Bio::Location Simple
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Summary
Bio::Location::Simple - Implementation of a Simple Location on a Sequence
Package variables
No package variables defined.
Inherit
Bio::Location::Atomic
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'.
Methods
new
No description
Code
startDescriptionCode
endDescriptionCode
lengthDescriptionCode
location_typeDescriptionCode
to_FTstringDescriptionCode
trunc
No description
Code
Methods description
startcode    nextTop
  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)
endcodeprevnextTop
  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.
lengthcodeprevnextTop
 Title   : length
Usage : $len = $loc->length();
Function: get the length in the coordinate space this location spans
Example :
Returns : an integer
Args : none
location_typecodeprevnextTop
  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 '^'
to_FTstringcodeprevnextTop
  Title   : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none
Methods code
newdescriptionprevnextTop
sub new {
     my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

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

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

    return $self;
}
startdescriptionprevnextTop
sub start {
    my ($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 $self->{'_start'};
}
enddescriptionprevnextTop
sub end {
    my ($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 $self->{'_end'};
}
lengthdescriptionprevnextTop
sub length {
    my ($self) = @_;
    if ($self->location_type eq 'IN-BETWEEN' ) {
        return 0;
    } else {
        return abs($self->end - $self->start) + 1;
    }
}
location_typedescriptionprevnextTop
sub location_type {
    my ($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 $self->{'_location_type'};
}
to_FTstringdescriptionprevnextTop
sub to_FTstring {
     my($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 $str;
}
truncdescriptionprevnextTop
sub trunc {
    my ($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
FEEDBACKTop
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 Top
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 BugsTop
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 LehvaslaihoTop
Email heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
strandTop
  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)
min_startTop
  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_startTop
  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_typeTop
  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_endTop
  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_endTop
  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_typeTop
  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
is_remoteTop
 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 $feat->seq_id (usually they will be the same). While this may sound weird, it reflects the location of the kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL feature tables. Example : Returns : TRUE if the location is a remote location, and FALSE otherwise Args : Value to set to
valid_LocationTop
 Title   : valid_Location
Usage : if ($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