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

BioPerl documentation Contained in the BioPerl distribution.

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NAME

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

SYNOPSIS

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    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

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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

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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:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho

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Email heikki-at-bioperl-dot-org

APPENDIX

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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   : $is_remote_loc = $loc->is_remote()
 Function: Whether or not a location is a remote location.

           A location is said to be remote if it is on a different
           'object' than the object which 'has' this
           location. Typically, features on a sequence will sometimes
           have a remote location, which means that the location of
           the feature is on a different sequence than the one that is
           attached to the feature. In such a case, $loc->seq_id will
           be different from $feat->seq_id (usually they will be the
           same).

           While this may sound weird, it reflects the location of the
           kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL
           feature tables.

 Example : 
 Returns : TRUE if the location is a remote location, and FALSE otherwise
 Args    : Value to set to

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
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Location::Simple
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code


# Let the code begin...


package Bio::Location::Simple;
use strict;

use base qw(Bio::Location::Atomic);

our %RANGEENCODE  = ('\.\.' => 'EXACT',
             '\^'   => 'IN-BETWEEN' );

our %RANGEDECODE  = ('EXACT'      => '..',
             'IN-BETWEEN' => '^' );

sub new { 
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    my ($locationtype) = $self->_rearrange([qw(LOCATION_TYPE)],@args);

    $locationtype && $self->location_type($locationtype);

    return $self;
}


sub start {
  my ($self, $value) = @_;
    $self->{'_start'} = $value if defined $value ;
  
    $self->throw("Only adjacent residues when location type ".
             "is IN-BETWEEN. Not [". $self->{'_start'}. "] and [".
             $self->{'_end'}. "]" )
        if defined $self->{'_start'} && defined $self->{'_end'} && 
        $self->location_type eq 'IN-BETWEEN' &&
        ($self->{'_end'} - 1 != $self->{'_start'});
    return $self->{'_start'};
}



sub end {
	my ($self, $value) = @_;
  
	$self->{'_end'} = $value if defined $value ;
	
	#assume end is the same as start if not defined
	if (!defined $self->{'_end'}) {
		if (!defined $self->{'_start'}) {
			$self->warn('Can not set Bio::Location::Simple::end() equal to start; start not set');
			return;
		}
		$self->warn('Setting end to equal start['. $self->{'_start'}. ']');
		$self->{'_end'} = $self->{'_start'};
	}
	$self->throw("Only adjacent residues when location type ".
			"is IN-BETWEEN. Not [". $self->{'_start'}. "] and [".
			 $self->{'_end'}. "]" )
		if defined $self->{'_start'} && defined $self->{'_end'} && 
		$self->location_type eq 'IN-BETWEEN' &&
		($self->{'_end'} - 1 != $self->{'_start'});
  
	return $self->{'_end'};
}


sub length {
   my ($self) = @_;
   if ($self->location_type eq 'IN-BETWEEN' ) {
       return 0;
   } else {
       return abs($self->end - $self->start) + 1;
   }

}


sub location_type {
    my ($self, $value) = @_;

    if( defined $value || ! defined $self->{'_location_type'} ) {
    $value = 'EXACT' unless defined $value;
    $value = uc $value;
    if (! defined $RANGEDECODE{$value}) {
        $value = '\^' if $value eq '^';
        $value = '\.\.' if $value eq '..';
        $value = $RANGEENCODE{$value};
    }
    $self->throw("Did not specify a valid location type. [$value] is no good")
        unless defined $value;
    $self->{'_location_type'} = $value;
    }
    $self->throw("Only adjacent residues when location type ".
         "is IN-BETWEEN. Not [". $self->{'_start'}. "] and [".
         $self->{'_end'}. "]" )
    if $self->{'_location_type'} eq 'IN-BETWEEN' &&
        defined $self->{'_start'} &&
        defined $self->{'_end'} &&
            ($self->{'_end'} - 1 != $self->{'_start'});

    return $self->{'_location_type'};
}


sub to_FTstring { 
    my($self) = @_;

    my $str;
    if( $self->start == $self->end ) {
    $str =  $self->start;
    } else {
        $str = $self->start . $RANGEDECODE{$self->location_type} . $self->end;
    }
    if($self->is_remote() && $self->seq_id()) {
    $str = $self->seq_id() . ":" . $str;
    }
    if( defined $self->strand &&
    $self->strand == -1 ) {
    $str = "complement(".$str.")";
    }
    return $str;
}


# comments, not function added by jason 
#
# trunc is untested, and as of now unannounced method for truncating a
# location.  This is to eventually be part of the procedure to
# truncate a sequence with annotatioin and properly remap the location
# of all the features contained within the truncated segment.

# presumably this might do things a little differently for the case 
# where the truncation splits the location in half
# 
# in short- you probably don't want to use  this method.

sub trunc {
  my ($self,$start,$end,$relative_ori) = @_;
  my $newstart  = $self->start - $start+1;
  my $newend    = $self->end   - $start+1;
  my $newstrand = $relative_ori * $self->strand;

  my $out;
  if( $newstart < 1 || $newend > ($end-$start+1) ) {
    $out = Bio::Location::Simple->new();
    $out->start($self->start);
    $out->end($self->end);
    $out->strand($self->strand);
    $out->seq_id($self->seqid);
    $out->is_remote(1);
  } else {
    $out = Bio::Location::Simple->new();
    $out->start($newstart);
    $out->end($newend);
    $out->strand($newstrand);
    $out->seq_id();
  }

  return $out;
}

1;