Ewan Birney

NAME

Bio::Location::Simple - Implementation of a Simple Location on a Sequence

SYNOPSIS

    use Bio::Location::Simple;

    my $location = new Bio::Location::Simple(-start => 1, -end => 100,
                                             -strand => 1 );

    if( $location->strand == -1 ) {
        printf "complement(%d..%d)\n", $location->start, $location->end;
    } else {
        printf "%d..%d\n", $location->start, $location->end;
    }

DESCRIPTION

This is an implementation of Bio::LocationI to manage simple location information on a Sequence.

FEEDBACK

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org             - General discussion
  http://bio.perl.org/MailList.html - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Jason Stajich

Email jason@chg.mc.duke.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

start

  Title   : start
  Usage   : $start = $loc->start();
  Function: get/set the start of this range
  Returns : the start of this range
  Args    : optionaly allows the start to be set
          : using $loc->start($start)

end

  Title   : end
  Usage   : $end = $loc->end();
  Function: get/set the end of this range
  Returns : the end of this range
  Args    : optionaly allows the end to be set
          : using $loc->end($start)

strand

  Title   : strand
  Usage   : $strand = $loc->strand();
  Function: get/set the strand of this range
  Returns : the strandidness (-1, 0, +1)
  Args    : optionaly allows the strand to be set
          : using $loc->strand($strand)

length

 Title   : length
 Usage   : $len = $loc->length();
 Function: get the length in the coordinate space this location spans
 Example :
 Returns : an integer
 Args    : none

min_start

  Title   : min_start
  Usage   : my $minstart = $location->min_start();
  Function: Get minimum starting location of feature startpoint   
  Returns : integer or undef if no minimum starting point.
  Args    : none

max_start

  Title   : max_start
  Usage   : my $maxstart = $location->max_start();
  Function: Get maximum starting location of feature startpoint.

            In this implementation this is exactly the same as min_start().

  Returns : integer or undef if no maximum starting point.
  Args    : none

start_pos_type

  Title   : start_pos_type
  Usage   : my $start_pos_type = $location->start_pos_type();
  Function: Get start position type (ie <,>, ^).

            In this implementation this will always be 'EXACT'.

  Returns : type of position coded as text 
            ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
  Args    : none

min_end

  Title   : min_end
  Usage   : my $minend = $location->min_end();
  Function: Get minimum ending location of feature endpoint 
  Returns : integer or undef if no minimum ending point.
  Args    : none

max_end

  Title   : max_end
  Usage   : my $maxend = $location->max_end();
  Function: Get maximum ending location of feature endpoint 

            In this implementation this is exactly the same as min_end().

  Returns : integer or undef if no maximum ending point.
  Args    : none

end_pos_type

  Title   : end_pos_type
  Usage   : my $end_pos_type = $location->end_pos_type();
  Function: Get end position type (ie <,>, ^) 

            In this implementation this will always be 'EXACT'.

  Returns : type of position coded as text 
            ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
  Args    : none

location_type

  Title   : location_type
  Usage   : my $location_type = $location->location_type();
  Function: Get location type encoded as text
  Returns : string ('EXACT', 'WITHIN', 'BETWEEN')
  Args    : none

is_remote

 Title   : is_remote
 Usage   : $self->is_remote($newval)
 Function: Getset for is_remote value
 Returns : value of is_remote
 Args    : newvalue (optional)

to_FTstring

  Title   : to_FTstring
  Usage   : my $locstr = $location->to_FTstring()
  Function: returns the FeatureTable string of this location
  Returns : string
  Args    : none