Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::Location::Simple.3pm

NAME

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

SYNOPSIS

     use Bio::Location::Simple;
 
     my $location = Bio::Location::Simple->new(-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 exact location information on a Sequence: '22' or '12..15' or '16^17'.

You can test the type of the location using length() function () or directly location_type() which can one of two values: 'EXACT' or 'IN-BETWEEN'.

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://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

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)
   Note    : If start is set but end is undefined, this now assumes that start
                     is the same as end but throws a warning (i.e. it assumes this is
                         a possible error). If start is undefined, this now throws an
                         exception.
 
 

strand

   Title   : strand
   Usage   : $strand = $loc->strand();
   Function: get/set the strand of this range
   Returns : the strandedness (-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 <,>, ^).
 
   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 <,>, ^) 
 
   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' or 'IN-BETWEEN')
   Args    : 'EXACT' or '..' or 'IN-BETWEEN' or '^'
 
 

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
 
 

valid_Location

  Title   : valid_Location
  Usage   : if ($location->valid_location) {...};
  Function: boolean method to determine whether location is considered valid
            (has minimum requirements for Simple implementation)
  Returns : Boolean value: true if location is valid, false otherwise
  Args    : none