Bio::Location
Simple
Toolbar
Summary
Bio::Location::Simple - Implementation of a Simple Location on a Sequence
Package variables
No package variables defined.
Included modules
Inherit
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 exact location
information on a Sequence: '22' or '12..15' or '16^17'.
You can test the type of the location using lenght() function () or
directly location_type() which can one of two values: 'EXACT' or
'IN-BETWEEN'.
Methods
Methods description
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) |
Title : length Usage : $len = $loc->length(); Function: get the length in the coordinate space this location spans Example : Returns : an integer Args : none |
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 '^' |
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) |
Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none |
Methods code
BEGIN { use vars qw( %RANGEENCODE %RANGEDECODE );
%RANGEENCODE = ('\.\.' => 'EXACT',
'\^' => 'IN-BETWEEN' );
%RANGEDECODE = ('EXACT' => '..',
'IN-BETWEEN' => '^' ); } |
sub end
{ my ($self, $value) = @_;
$self->{'_end'} = $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 $self->{'_end'}; } |
sub length
{ my ($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 $self->{'_location_type'}; } |
sub new
{ my ($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 $self->{'_start'}; } |
sub to_FTstring
{ my($self) = @_;
my $str;
if( $self->start == $self->end ) {
return $self->start;
}
$str = $self->start . $RANGEDECODE{$self->location_type} . $self->end;
if($self->is_remote() && $self->seq_id()) {
$str = $self->seq_id() . ":" . $str;
}
if( $self->strand == -1 ) {
$str = "complement(".$str.")";
}
return $str;
}
} |
sub trunc
{ my ($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; } |
General documentation
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
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://bugzilla.bioperl.org/
AUTHOR - Heikki Lehvaslaiho | Top |
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
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)
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
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
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', 'IN-BETWEEN')
Args : none
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
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
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', 'IN-BETWEEN')
Args : none
Title : is_remote
Usage : $self->is_remote($newval)
Function: Getset for is_remote value
Returns : value of is_remote
Args : newvalue (optional)