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# $Id: Simple.pm,v 1.20 2002/03/08 20:00:00 jason Exp $
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# $Id: Simple.pm,v 1.35 2003/12/18 13:15:20 jason Exp $
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# BioPerl module for Bio::Location::Simple
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# Cared for by Jason Stajich <jason@chg.mc.duke.edu>
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# Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
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# Copyright Jason Stajich
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# Copyright Heikki Lehvaslaiho
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# You may distribute this module under the same terms as perl itself
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# POD documentation - main docs before the code
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This is an implementation of Bio::LocationI to manage simple location
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information on a Sequence.
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This is an implementation of Bio::LocationI to manage exact location
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information on a Sequence: '22' or '12..15' or '16^17'.
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You can test the type of the location using lenght() function () or
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directly location_type() which can one of two values: 'EXACT' or
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bioperl-bugs@bio.perl.org
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http://bio.perl.org/bioperl-bugs/
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=head1 AUTHOR - Jason Stajich
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Email jason@chg.mc.duke.edu
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http://bugzilla.bioperl.org/
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=head1 AUTHOR - Heikki Lehvaslaiho
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Email heikki@ebi.ac.uk
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@ISA = qw(Bio::Root::Root Bio::LocationI);
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use Bio::Location::Atomic;
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@ISA = qw( Bio::Location::Atomic );
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use vars qw( %RANGEENCODE %RANGEDECODE );
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%RANGEENCODE = ('\.\.' => 'EXACT',
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'\^' => 'IN-BETWEEN' );
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%RANGEDECODE = ('EXACT' => '..',
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'IN-BETWEEN' => '^' );
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my ($class, @args) = @_;
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my ($v,$start,$end,$strand,$seqid) = $self->_rearrange([qw(VERBOSE
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defined $v && $self->verbose($v);
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defined $strand && $self->strand($strand);
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defined $start && $self->start($start);
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defined $end && $self->end($end);
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if( defined $self->start && defined $self->end &&
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$self->start > $self->end ) {
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$self->warn("When building a location start ($start) is expected to be less than end ($end), however it was not was not. Switching start and end and setting strand to -1");
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$seqid && $self->seq_id($seqid);
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my $self = $class->SUPER::new(@args);
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my ($locationtype) = $self->_rearrange([qw(LOCATION_TYPE)],@args);
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$locationtype && $self->location_type($locationtype);
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my ($self, $value) = @_;
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$self->min_start($value) if( defined $value );
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return $self->SUPER::start();
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$self->{'_start'} = $value if defined $value ;
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$self->throw("Only adjacent residues when location type ".
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"is IN-BETWEEN. Not [". $self->{'_start'}. "] and [".
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$self->{'_end'}. "]" )
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if defined $self->{'_start'} && defined $self->{'_end'} &&
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$self->location_type eq 'IN-BETWEEN' &&
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($self->{'_end'} - 1 != $self->{'_start'});
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return $self->{'_start'};
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my ($self, $value) = @_;
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$self->min_end($value) if( defined $value );
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return $self->SUPER::end();
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$self->{'_end'} = $value if defined $value ;
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$self->throw("Only adjacent residues when location type ".
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"is IN-BETWEEN. Not [". $self->{'_start'}. "] and [".
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$self->{'_end'}. "]" )
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if defined $self->{'_start'} && defined $self->{'_end'} &&
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$self->location_type eq 'IN-BETWEEN' &&
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($self->{'_end'} - 1 != $self->{'_start'});
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return $self->{'_end'};
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my ($self, $value) = @_;
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if ( defined $value ||
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! defined $self->{'_strand'} ) {
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# let's go ahead and force to '0' if
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# we are requesting the strand without it
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# having been set previously
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$value = 0 unless defined($value);
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if ( $value eq '+' ) { $value = 1; }
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elsif ( $value eq '-' ) { $value = -1; }
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elsif ( $value eq '.' ) { $value = 0; }
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elsif ( $value != -1 && $value != 1 && $value != 0 ) {
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$self->throw("$value is not a valid strand info");
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$self->{'_strand'} = $value
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return $self->{'_strand'};
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return abs($self->end() - $self->start()) + 1;
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if ($self->location_type eq 'IN-BETWEEN' ) {
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return abs($self->end - $self->start) + 1;
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Title : min_start
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Usage : my $minstart = $location->min_start();
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Function: Get minimum starting location of feature startpoint
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Function: Get minimum starting location of feature startpoint
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Returns : integer or undef if no minimum starting point.
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my ($self,$value) = @_;
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if(defined($value)) {
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$self->{'_start'} = $value;
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return $self->{'_start'};
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Title : max_start
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my ($self,@args) = @_;
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return $self->min_start(@args);
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=head2 start_pos_type
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Title : start_pos_type
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Usage : my $start_pos_type = $location->start_pos_type();
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Function: Get start position type (ie <,>, ^).
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In this implementation this will always be 'EXACT'.
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Returns : type of position coded as text
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('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
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('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN', 'IN-BETWEEN')
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my($self,@args) = @_;
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return $self->min_end(@args);
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=head2 end_pos_type
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Title : end_pos_type
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Usage : my $end_pos_type = $location->end_pos_type();
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Function: Get end position type (ie <,>, ^)
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In this implementation this will always be 'EXACT'.
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Returns : type of position coded as text
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('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
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('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN', 'IN-BETWEEN')
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=head2 location_type
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Title : location_type
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Usage : my $location_type = $location->location_type();
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Function: Get location type encoded as text
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Returns : string ('EXACT', 'WITHIN', 'BETWEEN')
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Returns : string ('EXACT' or 'IN-BETWEEN')
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Args : 'EXACT' or '..' or 'IN-BETWEEN' or '^'
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sub location_type {
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my ($self, $value) = @_;
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if( defined $value || ! defined $self->{'_location_type'} ) {
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$value = 'EXACT' unless defined $value;
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if (! defined $RANGEDECODE{$value}) {
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$value = '\^' if $value eq '^';
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$value = '\.\.' if $value eq '..';
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$value = $RANGEENCODE{$value};
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$self->throw("Did not specify a valid location type. [$value] is no good")
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unless defined $value;
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$self->{'_location_type'} = $value;
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$self->throw("Only adjacent residues when location type ".
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"is IN-BETWEEN. Not [". $self->{'_start'}. "] and [".
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$self->{'_end'}. "]" )
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if $self->{'_location_type'} eq 'IN-BETWEEN' &&
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defined $self->{'_start'} &&
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defined $self->{'_end'} &&
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($self->{'_end'} - 1 != $self->{'_start'});
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return $self->{'_location_type'};
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sub to_FTstring {
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if( $self->start == $self->end ) {
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my $str = $self->start . ".." . $self->end;
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if( $self->strand == -1 ) {
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$str = sprintf("complement(%s)", $str);
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$str = $self->start . $RANGEDECODE{$self->location_type} . $self->end;
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if($self->is_remote() && $self->seq_id()) {
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$str = $self->seq_id() . ":" . $str;
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if( defined $self->strand &&
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$self->strand == -1 ) {
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$str = "complement(".$str.")";
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# comments, not function added by jason
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# trunc is untested, and as of now unannounced method for truncating a
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# location. This is to eventually be part of the procedure to
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# truncate a sequence with annotatioin and properly remap the location
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# of all the features contained within the truncated segment.
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# presumably this might do things a little differently for the case
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# where the truncation splits the location in half
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# in short- you probably don't want to use this method.
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my ($self,$start,$end,$relative_ori) = @_;
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my $newstart = $self->start - $start+1;
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my $newend = $self->end - $start+1;
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my $newstrand = $relative_ori * $self->strand;
added
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Bio/Location/Simple.pm
