Bio::Location Fuzzy
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Summary
Bio::Location::Fuzzy - Implementation of a Location on a Sequence
which has unclear start and/or end locations
Package variables
No package variables defined.
Inherit
Bio::Location::Atomic Bio::Location::FuzzyLocationI
Synopsis
    use Bio::Location::Fuzzy;
my $fuzzylocation = Bio::Location::Fuzzy->new(
-start => '<30',
-end => 90,
-location_type => '..');
print "location string is ", $fuzzylocation->to_FTstring(), "\n"; print "location is of the type ", $fuzzylocation->location_type, "\n";
Description
This module contains the necessary methods for representing a
Fuzzy Location, one that does not have clear start and/or end points.
This will initially serve to handle features from Genbank/EMBL feature
tables that are written as 1^100 meaning between bases 1 and 100 or
<100..300 meaning it starts somewhere before 100. Advanced
implementations of this interface may be able to handle the necessary
logic of overlaps/intersection/contains/union. It was constructed to
handle fuzzy locations that can be represented in Genbank/EMBL and
Swissprot.
Methods
newDescriptionCode
location_typeDescriptionCode
startDescriptionCode
endDescriptionCode
min_startDescriptionCode
max_startDescriptionCode
start_pos_typeDescriptionCode
min_endDescriptionCode
max_endDescriptionCode
end_pos_typeDescriptionCode
to_FTstringDescriptionCode
_fuzzypointdecodeDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $fuzzyloc = Bio::Location::Fuzzy->new( @args);
Function:
Returns :
Args : -start => value for start (initialize by superclass)
-end => value for end (initialize by superclass)
-strand => value for strand (initialize by superclass)
-location_type => either ('EXACT','WITHIN','IN-BETWEEN',
'UNCERTAIN') OR ( 1,2,3,4)
-start_ext=> extension for start - defaults to 0,
-start_fuz= fuzzy code for start can be
('EXACT','WITHIN','BETWEEN','BEFORE','AFTER',
'UNCERTAIN' ) OR
a value 1 - 5 corresponding to index+1 above
-end_ext=> extension for end - defaults to 0,
-end_fuz= fuzzy code for end can be
('EXACT','WITHIN','BETWEEN','BEFORE','AFTER',
'UNCERTAIN') OR
a value 1 - 5 corresponding to index+1 above
location_typecodeprevnextTop
  Title   : location_type
Usage : my $location_type = $location->location_type();
Function: Get location type encoded as text
Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN', 'UNCERTAIN')
Args : none
startcodeprevnextTop
  Title   : start
Usage : $start = $fuzzy->start();
Function: get/set start of this range, handling fuzzy_starts
Returns : a positive integer representing the start of the location
Args : start location on set (can be fuzzy point string)
endcodeprevnextTop
  Title   : end
Usage : $end = $fuzzy->end();
Function: get/set end of this range, handling fuzzy_ends
Returns : a positive integer representing the end of the range
Args : end location on set (can be fuzzy string)
min_startcodeprevnextTop
  Title   : min_start
Usage : $min_start = $fuzzy->min_start();
Function: get/set the minimum starting point
Returns : the minimum starting point from the contained sublocations
Args : integer or undef on set
max_startcodeprevnextTop
  Title   : max_start
Usage : my $maxstart = $location->max_start();
Function: Get/set maximum starting location of feature startpoint
Returns : integer or undef if no maximum starting point.
Args : integer or undef on set
start_pos_typecodeprevnextTop
  Title   : start_pos_type
Usage : my $start_pos_type = $location->start_pos_type();
Function: Get/set start position type.
Returns : type of position coded as text
('BEFORE','AFTER','EXACT','WITHIN','BETWEEN','UNCERTAIN')
Args : a string on set
min_endcodeprevnextTop
  Title   : min_end
Usage : my $minend = $location->min_end();
Function: Get/set minimum ending location of feature endpoint
Returns : integer or undef if no minimum ending point.
Args : integer or undef on set
max_endcodeprevnextTop
  Title   : max_end
Usage : my $maxend = $location->max_end();
Function: Get/set maximum ending location of feature endpoint
Returns : integer or undef if no maximum ending point.
Args : integer or undef on set
end_pos_typecodeprevnextTop
  Title   : end_pos_type
Usage : my $end_pos_type = $location->end_pos_type();
Function: Get/set end position type.
Returns : type of position coded as text
('BEFORE','AFTER','EXACT','WITHIN','BETWEEN','UNCERTAIN')
Args : a string on set
to_FTstringcodeprevnextTop
  Title   : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: Get/Set seq_id that location refers to
Returns : seq_id
Args : [optional] seq_id value to set
_fuzzypointdecodecodeprevnextTop
  Title   : _fuzzypointdecode
Usage : ($type,$min,$max) = $self->_fuzzypointdecode('<5');
Function: Decode a fuzzy string.
Returns : A 3-element array consisting of the type of location, the
minimum integer, and the maximum integer describing the range
of coordinates this start or endpoint refers to. Minimum or
maximum coordinate may be undefined.
: Returns empty array on fail.
Args : fuzzypoint string
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($location_type, $start_ext, $start_fuz, $end_ext, $end_fuz) = 
        $self->_rearrange([ qw(LOCATION_TYPE START_EXT START_FUZ 
                   END_EXT END_FUZ )
                ], @args);

    $location_type  && $self->location_type($location_type);
    $start_ext && $self->max_start($self->min_start + $start_ext);
    $end_ext   && $self->max_end($self->min_end + $end_ext);
    $start_fuz && $self->start_pos_type($start_fuz);
    $end_fuz   && $self->end_pos_type($end_fuz);

    return $self;
}
location_typedescriptionprevnextTop
sub location_type {
    my ($self,$value) = @_;
    if( defined $value || ! defined $self->{'_location_type'} ) {
        $value = 'EXACT' unless defined $value;
        if(! defined $FUZZYCODES{$value} )  {
            $value = uc($value);
            if( $value =~ /\.\./ ) {
                $value = 'EXACT';
            } elsif( $value =~ /^\.$/ ) {
                $value = 'WITHIN';
            } elsif( $value =~ /\^/ ) {
                $value = 'IN-BETWEEN';
                $self->throw("Use Bio::Location::Simple for IN-BETWEEN locations [".
                             $self->start. "] and [". $self->end. "]")
                  if defined $self->start && defined $self->end &&
                            ($self->end - 1 == $self->start);
            } elsif( $value =~ /\?/ ) {
                $value = 'UNCERTAIN';
            } elsif( $value ne 'EXACT' && $value ne 'WITHIN' && 
                        $value ne 'IN-BETWEEN' ) {
                $self->throw("Did not specify a valid location type");
            }
        }
        $self->{'_location_type'} = $value;
    }
    return $self->{'_location_type'};
}
startdescriptionprevnextTop
sub start {
    my($self,$value) = @_;
    if( defined $value ) {
    my ($encode,$min,$max) = $self->_fuzzypointdecode($value);
    $self->start_pos_type($encode);
    $self->min_start($min);
    $self->max_start($max);
    }

    $self->throw("Use Bio::Location::Simple for IN-BETWEEN locations ["
                 . $self->SUPER::start. "] and [". $self->SUPER::end. "]")
    if $self->location_type eq 'IN-BETWEEN'  && defined $self->SUPER::end &&
                  ($self->SUPER::end - 1 == $self->SUPER::start);

    return $self->SUPER::start();
}
enddescriptionprevnextTop
sub end {
    my($self,$value) = @_;
    if( defined $value ) {
    my ($encode,$min,$max) = $self->_fuzzypointdecode($value);
    $self->end_pos_type($encode);
    $self->min_end($min);
    $self->max_end($max);
    }

    $self->throw("Use Bio::Location::Simple for IN-BETWEEN locations [".
                 $self->SUPER::start. "] and [". $self->SUPER::end. "]")
    if $self->location_type eq 'IN-BETWEEN' && defined $self->SUPER::start &&
                ($self->SUPER::end - 1 == $self->SUPER::start);

    return $self->SUPER::end();
}
min_startdescriptionprevnextTop
sub min_start {
    my ($self,@args) = @_;

    if(@args) {
    $self->{'_min_start'} = $args[0]; # the value may be undef!
} return $self->{'_min_start'};
}
max_startdescriptionprevnextTop
sub max_start {
    my ($self,@args) = @_;

    if(@args) {
        $self->{'_max_start'} = $args[0]; # the value may be undef!
} return $self->{'_max_start'};
}
start_pos_typedescriptionprevnextTop
sub start_pos_type {
    my ($self,$value) = @_;
    if(defined $value &&  $value =~ /^\d+$/ ) {
        if( $value == 0 ) { $value = 'EXACT'; }
        else { 
            my $v = $LOCATIONCODESBSANE[$value];
            if( ! defined $v ) {
                $self->warn("Provided value $value which I don't understand,".
                            " reverting to 'EXACT'");
                $v = 'EXACT';
            }
            $value = $v;
        }
    }
    if(defined($value)) {
        $self->{'_start_pos_type'} = $value;
    }
    return $self->{'_start_pos_type'};
}
min_enddescriptionprevnextTop
sub min_end {
    my ($self,@args) = @_;

    if(@args) {
        $self->{'_min_end'} = $args[0]; # the value may be undef!
} return $self->{'_min_end'};
}
max_enddescriptionprevnextTop
sub max_end {
    my ($self,@args) = @_;

    if(@args) {
        $self->{'_max_end'} = $args[0]; # the value may be undef!
} return $self->{'_max_end'};
}
end_pos_typedescriptionprevnextTop
sub end_pos_type {
    my ($self,$value) = @_;
    if( defined $value && $value =~ /^\d+$/ ) {
        if( $value == 0 ) { $value = 'EXACT'; }
        else { 
            my $v = $LOCATIONCODESBSANE[$value];
            if( ! defined $v ) {
                $self->warn("Provided value $value which I don't understand,".
                            " reverting to 'EXACT'");
                $v = 'EXACT';
            }
            $value = $v;
        }
    }

    if(defined($value)) {
        $self->{'_end_pos_type'} = $value;
    }
    return $self->{'_end_pos_type'};
}
to_FTstringdescriptionprevnextTop
sub to_FTstring {
    my ($self) = @_;    
    my (%vals) = ( 'start' => $self->start,
           'min_start' => $self->min_start,
           'max_start' => $self->max_start,
           'start_code' => $self->start_pos_type,
           'end' => $self->end,
           'min_end' => $self->min_end,
           'max_end' => $self->max_end,
           'end_code' => $self->end_pos_type );

    my (%strs) = ( 'start' => '',
           'end'   => '');
    my ($delimiter) = $FUZZYCODES{$self->location_type};
    $delimiter = $FUZZYCODES{'EXACT'} if ($self->location_type eq 'UNCERTAIN');
    
    my $policy = ref($self->coordinate_policy);
    
    # I'm lazy, lets do this in a loop since behaviour will be the same for 
# start and end
# The CoordinatePolicy now dictates start/end data here (bug 992) - cjf
foreach my $point ( qw(start end) ) { if( ($vals{$point."_code"} ne 'EXACT') && ($vals{$point."_code"} ne 'UNCERTAIN') ) { # must have max and min defined to use 'WITHIN', 'BETWEEN'
if ((!defined $vals{"min_$point"} || !defined $vals{"max_$point"}) && ( $vals{$point."_code"} eq 'WITHIN' || $vals{$point."_code"} eq 'BETWEEN')) { $vals{"min_$point"} = '' unless defined $vals{"min_$point"}; $vals{"max_$point"} = '' unless defined $vals{"max_$point"}; $self->warn("Fuzzy codes for start are in a strange state, (". join(",", ($vals{"min_$point"}, $vals{"max_$point"}, $vals{$point."_code"})). ")"); return ''; } if (defined $vals{$point."_code"} && ($vals{$point."_code"} eq 'BEFORE' || $vals{$point."_code"} eq 'AFTER')) { $strs{$point} .= $FUZZYCODES{$vals{$point."_code"}}; $strs{$point} .= $vals{"$point"}; } if( defined $vals{$point."_code"} && ($vals{$point."_code"} eq 'WITHIN' || $vals{$point."_code"} eq 'BETWEEN')) { # Expect odd results with anything but WidestCoordPolicy for now
$strs{$point} .= ($point eq 'start') ? $vals{"$point"}. $FUZZYCODES{$vals{$point."_code"}}. $vals{'max_'.$point} : $vals{'min_'.$point}. $FUZZYCODES{$vals{$point."_code"}}. $vals{"$point"}; $strs{$point} = "(".$strs{$point}.")"; } } elsif ($vals{$point."_code"} eq 'UNCERTAIN') { $strs{$point} = $FUZZYCODES{$vals{$point."_code"}}; $strs{$point} .= $vals{$point} if defined $vals{$point}; } else { $strs{$point} = $vals{$point}; } } my $str = $strs{'start'} . $delimiter . $strs{'end'}; if($self->is_remote() && $self->seq_id()) { $str = $self->seq_id() . ":" . $str; } if( defined $self->strand && $self->strand == -1 && $self->location_type() ne "UNCERTAIN") { $str = "complement(" . $str . ")"; } elsif($self->location_type() eq "WITHIN") { $str = "(".$str.")"; } return $str;
}
_fuzzypointdecodedescriptionprevnextTop
sub _fuzzypointdecode {
    my ($self, $string) = @_;
    return () if( !defined $string);
    # strip off leading and trailing space
$string =~ s/^\s*(\S+)\s*/$1/; foreach my $pattern ( keys %FUZZYPOINTENCODE ) { if( $string =~ /^$pattern$/ ) { my ($min,$max) = ($1,$2) unless (($1 eq '') && (!defined $2)); if( ($FUZZYPOINTENCODE{$pattern} eq 'EXACT') || ($FUZZYPOINTENCODE{$pattern} eq 'UNCERTAIN') ) { $max = $min; } else { $max = undef if((defined $max) && (length($max) == 0)); $min = undef if((defined $min) && (length($min) == 0)); } return ($FUZZYPOINTENCODE{$pattern},$min,$max); } } if( $self->verbose >= 1 ) { $self->warn("could not find a valid fuzzy encoding for $string"); } return (); } 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 - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
LocationI methodsTop
lengthTop
  Title   : length
Usage : $length = $fuzzy_loc->length();
Function: Get the length of this location.
Note that the length of a fuzzy location will always depend on the currently active interpretation of start and end. The result will therefore vary for different CoordinatePolicy objects. Returns : an integer Args : none
seq_idTop
  Title   : seq_id
Usage : my $seqid = $location->seq_id();
Function: Get/Set seq_id that location refers to
Returns : seq_id
Args : [optional] seq_id value to set
coordinate_policyTop
  Title   : coordinate_policy
Usage : $policy = $location->coordinate_policy(); $location->coordinate_policy($mypolicy); # set may not be possible Function: Get the coordinate computing policy employed by this object. See Bio::Location::CoordinatePolicyI for documentation about the policy object and its use. The interface *does not* require implementing classes to accept setting of a different policy. The implementation provided here does, however, allow to do so. Implementors of this interface are expected to initialize every new instance with a CoordinatePolicyI object. The implementation provided here will return a default policy object if none has been set yet. To change this default policy object call this method as a class method with an appropriate argument. Note that in this case only subsequently created Location objects will be affected. Returns : A Bio::Location::CoordinatePolicyI implementing object. Args : On set, a Bio::Location::CoordinatePolicyI implementing object.
See Bio::Location::CoordinatePolicyI
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