view release on metacpan or search on metacpan
lib/Bio/Community/IO.pm view on Meta::CPAN
A positive number (or undef)
=cut
method next_member () {
$self->throw_not_implemented;
}
=head2 next_community
lib/Bio/Community/IO.pm view on Meta::CPAN
}
method _next_community_init () {
# Driver-side method to initialize new community and return its name
$self->throw_not_implemented;
}
method _next_community_finish () {
# Driver-side method to finalize a community
$self->throw_not_implemented;
}
=head2 next_metacommunity
lib/Bio/Community/IO.pm view on Meta::CPAN
}
method _next_metacommunity_init () {
# Driver-side method to initialize new metacommunity and return its name
$self->throw_not_implemented;
}
method _next_metacommunity_finish () {
# Driver-side method to finalize reading a metacommunity
$self->throw_not_implemented;
}
=head2 write_member
lib/Bio/Community/IO.pm view on Meta::CPAN
Returns : 1 for success
=cut
method write_member (Bio::Community::Member $member, Count $count) {
$self->throw_not_implemented;
}
=head2 write_community
lib/Bio/Community/IO.pm view on Meta::CPAN
}
method _write_community_init (Bio::Community $community) {
# Driver-side method to initialize writing a community
$self->throw_not_implemented;
}
method _write_community_finish (Bio::Community $community) {
# Driver-side method to finalize writing a community
$self->throw_not_implemented;
}
=head2 write_metacommunity
lib/Bio/Community/IO.pm view on Meta::CPAN
}
method _write_metacommunity_init (Bio::Community::Meta $meta) {
# Driver-side method to initialize writing a metacommunity
$self->throw_not_implemented;
}
method _write_metacommunity_finish (Bio::Community::Meta $meta) {
# Driver-side method to finalize writing a metacommunity
$self->throw_not_implemented;
}
before 'close' => sub {
my $self = shift;
view release on metacpan or search on metacpan
lib/Bio/ConnectDots/ConnectorSet/HG_Focus_annot_csv.pm view on Meta::CPAN
package Bio::ConnectDots::ConnectorSet::HG_Focus_annot_csv;
use strict;
use vars qw(@ISA);
use Bio::ConnectDots::ConnectorSet;
@ISA = qw(Bio::ConnectDots::ConnectorSet);
view release on metacpan or search on metacpan
lib/Bio/Coordinate/MapperI.pm view on Meta::CPAN
sub in {
my ($self,$value) = @_;
$self->throw_not_implemented();
}
sub out {
my ($self,$value) = @_;
$self->throw_not_implemented();
}
sub swap {
my ($self) = @_;
$self->throw_not_implemented();
}
sub test {
my ($self) = @_;
$self->throw_not_implemented();
}
sub map {
my ($self,$value) = @_;
$self->throw_not_implemented();
}
sub return_match {
view release on metacpan or search on metacpan
# (They're explicitly set by the user, so we shouldn't fall back to
# finding another copy somewhere else.)
if ( my $dir = $self->args('libbigwig') ) {
return 1 if $self->find_libbigwig_in_build_dir($dir);
return 1 if $self->find_libbigwig_in_install_dir($dir);
$self->die_libbigwig_not_found(
"--libbigwig '$dir' command line parameter does not contain expected files\n"
);
}
elsif ( $dir = $ENV{'LIBBIGWIG_DIR'} ) {
return 1 if $self->find_libbigwig_in_build_dir($dir);
return 1 if $self->find_libbigwig_in_install_dir($dir);
$self->die_libbigwig_not_found(
"LIGBIGWIG_DIR=$ENV{LIBBIGWIG_DIR} environment variable does not contain expected files\n"
);
}
# Search through remaining possible (but not fatal) locations:
last;
}
}
return 1 if $found;
$self->die_libbigwig_not_found();
}
sub set_include_and_compiler_flags {
my ($self) = @_;
else {
return 0;
}
}
sub die_libbigwig_not_found {
my ( $self, $msg ) = @_;
$msg ||= '';
die $msg, <<END;
view release on metacpan or search on metacpan
lib/Bio/DB/Das/Chado.pm view on Meta::CPAN
=cut
sub types {
my $self = shift;
my ($enumerate) = $self->_rearrange([qw(ENUMERATE)],@_);
$self->throw_not_implemented;
#if lincoln didn't need to implement it, neither do I!
}
=head2 get_feature_by_alias, get_features_by_alias
view release on metacpan or search on metacpan
# (They're explicitly set by the user, so we shouldn't fall back to
# finding another copy somewhere else.)
if (my $dir = $self->args('htslib')) {
return 1 if $self->find_hts_in_build_dir($dir);
return 1 if $self->find_hts_in_install_dir($dir);
$self->die_hts_not_found(
"--htslib '$dir' command line parameter does not contain expected files\n"
);
}
elsif ($dir = $ENV{'HTSLIB_DIR'}) {
return 1 if $self->find_hts_in_build_dir($dir);
return 1 if $self->find_hts_in_install_dir($dir);
$self->die_hts_not_found(
"HTSLIB_DIR=$ENV{HTSLIB_DIR} environment variable does not contain expected files\n"
);
}
# Search through remaining possible (but not fatal) locations:
last;
}
}
return 1 if $found;
$self->die_hts_not_found();
}
sub set_include_and_compiler_flags {
my ($self) = @_;
else {
return 0;
}
}
sub die_hts_not_found {
my ($self, $msg) = @_;
$msg ||= '';
die $msg, <<END;
view release on metacpan or search on metacpan
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
Status : public
=cut
sub types {
shift->throw_not_implemented;
}
=head2 insert_sequence
Title : insert_sequence
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
=cut
sub attributes {
my $self = shift;
shift->throw_not_implemented;
}
=head2 start_bulk_update,finish_bulk_update
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
implemented by an adaptor that inherits from
Bio::DB::SeqFeature::Store. It returns true on success. @features = $db->features(-seqid=>'Chr1');
=cut
sub _init_database { shift->throw_not_implemented }
=head2 _store
Title : _store
Usage : $success = $db->_store($indexed,@objects)
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
# _store($indexed,@objs)
sub _store {
my $self = shift;
my $indexed = shift;
my @objs = @_;
$self->throw_not_implemented;
}
=head2 _fetch
Title : _fetch
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
method to unserialize it and synchronize the primary_id.
=cut
# _fetch($id)
sub _fetch { shift->throw_not_implemented }
=head2 _fetch_many
Title : _fetch_many
Usage : $feature = $db->_fetch_many(@primary_ids)
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
for a feature object that has changed.
=cut
# this is called to index a feature
sub _update_indexes { shift->throw_not_implemented }
=head2 _start_reindexing, _end_reindexing
Title : _start_reindexing, _end_reindexing
Usage : $db->_start_reindexing()
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
recognized.
=cut
# bottleneck query generator
sub _features { shift->throw_not_implemented }
=head2 _search_attributes
Title : _search_attributes
Usage : @result_list = $db->_search_attributes("text search string",[$tag1,$tag2...],$limit)
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
difference between this and the public method is that the tag list is
guaranteed to be an array reference.
=cut
sub _search_attributes { shift->throw_not_implemented }
=head2 can_store_parentage
Title : can_store_parentage
Usage : $flag = $db->can_store_parentage
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
(e.g. Bio::DB::SeqFeature) will invoke this method to store
feature/subfeature relationships in a normalized table.
=cut
sub _add_SeqFeature { shift->throw_not_implemented }
=head2 _fetch_SeqFeatures
Title : _fetch_SeqFeatures
Usage : @children = $db->_fetch_SeqFeatures($parent_feature)
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
feature/subfeature relationships from the database.
=cut
# _get_SeqFeatures($parent,@list_of_child_types)
sub _fetch_SeqFeatures {shift->throw_not_implemented }
=head2 _insert_sequence
Title : _insert_sequence
Usage : $success = $db->_insert_sequence($seqid,$sequence_string,$offset)
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
this method in order to store and retrieve nucleotide or protein
sequence.
=cut
sub _insert_sequence { shift->throw_not_implemented }
# _fetch_sequence() is similar to old dna() method
=head2 _fetch_sequence
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
this method in order to store and retrieve nucleotide or protein
sequence.
=cut
sub _fetch_sequence { shift->throw_not_implemented }
sub seq {
my $self = shift;
my ($seq_id,$start,$end) = @_;
if (my $a = $self->dna_accessor) {
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
This method is invoked by seq_ids() to return all sequence IDs
(coordinate systems) known to the database.
=cut
sub _seq_ids { shift->throw_not_implemented }
=head2 _start_bulk_update,_finish_bulk_update
Title : _start_bulk_update, _finish_bulk_update
Usage : $db->_start_bulk_update
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
=back
=cut
sub _firstid { shift->throw_not_implemented }
sub _nextid { shift->throw_not_implemented }
sub _existsid { shift->throw_not_implemented }
sub _deleteid { shift->throw_not_implemented }
sub _clearall { shift->throw_not_implemented }
sub _featurecount { shift->throw_not_implemented }
=head1 Internal Methods
These methods are internal to Bio::DB::SeqFeature::Store and adaptors.
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
1000 bp, you may see some shifting of counts between adjacent bins.
=cut
sub coverage_array {
shift->throw_not_implemented;
}
package Bio::DB::SeqFeature::Store::FeatureIterator;
$Bio::DB::SeqFeature::Store::FeatureIterator::VERSION = '1.7.5';
view release on metacpan or search on metacpan
lib/Bio/DOOP/Sequence.pm view on Meta::CPAN
sub get_ver {
my $self = shift;
return($self->{VERSION});
}
=head2 get_annot_id
Returns the sequence annotation primary id. This is the internal ID from the MySQL database.
Return type: string
my $annotation_id = $seq->get_annot_id;
=cut
sub get_annot_id {
my $self = shift;
return($self->{ANNOT});
}
=head2 get_orig_id
view release on metacpan or search on metacpan
lib/Bio/Tools/EUtilities/EUtilDataI.pm view on Meta::CPAN
shift->warn("Object may not need an iterator. Please check the documentation.");
}
sub _add_data {
shift->throw_not_implemented;
}
sub to_string {
shift->throw_not_implemented;
}
sub _text_wrap {
shift;
view release on metacpan or search on metacpan
nextchar|||
ninstr|||
no_bareword_allowed|||
no_fh_allowed|||
no_op|||
not_a_number|||
nothreadhook||5.008000|
nuke_stacks|||
num_overflow|||n
offer_nice_chunk|||
oopsAV|||
# if !defined(__PATCHLEVEL_H_INCLUDED__) && !(defined(PATCHLEVEL) && defined(SUBVERSION))
# define PERL_PATCHLEVEL_H_IMPLICIT
# include <patchlevel.h>
# endif
# if !(defined(PERL_VERSION) || (defined(SUBVERSION) && defined(PATCHLEVEL)))
# include <could_not_find_Perl_patchlevel.h>
# endif
# ifndef PERL_REVISION
# define PERL_REVISION (5)
/* Replace: 1 */
# define PERL_VERSION PATCHLEVEL
view release on metacpan or search on metacpan
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
=cut
sub fetch_all_by_outward_search {
my $self = shift;
my ($ref_feature, $respect_strand, $opposite_strand, $downstream, $upstream, $start_search_range,
$limit,$not_overlapping,$five_prime,$three_prime, $max_range) =
rearrange([qw(FEATURE SAME_STRAND OPPOSITE_STRAND DOWNSTREAM UPSTREAM RANGE LIMIT NOT_OVERLAPPING FIVE_PRIME THREE_PRIME MAX_RANGE)], @_);
my $factor = 1;
$limit ||= 1;
$start_search_range ||= 1000;
my $current_search_range = $start_search_range;
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
-SAME_STRAND => $respect_strand,
-OPPOSITE_STRAND => $opposite_strand,
-DOWNSTREAM => $downstream,
-UPSTREAM => $upstream,
-LIMIT => $limit,
-NOT_OVERLAPPING => $not_overlapping,
-FIVE_PRIME => $five_prime,
-THREE_PRIME => $three_prime,
)
};
$factor++;
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
Caller : general
=cut
sub fetch_all_nearest_by_Feature{
my $self = shift;
my ($ref_feature, $respect_strand, $opposite_strand, $downstream, $upstream, $search_range,$limit,$not_overlapping,$five_prime,$three_prime) =
rearrange([qw(FEATURE SAME_STRAND OPPOSITE_STRAND DOWNSTREAM UPSTREAM RANGE LIMIT NOT_OVERLAPPING FIVE_PRIME THREE_PRIME)], @_);
if ( !defined($search_range)) {
$search_range ||= 1000;
}
$limit ||= 1;
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
@candidates = grep { ($_->strand == 1) ? $_->seq_region_end > $ref_feature->end : $_->seq_region_start > $ref_feature->end } @candidates;
}
}
# Then sort and prioritise the candidates
my $finalists; # = [[feature, distance, centre-weighted distance, length, dbID],..]
$finalists = $self->select_nearest($ref_feature,\@candidates,$limit,$not_overlapping,$five_prime,$three_prime);
$finalists = [ map { [ splice @$_,0,2 ]} @$finalists ]; # Remove the ugly bits from the sight of users.
return $finalists;
}
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
Arg [2] : Listref of Features to be considered for nearness.
Arg [3] : Integer, limited number of Features to return. Equally near features are all returned in spite of this limit
Arg [4] : Boolean, Overlapping prohibition. Overlapped Features are forgotten
Arg [5] : Boolean, use the 5' ends of the nearby features for distance calculation
Arg [6] : Boolean, use the 3' ends of the nearby features for distance calculation
Example : $feature_list = $feature_adaptor->select_nearest($ref_feature,\@candidates,$limit,$not_overlapping)
Description: Take a list of possible features, and determine which is nearest. Nearness is a
tricky concept. Beware of using the distance between Features, as it may not be the number you think
it should be.
Returntype : listref of Features ordered by proximity
Caller : BaseFeatureAdaptor->fetch_all_nearest_by_Feature
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
sub select_nearest {
my $self = shift;
my $ref_feature = shift;
my $candidates = shift;
my $limit = shift;
my $not_overlapping = shift;
my $five_prime = shift;
my $three_prime = shift;
# Convert circular coordinates to linear ones for distance calculation
my $ref_start = ($ref_feature->start < $ref_feature->end) ? $ref_feature->start : $ref_feature->start - $ref_feature->length; # Not ->end, in case circular
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
? $neighbour->seq_region_start : $neighbour->seq_region_start - $neighbour->length; # Not ->end, in case it is circular
my $neigh_midpoint = $self->_compute_midpoint($neighbour);
my $neigh_end = $neighbour->seq_region_end;
# discard overlaps early if not required.
next if ( $not_overlapping
&& (
( $neigh_start >= $ref_start && $neigh_end <= $ref_end )
|| ( $neigh_end <= $ref_end && $neigh_end >= $ref_start )
)
);
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
next unless ($shortest_distance || $adjusted_distance);
}
else {
($shortest_distance,$adjusted_distance) = $self->_compute_nearest_end(@args);
}
push @$position_matrix,[ $neighbour, $shortest_distance, $adjusted_distance, $neighbour->length, $neighbour->display_id] unless ($not_overlapping && $shortest_distance == 0);
}
# Order by distance, then centre-to-centre distance, then smallest feature first, then an arbitrary ID.
# $position_matrix looks like this:
# [ [ $feature, closest measure of distance, size, dbID ] ]
view release on metacpan or search on metacpan
lib/Bio/FeatureIO.pm view on Meta::CPAN
=cut
sub next_feature {
my ($self, $seq) = @_;
$self->throw_not_implemented;
}
=head2 write_feature
Title : write_feature
lib/Bio/FeatureIO.pm view on Meta::CPAN
=cut
sub write_feature {
my ($self, $seq) = @_;
$self->throw_not_implemented();
}
=head2 _load_format_module
Title : _load_format_module
view release on metacpan or search on metacpan
t/boilerplate.t view on Meta::CPAN
use 5.006;
use strict;
use warnings;
use Test::More tests => 13;
sub not_in_file_ok
{
my ($filename, %regex) = @_;
open(my $fh, '<', $filename) || die "couldn't open $filename for reading: $!";
my $ref = do {local $/; <$fh>};
t/boilerplate.t view on Meta::CPAN
}
sub module_boilerplate_ok
{
my ($module) = @_;
not_in_file_ok($module =>
'the great new $MODULENAME' => qr/ - The great new /,
'boilerplate description' => qr/Quick summary of what the module/,
'stub function definition' => qr/function[12]/,
);
return;
t/boilerplate.t view on Meta::CPAN
TODO:
{
local $TODO = "Need to replace the boilerplate text";
not_in_file_ok(README =>
"The README is used..." => qr/The README is used/,
"'version information here'" => qr/to provide version information/,
);
not_in_file_ok(Changes =>
"placeholder date/time" => qr(Date/time)
);
module_boilerplate_ok('lib/Bio/GeneDesign.pm');
module_boilerplate_ok('lib/Bio/GeneDesign/Basic.pm');
view release on metacpan or search on metacpan
bin/gonz_compcol.pl view on Meta::CPAN
= dict_slurp( $a_f, { key_idx => $opt{a}, val_idx => $opt{va}, uniq => 0, concat_keys => $opt{concat} } );
my $b_data
= dict_slurp( $b_f, { key_idx => $opt{b}, val_idx => $opt{vb}, uniq => 0, concat_keys => $opt{concat} } );
my @both = grep { exists( $b_data->{$_} ) } keys %$a_data;
my @not_in_a = grep { !exists( $a_data->{$_} ) } keys %$b_data;
my @not_in_b = grep { !exists( $b_data->{$_} ) } keys %$a_data;
say "A: $a_f";
say "B: $b_f";
say "";
bin/gonz_compcol.pl view on Meta::CPAN
say "first 3:";
say " " . join( "\n ", @both[ 0 .. 2 ] );
}
say "";
say "UNIQUE TO A: " . scalar @not_in_b;
if ( scalar @not_in_b > 0 ) {
say "first 3:";
say " " . join( "\n ", @not_in_b[ 0 .. 2 ] );
}
say "";
say "UNIQUE TO B: " . scalar @not_in_a;
if ( scalar @not_in_a > 0 ) {
say "first 3:";
say " " . join( "\n ", @not_in_a[ 0 .. 2 ] );
}
say "";
my %both = map { $_ => 1 } @both;