pappso::specpeptidoms::LocationSaver Class Reference

#include <locationsaver.h>

Public Member Functions
	LocationSaver ()
	~LocationSaver ()
void	addLocation (std::size_t beginning, std::size_t length, int tree, int score, const SpOMSProtein *protein_ptr)
	Adds a location to the locations heap. If a saved location has the same tree_id, it will replace it. Otherwise, it replaces the location with the lowest score.
std::vector< Location >	getLocations () const
	Returns a vector containing the saved locations.
std::size_t	getNextTree ()
	Creates a new alignment tree and returns its id.
int	getMinScore (int tree_id) const
	Returns the minimum score for a location with the provided tree_id to be saved in the heap.
void	resetLocationSaver ()

Static Private Member Functions
static bool	locationCompare (const Location &loc1, const Location &loc2)

Private Attributes
std::vector< Location >	m_locations_heap
std::vector< int >	m_tree_scores
std::vector< bool >	m_tree_in_heap

Detailed Description

Definition at line 78 of file locationsaver.h.

Constructor & Destructor Documentation

LocationSaver()

pappso::specpeptidoms::LocationSaver::LocationSaver

(

)

Constructor

Definition at line 59 of file locationsaver.cpp.

{
  Location location_zero;
  location_zero.beginning  = 0;
  location_zero.length     = 0;
  location_zero.proteinPtr = nullptr;
  location_zero.score      = MIN_ALIGNMENT_SCORE;
  location_zero.tree       = -1;
 
  m_locations_heap.resize(MAX_SAVED_ALIGNMENTS, location_zero);
  // std::make_heap(m_locations_heap.begin(), m_locations_heap.end(),
  // LocationSaver::locationCompare); ?
  // m_tree_scores.reserve ?
}

References pappso::specpeptidoms::Location::beginning, pappso::specpeptidoms::Location::length, m_locations_heap, pappso::specpeptidoms::MAX_SAVED_ALIGNMENTS(), pappso::specpeptidoms::MIN_ALIGNMENT_SCORE(), pappso::specpeptidoms::Location::proteinPtr, pappso::specpeptidoms::Location::score, and pappso::specpeptidoms::Location::tree.

~LocationSaver()

pappso::specpeptidoms::LocationSaver::~LocationSaver

(

)

Destructor

Definition at line 181 of file locationsaver.cpp.

{
}

Member Function Documentation

addLocation()

void pappso::specpeptidoms::LocationSaver::addLocation	(	std::size_t	beginning,
		std::size_t	length,
		int	tree,
		int	score,
		const SpOMSProtein *	protein_ptr )

Adds a location to the locations heap. If a saved location has the same tree_id, it will replace it. Otherwise, it replaces the location with the lowest score.

Definition at line 82 of file locationsaver.cpp.

{
  try
    {
      m_tree_scores.at(tree) = score;
      if(m_tree_in_heap.at(tree))
        {
          for(std::vector<Location>::iterator iter = m_locations_heap.begin();
              iter != m_locations_heap.end();
              iter++)
            {
              if(iter->tree == tree)
                {
                  iter->score  = score;
                  iter->length = length;
                }
            }
          std::make_heap(
            m_locations_heap.begin(), m_locations_heap.end(), LocationSaver::locationCompare);
        }
      else
        {
          if(m_locations_heap.begin()->tree >= 0)
            {
              m_tree_in_heap.at(m_locations_heap.begin()->tree) = false;
            }
          m_tree_in_heap.at(tree) = true;
          std::pop_heap(
            m_locations_heap.begin(), m_locations_heap.end(), LocationSaver::locationCompare);
          m_locations_heap.pop_back();
          m_locations_heap.push_back({beginning, length, tree, score, protein_ptr});
          std::push_heap(
            m_locations_heap.begin(), m_locations_heap.end(), LocationSaver::locationCompare);
        }
    }
  catch(const std::exception &error)
    {
      throw pappso::PappsoException(
        QObject::tr("addLocation failed std::exception :\n%1").arg(error.what()));
    }
}

References locationCompare(), m_locations_heap, m_tree_in_heap, and m_tree_scores.

getLocations()

std::vector< pappso::specpeptidoms::Location > pappso::specpeptidoms::LocationSaver::getLocations

(

)

const

Returns a vector containing the saved locations.

Returns

vector of Location of size MAX_SAVED_ALIGNMENTS

Definition at line 126 of file locationsaver.cpp.

{
  std::vector<Location> locations;
  locations.reserve(m_locations_heap.size());
  for(std::vector<Location>::const_iterator iter = m_locations_heap.begin();
      iter != m_locations_heap.end();
      iter++)
    {
      if(iter->tree >= 0)
        {
          locations.push_back(*iter);
        }
    }
  return locations;
}

References m_locations_heap.

Referenced by pappso::cbor::psm::PsmSpecPeptidOmsScan::sequenceAlignment().

getMinScore()

int pappso::specpeptidoms::LocationSaver::getMinScore

(

int

tree_id

)

const

Returns the minimum score for a location with the provided tree_id to be saved in the heap.

Definition at line 151 of file locationsaver.cpp.

{
  if(m_tree_scores.size() == 0)
    {
      return m_locations_heap.begin()->score;
    }
  else
    {
      if(tree_id > (int)m_tree_scores.size())
        {
 
          throw pappso::ExceptionOutOfRange(
            QObject::tr("LocationSaver::getMinScore failed :\nout of "
                        "range access %1 with m_tree_scores.size() %2")
              .arg(tree_id)
              .arg(m_tree_scores.size()));
        }
 
      /*To be stored, an alignment's score must be higher than: its tree's current score, the
       * current worse stored alignment's score and a score that depends of the current best
       * alignment's score
       */
      return std::max(
        m_tree_scores.at(tree_id),
        std::max(m_locations_heap.begin()->score,
                 (int)std::ceil(ALIGNMENT_FILTER *
                                *(std::max_element(m_tree_scores.begin(), m_tree_scores.end())))));
    }
}

References pappso::specpeptidoms::ALIGNMENT_FILTER(), m_locations_heap, and m_tree_scores.

getNextTree()

std::size_t pappso::specpeptidoms::LocationSaver::getNextTree

(

)

Creates a new alignment tree and returns its id.

Definition at line 143 of file locationsaver.cpp.

{
  m_tree_scores.push_back(MIN_ALIGNMENT_SCORE);
  m_tree_in_heap.push_back(false);
  return m_tree_scores.size() - 1;
}

References m_tree_in_heap, m_tree_scores, and pappso::specpeptidoms::MIN_ALIGNMENT_SCORE().

locationCompare()

bool pappso::specpeptidoms::LocationSaver::locationCompare ( const Location & loc1, const Location & loc2 )

staticprivate

Definition at line 75 of file locationsaver.cpp.

{
  return loc1.score > loc2.score;
}

References pappso::specpeptidoms::Location::score.

Referenced by addLocation().

resetLocationSaver()

void pappso::specpeptidoms::LocationSaver::resetLocationSaver

(

)

Definition at line 186 of file locationsaver.cpp.

{
  Location location_zero;
  location_zero.beginning  = 0;
  location_zero.length     = 0;
  location_zero.proteinPtr = nullptr;
  location_zero.score      = MIN_ALIGNMENT_SCORE;
  location_zero.tree       = -1;
 
  std::fill(m_locations_heap.begin(), m_locations_heap.end(), location_zero);
  m_tree_scores.clear();
  m_tree_in_heap.clear();
 
 
  // int m_min_score, m_max_score;
}

References pappso::specpeptidoms::Location::beginning, pappso::specpeptidoms::Location::length, m_locations_heap, m_tree_in_heap, m_tree_scores, pappso::specpeptidoms::MIN_ALIGNMENT_SCORE(), pappso::specpeptidoms::Location::proteinPtr, pappso::specpeptidoms::Location::score, and pappso::specpeptidoms::Location::tree.

Member Data Documentation

m_locations_heap

std::vector<Location> pappso::specpeptidoms::LocationSaver::m_locations_heap

private

Definition at line 123 of file locationsaver.h.

Referenced by LocationSaver(), addLocation(), getLocations(), getMinScore(), and resetLocationSaver().

m_tree_in_heap

std::vector<bool> pappso::specpeptidoms::LocationSaver::m_tree_in_heap

private

Definition at line 125 of file locationsaver.h.

Referenced by addLocation(), getNextTree(), and resetLocationSaver().

m_tree_scores

std::vector<int> pappso::specpeptidoms::LocationSaver::m_tree_scores

private

Definition at line 124 of file locationsaver.h.

Referenced by addLocation(), getMinScore(), getNextTree(), and resetLocationSaver().

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The documentation for this class was generated from the following files:

• pappsomspp/core/processing/specpeptidoms/locationsaver.h
• pappsomspp/core/processing/specpeptidoms/locationsaver.cpp