Bio::Location Atomic
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Summary
Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence
Package variables
No package variables defined.
Included modules
Bio::LocationI
Bio::Root::Root
Inherit
Bio::LocationI Bio::Root::Root
Synopsis
    use Bio::Location::Atomic;
my $location = new Bio::Location::Atomic(-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.
Methods
each_LocationDescriptionCode
endDescriptionCode
end_pos_typeDescriptionCode
is_remoteDescriptionCode
lengthDescriptionCode
location_typeDescriptionCode
max_endDescriptionCode
max_startDescriptionCode
min_endDescriptionCode
min_startDescriptionCode
new
No description
Code
startDescriptionCode
start_pos_typeDescriptionCode
strandDescriptionCode
to_FTstringDescriptionCode
trunc
No description
Code
Methods description
each_Locationcode    nextTop
 Title   : each_Location
Usage : @locations = $locObject->each_Location($order);
Function: Conserved function call across Location:: modules - will
return an array containing the component Location(s) in
that object, regardless if the calling object is itself a
single location or one containing sublocations.
Returns : an array of Bio::LocationI implementing objects - for
Simple locations, the return value is just itself.
Args :
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)
end_pos_typecodeprevnextTop
  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
is_remotecodeprevnextTop
 Title   : is_remote
Usage : $self->is_remote($newval)
Function: Getset for is_remote value
Returns : value of is_remote
Args : newvalue (optional)
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', 'WITHIN', 'BETWEEN')
Args : none
max_endcodeprevnextTop
  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
max_startcodeprevnextTop
  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
min_endcodeprevnextTop
  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
min_startcodeprevnextTop
  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
startcodeprevnextTop
  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)
start_pos_typecodeprevnextTop
  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
strandcodeprevnextTop
  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)
to_FTstringcodeprevnextTop
  Title   : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none
Methods code
each_LocationdescriptionprevnextTop
sub each_Location {
   my ($self) = @_;
   return ($self);
}
enddescriptionprevnextTop
sub end {
  my ($self, $value) = @_;

  $self->min_end($value) if( defined $value );
  return $self->SUPER::end();
}
end_pos_typedescriptionprevnextTop
sub end_pos_type {
    my($self) = @_;
    return 'EXACT';
}
is_remotedescriptionprevnextTop
sub is_remote {
   my $self = shift;
   if( @_ ) {
       my $value = shift;
       $self->{'is_remote'} = $value;
   }
   return $self->{'is_remote'};
}
lengthdescriptionprevnextTop
sub length {
   my ($self) = @_;
   return abs($self->end() - $self->start()) + 1;
}
location_typedescriptionprevnextTop
sub location_type {
    my ($self) = @_;
    return 'EXACT';
}
max_enddescriptionprevnextTop
sub max_end {
    my($self,@args) = @_;
    return $self->min_end(@args);
}
max_startdescriptionprevnextTop
sub max_start {
    my ($self,@args) = @_;
    return $self->min_start(@args);
}
min_enddescriptionprevnextTop
sub min_end {
    my($self,$value) = @_;

    if(defined($value)) {
	$self->{'_end'} = $value;
    }
    return $self->{'_end'};
}
min_startdescriptionprevnextTop
sub min_start {
    my ($self,$value) = @_;

    if(defined($value)) {
	$self->{'_start'} = $value;
    }
    return $self->{'_start'};
}
newdescriptionprevnextTop
sub new {
     my ($class, @args) = @_;
    my $self = {};

    bless $self,$class;

    my ($v,$start,$end,$strand,$seqid) = $self->_rearrange([qw(VERBOSE
							       START
							       END
							       STRAND
							       SEQ_ID)],@args);
    defined $v && $self->verbose($v);
    defined $strand && $self->strand($strand);

    defined $start  && $self->start($start);
    defined $end    && $self->end($end);
    if( defined $self->start && defined $self->end &&
	$self->start > $self->end && $self->strand != -1 ) {
	$self->warn("When building a location, start ($start) is expected to be less than end ($end), ".
		    "however it was not. Switching start and end and setting strand to -1");

	$self->strand(-1);
	my $e = $self->end;
	my $s = $self->start;
	$self->start($e);
	$self->end($s);
    }
    $seqid          && $self->seq_id($seqid);

    return $self;
}
startdescriptionprevnextTop
sub start {
  my ($self, $value) = @_;
  $self->min_start($value) if( defined $value );
  return $self->SUPER::start();
}
start_pos_typedescriptionprevnextTop
sub start_pos_type {
    my($self) = @_;
    return 'EXACT';
}
stranddescriptionprevnextTop
sub strand {
  my ($self, $value) = @_;

  if ( defined $value ) {
       if ( $value eq '+' ) { $value = 1; }
       elsif ( $value eq '-' ) { $value = -1; }
       elsif ( $value eq '.' ) { $value = 0; }
       elsif ( $value != -1 && $value != 1 && $value != 0 ) {
	   $self->throw("$value is not a valid strand info");
       }
       $self->{'_strand'} = $value
   }
  # let's go ahead and force to '0' if
# we are requesting the strand without it
# having been set previously
return $self->{'_strand'} || 0;
}
to_FTstringdescriptionprevnextTop
sub to_FTstring {
     my($self) = @_;
    if( $self->start == $self->end ) {
	return $self->start;
    }
    my $str = $self->start . ".." . $self->end;
    if( $self->strand == -1 ) {
	$str = sprintf("complement(%s)", $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::Atomic->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::Atomic->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://bio.perl.org/MailList.html - About the mailing lists
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 email
or the web:
  bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _