#include <scenario.h>

Public Member Functions
	Scenario ()
	~Scenario ()
void	saveOrigin (std::size_t current_row, std::size_t current_column, std::size_t previous_row, std::size_t previous_column, int score, AlignType alignment_type)
	Stores the origin (cell location and alignment type) of the provided cell in the backtracking matrix.
void	reserve (std::size_t n_rows, std::size_t n_columns)
	Allocate new storage to the backtracking matrix if needed.
std::pair< std::vector< ScenarioCell >, int >	getBestAlignment () const
	Returns the scenario cells corresponding to the best alignment and the best alignment's score.
int	getBestScore () const
void	resetScenario ()
void	clear ()

Private Attributes
std::vector< std::vector< ScenarioCell > >	m_origin_matrix
std::pair< ScenarioCell, int >	m_best_alignment = {{0, 0, AlignType::init}, -15}

Detailed Description

Definition at line 55 of file scenario.h.

Constructor & Destructor Documentation

◆ Scenario()

pappso::specpeptidoms::Scenario::Scenario ( )

Constructor

Definition at line 75 of file scenario.cpp.

76{

77}

◆ ~Scenario()

pappso::specpeptidoms::Scenario::~Scenario ( )

Destructor

Definition at line 79 of file scenario.cpp.

80{

81}

Member Function Documentation

◆ clear()

void pappso::specpeptidoms::Scenario::clear ( )

Definition at line 120 of file scenario.cpp.

{
  m_origin_matrix.clear();
  m_best_alignment = {{0, 0, AlignType::init}, -15};
}

References pappso::specpeptidoms::init, m_best_alignment, and m_origin_matrix.

◆ getBestAlignment()

std::pair< std::vector< pappso::specpeptidoms::ScenarioCell >, int > pappso::specpeptidoms::Scenario::getBestAlignment ( ) const

Returns the scenario cells corresponding to the best alignment and the best alignment's score.

Definition at line 91 of file scenario.cpp.

{
  std::pair<std::vector<ScenarioCell>, int> best_alignment;
  ScenarioCell current_cell   = m_best_alignment.first;
  current_cell.alignment_type = AlignType::init;
  while(current_cell.previous_column > 0 && current_cell.previous_row > 0)
    {
      best_alignment.first.push_back(current_cell);
      current_cell = m_origin_matrix.at(current_cell.previous_row).at(current_cell.previous_column);
    }
  best_alignment.first.push_back(current_cell);
  best_alignment.second = m_best_alignment.second;
  return best_alignment;
}

References pappso::specpeptidoms::ScenarioCell::alignment_type, pappso::specpeptidoms::init, m_best_alignment, m_origin_matrix, pappso::specpeptidoms::ScenarioCell::previous_column, and pappso::specpeptidoms::ScenarioCell::previous_row.

◆ getBestScore()

int pappso::specpeptidoms::Scenario::getBestScore ( ) const

Definition at line 107 of file scenario.cpp.

{
  return m_best_alignment.second;
}

References m_best_alignment.

◆ reserve()

void pappso::specpeptidoms::Scenario::reserve	(	std::size_t	n_rows,
		std::size_t	n_columns )

Allocate new storage to the backtracking matrix if needed.

Definition at line 84 of file scenario.cpp.

{
  m_origin_matrix = std::vector<std::vector<ScenarioCell>>(
    n_rows, std::vector<ScenarioCell>(n_columns, {0, 0, AlignType::init}));
}

References pappso::specpeptidoms::init, and m_origin_matrix.

◆ resetScenario()

void pappso::specpeptidoms::Scenario::resetScenario ( )

Definition at line 113 of file scenario.cpp.

{
  // m_origin_matrix.clear();
  m_best_alignment = {{0, 0, AlignType::init}, -15};
}

References pappso::specpeptidoms::init, and m_best_alignment.

◆ saveOrigin()

void pappso::specpeptidoms::Scenario::saveOrigin	(	std::size_t	current_row,
		std::size_t	current_column,
		std::size_t	previous_row,
		std::size_t	previous_column,
		int	score,
		AlignType	alignment_type )

Stores the origin (cell location and alignment type) of the provided cell in the backtracking matrix.

Definition at line 42 of file scenario.cpp.

{
  if(score > m_best_alignment.second)
    {
      m_best_alignment = {{current_row, current_column, alignment_type}, score};
    }
  try
    {
      m_origin_matrix.at(current_row).at(current_column) = {
        previous_row, previous_column, alignment_type};
    }
  catch(const std::exception &error)
    {
      int max_column_size = 0;
      if(current_row < m_origin_matrix.size())
        {
          max_column_size = m_origin_matrix.at(current_row).size();
        }
      throw pappso::ExceptionOutOfRange(
        QObject::tr(
          "Scenario::saveOrigin failed for current_row %1 (size %2)  current_column %3 (size %4)")
          .arg(current_row)
          .arg(m_origin_matrix.size())
          .arg(current_column)
          .arg(max_column_size));
    }
}

References m_best_alignment, and m_origin_matrix.

Member Data Documentation

◆ m_best_alignment

std::pair<ScenarioCell, int> pappso::specpeptidoms::Scenario::m_best_alignment = {{0, 0, AlignType::init}, -15}

private

Definition at line 98 of file scenario.h.

98{{0, 0, AlignType::init}, -15};

Referenced by clear(), getBestAlignment(), getBestScore(), resetScenario(), and saveOrigin().

◆ m_origin_matrix

std::vector<std::vector<ScenarioCell> > pappso::specpeptidoms::Scenario::m_origin_matrix