DelimitedTextOccurrences.cpp

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#include <openmodeller/occ_io/DelimitedTextOccurrences.hh>

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

#include <vector>
using std::vector;

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

// Win32 defines
#ifdef WIN32
#include <fcntl.h>
#include <io.h>
#define strcasecmp _stricmp

#define open  _open
#define close _close
#define fdopen  _fdopen

#else
#include <fcntl.h>
#include <unistd.h>
#endif

/*****************************************/
/*** create OccurrencesReader callback ***/
OccurrencesReader * 
DelimitedTextOccurrences::CreateOccurrencesReaderCallback( const char *source, const char *coordSystem )
{
  return new DelimitedTextOccurrences( source, coordSystem );
}


/*******************/
/*** Constructor ***/
DelimitedTextOccurrences::DelimitedTextOccurrences( const char *source, const char *coordSystem )
{
  _source = (char *) source; // should be a file name

  _coord_system = (char *) coordSystem;

  _loaded = false;
}


/******************/
/*** Destructor ***/
DelimitedTextOccurrences::~DelimitedTextOccurrences()
{
}


/***********************/
/*** load Ocurrences ***/
bool
DelimitedTextOccurrences::load()
{
  if ( _loaded ) {

    return true;
  }

  // Opens the input file.
  FILE *file = fopen( _source, "r" );

  if ( ! file ) {

    Log::instance()->error( "Can't open file %s.\n", _source );
    return false;
  }

  Log::instance()->debug( "Reading occurrences from file %s.\n", _source );

  // Fixme: read this from file.
  Scalar error      = -1.0;
  int    num_attributes = 0;
  Scalar *attributes    = 0;

  // Columns to be read.
  char id[100];
  char label[150];
  double x, y;
  int abundance;

  // Read all occurrences line by line inserting into the
  // appropriate object.
  const int line_len = 600;
  char line[line_len];
  char *pos;

  while ( fgets( line, line_len, file ) ) {

    // Remove \r that DOS loves to use.
    pos = strchr( line, '\r' );

    if ( pos ) {

      *pos = '\0';
    }

    if ( *line != '#' && sscanf( line, "%[^\t] %[^\t] %lf %lf %u", id, label, &x, &y, &abundance ) == 5 ) {

      Coord lg = Coord( x );
      Coord lt = Coord( y );

      _addOccurrence( id, label, lg, lt, error, (Scalar)abundance, num_attributes, attributes );
    }
    else if ( *line != '#' && sscanf( line, "%[^\t] %[^\t] %lf %lf", id, label, &x, &y ) == 4 ) {

      // When no abundance is provided, assume 1 (single presence)

      Coord lg = Coord( x );
      Coord lt = Coord( y );

      _addOccurrence( id, label, lg, lt, error, 1.0, num_attributes, attributes );
    }
    else if ( *line != '#' && sscanf( line, "%[^,],%[^,],%lf,%lf,%u", id, label, &x, &y, &abundance ) == 5 ) {

      Coord lg = Coord( x );
      Coord lt = Coord( y );

      _addOccurrence( id, label, lg, lt, error, (Scalar)abundance, num_attributes, attributes );
    }
    else if ( *line != '#' && sscanf( line, "%[^,],%[^,],%lf,%lf", id, label, &x, &y ) == 4 ) {

      // When no abundance is provided, assume 1 (single presence)

      Coord lg = Coord( x );
      Coord lt = Coord( y );

      _addOccurrence( id, label, lg, lt, error, 1.0, num_attributes, attributes );
    }
    else {

      Log::instance()->debug( "Skipping line: %s", line );
    }
  }

  fclose( file );

  _loaded = true;

  return true;
}