OccurrencesReader.cpp

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#include <openmodeller/occ_io/OccurrencesReader.hh>
#include <openmodeller/Occurrences.hh>  // List of occurrences.

#include <vector>
using std::vector;

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

/*********************/
/*** get Presences ***/
OccurrencesPtr
OccurrencesReader::getPresences( const char *groupId )
{
  // If group was not specified, return empty set
  if ( ! groupId ) {

    return new OccurrencesImpl( 1 );
  }

  LstOccurrences::iterator ocs = _presences.begin();
  LstOccurrences::iterator end = _presences.end();

  while ( ocs != end ) {

    OccurrencesPtr oc = *ocs;

    if ( ! strcasecmp( groupId, oc->label() ) ) {

      _presences.erase( ocs );

      return oc;
    }

    ++ocs;
  }

  return new OccurrencesImpl( 1 );
}


/********************/
/*** get Absences ***/
OccurrencesPtr
OccurrencesReader::getAbsences( const char *groupId )
{
  // If group was not specified, return empty set
  if ( ! groupId ) {

    return new OccurrencesImpl( 0 );
  }

  LstOccurrences::iterator ocs = _absences.begin();
  LstOccurrences::iterator end = _absences.end();

  while ( ocs != end ) {

    OccurrencesPtr oc = *ocs;

    if ( ! strcasecmp( groupId, oc->label() ) ) {

      _absences.erase( ocs );

      return oc;
    }

    ++ocs;
  }

  return new OccurrencesImpl( 0 );
}


/*************/
/*** print ***/
void
OccurrencesReader::printOccurrences( const std::string& msg )
{
  printf( "%s", msg.c_str() );

  printf( "\nPresences" );

  LstOccurrences::const_iterator ocs = _presences.begin();
  LstOccurrences::const_iterator end = _presences.end();

  while ( ocs != end ) {

    (*ocs)->dump( "\n****************" );
    ++ocs;
  }

  printf( "\nAbsences" );

  ocs = _absences.begin();
  end = _absences.end();

  while ( ocs != end ) {

    (*ocs)->dump( "\n****************" );
    ++ocs;
  }
}

/**********************/
/*** add Occurrence ***/
int
OccurrencesReader::_addOccurrence( const char *id, const char *groupId, Coord lg, Coord lt,
                                   Scalar error, Scalar abundance,
                                   int num_attributes, Scalar *attributes )
{
  if ( abundance > 0 ) {

    _addPresence( id, groupId, lg, lt, error, abundance, num_attributes, attributes );
  }
  else {

    _addAbsence( id, groupId, lg, lt, error, num_attributes, attributes );
  }

  return 1;
}

/********************/
/*** add Presence ***/
int
OccurrencesReader::_addPresence( const char *id, const char *groupId, Coord lg, Coord lt,
                                 Scalar error, Scalar abundance,
                                 int num_attributes, Scalar *attributes )
{
  // If a presence group with the same name already exists, 
  // just add another occurrence to it.

  // We search backwards because new Occurrences are pushed
  // onto the back, so most likely, the Occurrences we are looking
  // for is at the back.
  LstOccurrences::const_reverse_iterator ocs = _presences.rbegin();
  LstOccurrences::const_reverse_iterator end = _presences.rend();
  while ( ocs != end ) {

    OccurrencesPtr const & group = *ocs;

    if ( ! strcasecmp( group->label(), groupId ) ) {

      group->createOccurrence( id, lg, lt, error, abundance, num_attributes, attributes );
      return 0;
    }

    ++ocs;
  }

  // If the occurrences group does not exist, create it.
  OccurrencesImpl *newgroup = new OccurrencesImpl( groupId, _coord_system );
  newgroup->createOccurrence( id, lg, lt, error, abundance, num_attributes, attributes );
  _presences.push_back( newgroup );

  return 1;
}

/*******************/
/*** add Absence ***/
int
OccurrencesReader::_addAbsence( const char *id, const char *groupId, Coord lg, Coord lt,
                                Scalar error, int num_attributes, Scalar *attributes )
{
  // If an absence group with the same name already exists, 
  // just add another occurrence to it.

  // We search backwards because new Occurrences are pushed
  // onto the back, so most likely, the Occurrences we are looking
  // for is at the back.
  LstOccurrences::const_reverse_iterator ocs = _absences.rbegin();
  LstOccurrences::const_reverse_iterator end = _absences.rend();
  while ( ocs != end ) {

      OccurrencesPtr const & group = *ocs;

      if ( ! strcasecmp( group->label(), groupId ) ) {

        group->createOccurrence( id, lg, lt, error, 0.0, num_attributes, attributes );
        return 0;
      }

      ++ocs;
  }

  // If the occurrences group does not exist, create it.
  OccurrencesImpl *newgroup = new OccurrencesImpl( groupId, _coord_system );
  newgroup->createOccurrence( id, lg, lt, error, 0.0, num_attributes, attributes );
  _absences.push_back( newgroup );

  return 1;
}