphabet.hasName("nitrogen"), true)
    TEST_EQUAL(alphabet.hasName("oxygen"), true)
    TEST_EQUAL(alphabet.hasName("oxygen2"), false)
  }
  END_SECTION
  
  START_SECTION((void push_back(const name_type &name, mass_type value)))
  {
    IMSAlphabet alphabet_copy(alphabet);
    alphabet_copy.push_back("carbon", carbon_mass);
    TEST_EQUAL(alphabet_copy.size(), 4)
    ABORT_IF(alphabet_copy.size() != 4)
  
    TEST_EQUAL(alphabet_copy.getElement(3).getName(), "carbon")
    TEST_EQUAL(alphabet_copy.hasName("carbon"),true)
    TEST_EQUAL(alphabet_copy.getMass(3), carbon_mass)
  }
  END_SECTION
  
  START_SECTION((void push_back(const element_type &element)))
  {
    IMSAlphabet alphabet_copy(alphabet);
    alphabet_copy.push_back(carbon);
    TEST_EQUAL(alphabet_copy.size(), 4)
    ABORT_IF(alphabet_copy.size() != 4)
  
    TEST_EQUAL(alphabet_copy.getElement(3).getName(), "carbon")
    TEST_EQUAL(alphabet_copy.hasName("carbon"),true)
    TEST_EQUAL(alphabet_copy.getMass(3), carbon.getMass())
  }
  END_SECTION
  
  START_SECTION((void clear()))
  {
    IMSAlphabet alphabet_copy(alphabet);
    alphabet_copy.clear();
    TEST_EQUAL(alphabet_copy.size(), 0)
    TEST_EQUAL(alphabet_copy.hasName("oxygen"), false)
  }
  END_SECTION
  
  START_SECTION((virtual void sortByNames()))
  {
    IMSAlphabet alphabet_copy(alphabet);
    alphabet_copy.sortByNames();
    TEST_EQUAL(alphabet_copy.size(), 3)
    TEST_EQUAL(alphabet_copy.getElement(0), hydrogen)
    TEST_EQUAL(alphabet_copy.getElement(1), nitrogen)
    TEST_EQUAL(alphabet_copy.getElement(2), oxygen)
  }
  END_SECTION
  
  START_SECTION((virtual void sortByValues()))
  {
    IMSAlphabet alphabet_copy(alphabet);
    alphabet_copy.push_back(carbon);
    alphabet_copy.sortByValues();
    TEST_EQUAL(alphabet_copy.size(), 4)
    TEST_EQUAL(alphabet_copy.getElement(0), hydrogen)
    TEST_EQUAL(alphabet_copy.getElement(1), carbon)
    TEST_EQUAL(alphabet_copy.getElement(2), nitrogen)
    TEST_EQUAL(alphabet_copy.getElement(3), oxygen)
  }
  END_SECTION
  
  START_SECTION((virtual void load(const std::string &fname)))
  {
    NOT_TESTABLE // will be tested in virtual void load(const std::string &fname, IMSAlphabetParser<> *parser)
  }
  END_SECTION
  
  START_SECTION((virtual void load(const std::string &fname, IMSAlphabetParser<> *parser)))
  {
    IMSAlphabet load_copy(alphabet);
    TEST_EQUAL(load_copy.size(), 3)
  
    TEST_EXCEPTION(Exception::IOException, load_copy.load(""))
  
    // this should not clear the alphabet
    TEST_EQUAL(load_copy.size(), 3)
  
    // create file with minimal content
    String filename;
    NEW_TMP_FILE(filename)
  
    // just create the file
    ofstream of;
    of.open(filename.c_str());
    of << "# a comment which should be ignored" << std::endl;
    of << "hydrogen\t1.0" << std::endl;
    of << "oxygen\t16.0" << std::endl;
    of << "nitrogen\t14.0" << std::endl;
    of.close();
  
    load_copy.load(filename, new IMSAlphabetTextParser);
  
    TEST_EQUAL(load_copy.size(), 3)
    TEST_EQUAL(load_copy.hasName("hydrogen"), true)
    TEST_REAL_SIMILAR(load_copy.getMass("hydrogen"), 1.0)
    TEST_EQUAL(load_copy.hasName("nitrogen"), true)
    TEST_REAL_SIMILAR(load_copy.getMass("nitrogen"), 14.0)
    TEST_EQUAL(load_copy.hasName("oxygen"), true)
    TEST_REAL_SIMILAR(load_copy.getMass("oxygen"), 16.0)
  }
  END_SECTION
  
  START_SECTION((size_type size() const ))
  {
    TEST_EQUAL(alphabet.size(),3)
  
    IMSAlphabet alphabet_copy(alphabet);
    TEST_EQUAL(alphabet_copy.size(),3)
  
    alphabet_copy.push_back(carbon);
    TEST_EQUAL(alphabet_copy.size(), 4)
  }
  END_SECTION
  
  START_SECTION((bool erase(const name_type &name)))
  {
    IMSAlphabet alphabet_copy(alphabet);
    TEST_EQUAL(alphabet_copy.size(),3)
  
    TEST_EQUAL(alphabet_copy.erase("hydrogen"), true)
    TEST_EQUAL(alphabet_copy.size(),2)
    TEST_EQUAL(alphabet_copy.erase("hydrogen"), false)
  
    TEST_EQUAL(alphabet_copy.erase("oxygen"), true)
    TEST_EQUAL(alphabet_copy.size(),1)
  
    TEST_EQUAL(alphabet_copy.erase("nitrogen"), true)
    TEST_EQUAL(alphabet_copy.size(),0)
  }
  END_SECTION
  
  
  /////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////
  END_TEST
  
  
  
  