FAST

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lib/FAST/Bio/Location/Atomic.pm  view on Meta::CPAN

sub start_pos_type {
    my($self) = @_;
    return 'EXACT';
}

=head2 min_end

  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

=cut

sub min_end {
    my($self,$value) = @_;

    if(defined($value)) {
	$self->{'_end'} = $value;
    }
    return $self->{'_end'};
}

=head2 max_end

  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

=cut

sub max_end {
    my($self,@args) = @_;

lib/FAST/Bio/Location/Fuzzy.pm  view on Meta::CPAN

    if(defined($value)) {
        $self->{'_start_pos_type'} = $value;
    }
    return $self->{'_start_pos_type'};
}

=head2 min_end

  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

=cut

sub min_end {
    my ($self,@args) = @_;

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

=head2 max_end

  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

=cut

sub max_end {
    my ($self,@args) = @_;

    if(@args) {
        $self->{'_max_end'} = $args[0]; # the value may be undef!

lib/FAST/Bio/Location/Fuzzy.pm  view on Meta::CPAN

=cut

=head2 _fuzzypointdecode

  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

=cut

sub _fuzzypointdecode {
    my ($self, $string) = @_;
    return () if( !defined $string);
    # strip off leading and trailing space

lib/FAST/Bio/Location/FuzzyLocationI.pm  view on Meta::CPAN

  Returns : type of position coded as text 
            ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
  Args    : none

=cut

=head2 min_end

  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

=cut

=head2 max_end

  Title   : max_end
  Usage   : my $maxend = $location->max_end();
  Function: Get maximum ending location of feature endpoint 
  Returns : integer or undef if no maximum ending point.
  Args    : none

=cut

=head2 end_pos_type

  Title   : end_pos_type
  Usage   : my $end_pos_type = $location->end_pos_type();
  Function: Get end position type (ie <,>, ^) 

lib/FAST/Bio/Location/Simple.pm  view on Meta::CPAN

  Returns : type of position coded as text 
            ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
  Args    : none

=cut

=head2 min_end

  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

=cut


=head2 max_end

  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

=cut

=head2 end_pos_type

lib/FAST/Bio/Location/Split.pm  view on Meta::CPAN

				 "that is not possible, try manipulating the sub Locations");
    }
    my @locs = $self->sub_Location();
    return ( @locs ) ? $locs[0]->start_pos_type() : undef;    
}

=head2 min_end

  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

=cut

sub min_end {
    my ($self,$value) = @_;

    if( defined $value ) {
	$self->throw("Trying to set the minimum end point of a split location, ".

lib/FAST/Bio/Location/Split.pm  view on Meta::CPAN

    # reverse sort locations by largest ending to smallest ending
    my @locs = $self->sub_Location(-1);
    return $locs[0]->min_end() if @locs; 
    return;
}

=head2 max_end

  Title   : max_end
  Usage   : my $maxend = $location->max_end();
  Function: Get maximum ending location of feature endpoint 
  Returns : integer or undef if no maximum ending point.
  Args    : none

=cut

sub max_end {
    my ($self,$value) = @_;

    if( defined $value ) {
	$self->throw("Trying to set the maximum end point of a split location, ".

lib/FAST/Bio/Location/SplitLocationI.pm  view on Meta::CPAN

  Returns : type of position coded as text 
            ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
  Args    : none

=cut

=head2 min_end

  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

=cut

=head2 max_end

  Title   : max_end
  Usage   : my $maxend = $location->max_end();
  Function: Get maximum ending location of feature endpoint 
  Returns : integer or undef if no maximum ending point.
  Args    : none

=cut

=head2 end_pos_type

  Title   : end_pos_type
  Usage   : my $end_pos_type = $location->end_pos_type();
  Function: Get end position type (ie <,>, ^) 

lib/FAST/Bio/Search/HSP/GenericHSP.pm  view on Meta::CPAN

sub _calculate_seq_positions {
    my ($self,@args) = @_;
    return unless ( $self->{'_sequenceschanged'} );
    $self->{'_sequenceschanged'} = 0;
    my ($seqString, $qseq,$sseq) = ( $self->homology_string(),
                                     $self->query_string(),
                                     $self->hit_string() );
    my ($mlen, $qlen, $slen) = (CORE::length($seqString), CORE::length($qseq), CORE::length($sseq));
    my $qdir = $self->query->strand || 1;
    my $sdir = $self->hit->strand || 1;
    my ($resCount_query, $endpoint_query) = ($qdir <=0) ? ($self->query->end, $self->query->start)
        : ($self->query->start, $self->query->end);
    my ($resCount_sbjct, $endpoint_sbjct) = ($sdir <=0) ? ($self->hit->end, $self->hit->start)
        : ($self->hit->start, $self->hit->end);
    
    my $prog = $self->algorithm;
    
    if( $prog  =~ /FAST|SSEARCH|SMITH-WATERMAN/i ) {
    
        # we infer the end of the regional sequence where the first and last
        # non spaces are in the homology string
        # then we use the HSP->length to tell us how far to read
        # to cut off the end of the sequence

lib/FAST/List/Gen.pm  view on Meta::CPAN

    say <A .. ZZ>->str;         # 'A B C D E ... ZX ZY ZZ'

    <1..>->zip(<a..>)->say(10); # '1 a 2 b 3 c 4 d 5 e'

to specify an infinite range, you can pass C< range > an infinite value
(C< 9**9**9 > works well), or the glob C< ** >, or the string C< '*' >

    range(1, 9**9**9) ~~ range(1, **) ~~ range(1, '*') ~~ <1..*> ~~ <1..>

ranges only store their endpoints, and ranges of all sizes take up the same
amount of memory.

=cut

    sub range ($;$$) {
        splice @_, 1, 1, 9**9**9
            if @_ > 1 and $_[1] eq '*'
                      || \$_[1] == \**;
        for (@_) {
            defined