Bio::Factory FTLocationFactory
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Bio::Factory::FTLocationFactory - A FeatureTable Location Parser
Package variables
No package variables defined.
Included modules
Bio::Factory::LocationFactoryI Bio::Root::Root
    # parse a string into a location object
$loc = Bio::Factory::FTLocationFactory->from_string("join(100..200, 400..500");
Implementation of string-encoded location parsing for the Genbank feature table
encoding of locations.
Methods description
_parse_locationcode    nextTop
 Title   : _parse_location
Usage : $loc = $locfactory->_parse_location( $loc_string)
Function: Parses the given location string and returns a location object with start() and end() and strand() set appropriately. Note that this method is private. Returns : A Bio::LocationI implementing object or undef on failure Args : location string
 Title   : from_string
Usage : $loc = $locfactory->from_string("100..200");
Function: Parses the given string and returns a Bio::LocationI implementing
object representing the location encoded by the string.
This implementation parses the Genbank feature table encoding of locations. Example : Returns : A Bio::LocationI implementing object. Args : A string.
Methods code
sub _parse_location {
    my ($self, $locstr) = @_;
    my ($loc, $seqid);

    $self->debug( "Location parse, processing $locstr\n");

    # 'remote' location?
if($locstr =~ /^(\S+):(.*)$/) { # yes; memorize remote ID and strip from location string
$seqid = $1; $locstr = $2; } # split into start and end
my ($start, $end) = split(/\.\./, $locstr); # remove enclosing parentheses if any; note that because of parentheses
# possibly surrounding the entire location the parentheses around start
# and/or may be asymmetrical
$start =~ s/^\(+//; $start =~ s/\)+$//; $end =~ s/^\(+// if $end; $end =~ s/\)+$// if $end; # Is this a simple (exact) or a fuzzy location? Simples have exact start
# and end, or is between two adjacent bases. Everything else is fuzzy.
my $loctype = ".."; # exact with start and end as default
my $locclass = "Bio::Location::Simple"; if(! defined($end)) { if($locstr =~ /(\d+)([\.\^])(\d+)/) { $start = $1; $end = $3; $loctype = $2; $locclass = "Bio::Location::Fuzzy" unless (abs($end - $start) <= 1) && ($loctype eq "^"); } else { $end = $start; } } if ( ($start =~ /[\>\<\?\.\^]/) || ($end =~ /[\>\<\?\.\^]/) ) { $locclass = 'Bio::Location::Fuzzy'; } # instantiate location and initialize
$loc = $locclass->new(-verbose => $self->verbose, -start => $start, -end => $end, -strand => 1, -location_type => $loctype); # set remote ID if remote location
if($seqid) { $loc->is_remote(1); $loc->seq_id($seqid); } # done (hopefully)
return $loc; } 1;
sub from_string {
    # the third parameter is purely optional and indicates a recursive
# call if set
my ($self,$locstr,$is_rec) = @_; my $loc; # there is no place in FT-formatted location strings where whitespace
# carries meaning, so strip it off entirely upfront
$locstr =~ s/\s+//g if ! $is_rec; # does it contain an operator?
if($locstr =~ /^([A-Za-z]+)\((.*)\)$/) { # yes:
my $op = $1; my $oparg = $2; if($op eq "complement") { # parse the argument recursively, then set the strand to -1
$loc = $self->from_string($oparg, 1); $loc->strand(-1); } elsif(($op eq "join") || ($op eq "order") || ($op eq "bond")) { # This is a split location. Split into components and parse each
# one recursively, then gather into a SplitLocationI instance.
# Note: The following code will /not/ work with nested
# joins (you want to have grammar-based parsing for that).
$loc = Bio::Location::Split->new(-verbose => $self->verbose, -splittype => $op); foreach my $substr (split(/,/, $oparg)) { $loc->add_sub_Location($self->from_string($substr, 1)); } } else { $self->throw("operator\" $op\" unrecognized by parser"); } } else { # no operator, parse away
$loc = $self->_parse_location($locstr); } return $loc;
General documentation
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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
the Bioperl mailing list. Your participation is much appreciated.              - General discussion - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
AUTHOR - Hilmar LappTop
Email hlapp at
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
 Title   : new
Usage : my $obj = new Bio::Factory::FTLocationFactory();
Function: Builds a new Bio::Factory::FTLocationFactory object
Returns : an instance of Bio::Factory::FTLocationFactory
Args :