view release on metacpan or  search on metacpan

lib/B/DeparseTree/TreeMain.pm  view on Meta::CPAN

    $info->{other_ops} = \@skipped_ops;
    return $info;

}

sub update_node($$$$)
{
    my ($self, $node, $prev_expr, $op) = @_;
    $node->{prev_expr} = $prev_expr;
    my $addr = $prev_expr->{addr};
    if ($addr && ! exists $self->{optree}{$addr}) {

 view release on metacpan or  search on metacpan

eg/nagios2bugzilla/talktobugzilla.pl  view on Meta::CPAN

    return 1

}

sub update_bug {

    my $f = shift;
    my $bug = shift;
    my $params = shift;

 view release on metacpan or  search on metacpan

lib/Backed_Objects.pm  view on Meta::CPAN

  $self->on_update($obj);
  $self->on_order_change;
  $self->on_any_change;
}

sub update {
  my ($self, $obj) = @_;
  die "Updating an object not in DB!" unless $self->id($obj);
  $self->before_update($obj);
  $self->do_update($obj);
  $self->post_process($obj);

 view release on metacpan or  search on metacpan

lib/BalanceOfPower/Relations/RelPack.pm  view on Meta::CPAN

    else
    {
        return 0;
    }
}
sub update_link
{
    my $self = shift;
    my $link = shift;
    $self->delete_link($link->node1, $link->node2);
    $self->add_link($link);

 view release on metacpan or  search on metacpan

lib/Basset/DB/Table.pm  view on Meta::CPAN

=cut

__PACKAGE__->add_attr('_cached_bindables');

sub update_bindables {
	my $self = shift;
	if (my $bindables = $self->_cached_bindables->{'update'}) {
		return @$bindables;
	} else {
        my @excess = $self->primary_cols;

lib/Basset/DB/Table.pm  view on Meta::CPAN

=end btest

=cut

sub update_query {
	my $self = shift;

	my @cols = @_;

	if (@cols){

 view release on metacpan or  search on metacpan

lib/Bb/Collaborate/V3.pm  view on Meta::CPAN

                                                   startTime => '1448922188000',
                                                   ... });

=cut

sub update {
    my ($class, $data, %opt) = @_;

    $opt{command} ||= 'Set'.$class->entity_name;

    return $class->SUPER::update($data, %opt);

 view release on metacpan or  search on metacpan

lib/Beagle/Backend/base.pm  view on Meta::CPAN

        }
    }
    return %file;
}

sub update {
    my $self   = shift;
    my $object = shift;
}

sub delete {
    my $self   = shift;
    my $object = shift;
}

sub updated {
    my $self = shift;
}

no Any::Moose;
__PACKAGE__->meta->make_immutable;

 view release on metacpan or  search on metacpan

lib/Benchmark/Perl/Formance/Plugin/Shootout/knucleotide.pm  view on Meta::CPAN

        }

        print $output if $PRINT;
}

sub update_hash_for_frame {
  my $frame = $_[0];
  my @threads;
  for my $i (0 .. $threads - 1) {
    use integer;
    my $begin = $l * $i / $threads;

lib/Benchmark/Perl/Formance/Plugin/Shootout/knucleotide.pm  view on Meta::CPAN

    my $count = $thread->join;
    $h{$_} += $count->{$_} for keys %$count;
  }
}

sub update_hash_slice {
  my ($frame, $begin, $end) = @_;
  my %local;
  $local{substr($sequence,$_,$frame)}++ for $begin .. $end;
  return \%local;
}

 view release on metacpan or  search on metacpan

lib/BenchmarkAnything/Storage/Backend/SQL/Query/common.pm  view on Meta::CPAN

            bench_value_id = ?
    ", @{$hr_vals}{qw/ new_bench_value_id old_bench_value_id /} );

}

sub update_benchmark_backup_value {

    my ( $or_self, $hr_vals ) = @_;

    return $or_self->execute_query( "
        UPDATE $or_self->{config}{tables}{benchmark_backup_value_table}

lib/BenchmarkAnything/Storage/Backend/SQL/Query/common.pm  view on Meta::CPAN

        WHERE raw_bench_bundle_id IN (".join(',', ('?') x @a_vals).")
    ", @a_vals );

}

sub update_raw_bench_bundle_set_processed {

    my ( $or_self, @a_vals ) = @_;

    return $or_self->execute_query( "
        UPDATE raw_bench_bundles

lib/BenchmarkAnything/Storage/Backend/SQL/Query/common.pm  view on Meta::CPAN

              raw_bench_bundle_id = ?
    ", @a_vals );

}

sub update_raw_bench_bundle_set_processed2 {

    my ( $or_self, @a_vals ) = @_;

    return $or_self->execute_query( "
        UPDATE raw_bench_bundles

lib/BenchmarkAnything/Storage/Backend/SQL/Query/common.pm  view on Meta::CPAN

              raw_bench_bundle_id IN (".join(',', ('?') x @a_vals).")
    ", @a_vals );

}

sub update_raw_bench_bundle_set_processed3 {

    my ( $or_self, @a_vals ) = @_;

    return $or_self->execute_query( "
        UPDATE raw_bench_bundles

 view release on metacpan or  search on metacpan

lib/Biblio/SIF/Patron.pm  view on Meta::CPAN

sub country         { shift()->_string( 299, 20, @_ ) }
sub phone           { shift()->_string( 319, 25, @_ ) }
sub cell_phone      { shift()->_string( 344, 25, @_ ) }
sub fax             { shift()->_string( 369, 25, @_ ) }
sub other_phone     { shift()->_string( 394, 25, @_ ) }
sub update_date     { shift()->_date(   419,     @_ ) }

sub postal_code     { shift()->_string( 289, 10, @_ ) }  # Alias
sub state_province  { shift()->_string( 282,  7, @_ ) }  # Alias
sub zip_postal      { shift()->_string( 289, 10, @_ ) }  # Alias

 view release on metacpan or  search on metacpan

lib/Bigtop/Parser.pm  view on Meta::CPAN

    return [ $self->{__IDENT__} => $self->{__NAME__} ];
}

# if a renamed field is in foreign_display, update it
sub update_foreign_display {
    my $self = shift;
    shift;
    my $data = shift;

    return unless $self->{ __TYPE__ } eq 'foreign_display';

lib/Bigtop/Parser.pm  view on Meta::CPAN

    return [ $self->{ __DEF__ }{ __ARGS__ } ];
}

# If the old label was the default, the label will be changed to default
# for new name.
sub update_label {
    my $self         = shift;
    my $child_output = shift;
    my $data         = shift;

    return unless $self->{ __KEYWORD__ } eq 'label';

lib/Bigtop/Parser.pm  view on Meta::CPAN

    };

    return bless $self, $class;
}

sub update_label {
    my $self = shift;

    return [ $self->{ __ARGS__ }->get_first_arg ];
}

lib/Bigtop/Parser.pm  view on Meta::CPAN

        $ident . '::form_name'  => $table,
        $ident . '::extra_keys' => $extra_keys,
    ];
}

sub update_field_name {
    my $self         = shift;
    my $child_output = shift;
    my $data         = shift;

    my $count = 0;

lib/Bigtop/Parser.pm  view on Meta::CPAN

        keyword     => $self->{__KEYWORD__},
        values      => $self->{__ARGS__},
    } ];
}

sub update_field_name {
    my $self = shift;
    shift;
    my $data = shift;

    unless ( $self->{ __KEYWORD__ } eq 'cols'

lib/Bigtop/Parser.pm  view on Meta::CPAN

    my $self = shift;

    return [ $self->{__KEYWORD__} => $self->{__ARGS__} ];
}

sub update_config_statement {
    my $self   = shift;
    shift;
    my $data   = shift;

    return unless ( $data->{ ident } eq $self->{__PARENT__}->get_ident );

lib/Bigtop/Parser.pm  view on Meta::CPAN

        keyword     => $self->{__KEYWORD__},
        value       => $self->{__ARGS__}[0],
    } ];
}

sub update_config_statement {
    my $self   = shift;
    shift;
    my $data   = shift;

    return unless ( $data->{ ident } eq $self->{__PARENT__}->{__IDENT__} );

 view release on metacpan or  search on metacpan

lib/Bintray/API/Package.pm  view on Meta::CPAN

        anon => 1,
    );
} ## end sub info

## Update Package
sub update {
    my ( $self, @args ) = @_;

    my %opts = validate_with(
        params => [@args],
        spec   => {

lib/Bintray/API/Package.pm  view on Meta::CPAN

            'packages',            $self->repo()->subject()->name(),
            $self->repo()->name(), $self->name(),
        ),
        content => $json,
    );
} ## end sub update

## Create Version
sub create_version {
    my ( $self, @args ) = @_;

lib/Bintray/API/Package.pm  view on Meta::CPAN

        content => $json,
    );
} ## end sub set_attributes

## Update Attributes
sub update_attributes { return shift->set_attributes( @_, update => 1, ); }

## Add WebHook
sub set_webhook {
    my ( $self, @args ) = @_;

 view release on metacpan or  search on metacpan

lib/Bio/BPWrapper/SeqManipulations.pm  view on Meta::CPAN

	$out->write_seq($seqobj);
    }
}


sub update_longest_orf {
    while( my $seqobj  = $in->next_seq() ) {
	my $pep_string = $seqobj->translate( undef, undef, 0 )->seq();
	unless ($pep_string =~ /\*[A-Z]/) { # no internal stop; don't proceed
	    my $id = $seqobj->id();
	    $seqobj->id($id . "|+1");

 view release on metacpan or  search on metacpan

lib/Bio/BioStudio/Foswiki.pm  view on Meta::CPAN

=head2 update_wiki

=cut

sub update_wiki
{
  my ($BS, $pa, $commentarr) = @_;
  my $VERPATH = $pa->{CHRPATH} . "/$pa->{NEWCHROMOSOME}.txt";
  my @arr = @{$commentarr};
  if ($BS->{enable_gbrowse})

 view release on metacpan or  search on metacpan

lib/Bio/BioVeL/AsynchronousService.pm  view on Meta::CPAN

the process that was launched by launch(), and will update the status, e.g. from RUNNING
to DONE or ERROR.

=cut

sub update { 
	my $self   = shift;
	my $log    = $self->logger;
	my $status = DONE;
	if ( my $pid = $self->pid ) {
		my $timestamp = $self->timestamp;

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lib/Bio/Cellucidate/Base.pm  view on Meta::CPAN

    my $id = shift;
    my $format = shift;
    $self->rest('GET', $self->route . "/" . $id, $format)->processResponse;
}

sub update {
    my $self = shift;
    my $id = shift;
    my $data = $self->args(shift);
    my $format = shift;

 view release on metacpan or  search on metacpan

lib/Bio/DB/GFF/Adaptor/dbi/pg.pm  view on Meta::CPAN

  }
  $sth->finish;
  return $count;
}

sub update_sequences {
  my $self = shift;
  my $dbh  = $self->features_db;
 
  $dbh->do("SELECT setval('public.fdata_fid_seq', max(fid)+1) FROM fdata");
  $dbh->do("SELECT setval('public.fattribute_fattribute_id_seq', max(fattribute_id)+1) FROM fattribute");

 view release on metacpan or  search on metacpan

lib/Bio/DB/SeqFeature/NormalizedFeature.pm  view on Meta::CPAN

the database. This is not needed for add_SeqFeature() as update() is
invoked automatically.

=cut

sub update {
  my $self = shift;
  my $store = $self->object_store or return;
  $store->store($self);
}

 view release on metacpan or  search on metacpan

lib/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm  view on Meta::CPAN

               the altered version.
  Returntype : Integer - the return value of the store method, viz. whether the
               insert was successful.
=cut

sub update {
    my $self = shift;
    my $allele_group = shift;
    assert_ref($allele_group, 'Bio::EnsEMBL::AltAlleleGroup', 'allele_group');
    throw "Cannot update an AltAlleleGroup without a dbID. AltAlleleGroups should be fetched from the DB prior to updating them" if ! $allele_group->dbID();
    my $keep_group = 1;

 view release on metacpan or  search on metacpan

lib/Bio/GMOD/Blast/Graph/MapSpace.pm  view on Meta::CPAN

    return( $fitsP );
}

#######################################################################
sub updateFromWrapper {
#######################################################################
    my( $self, $wrap ) = @_;
    my( $space );
    my( $count );
    my( $wheight );

 view release on metacpan or  search on metacpan

GMOD/Admin/Update.pm  view on Meta::CPAN

@ISA = qw/Bio::GMOD Bio::GMOD::Util::CheckVersions/;

# Currently, there is no generic update method.  Bio::GMOD::Admin::Update
# must be subclassed for your particular MOD
sub update {
  my $self = shift;
  my $adaptor = $self->adaptor;
  my $name = $adaptor->name;
  $self->logit("$name does not currently support automated updates at this time. Please ask the administrators of $name to add this functionality.",
	       -die => 1);

 view release on metacpan or  search on metacpan

AL_Spots/AL_Spots.pm  view on Meta::CPAN

  $self->id($pkey);
  $self->als_pk($pkey);
  return $pkey;
}

sub update_db {
  my ($self,$dbh) = @_;
  assert_dbh($dbh);
  die "Bio::Genex::AL_Spots::update_db: object not in DB"
    unless defined $self->id() && defined $self->als_pk();

 view release on metacpan or  search on metacpan

lib/Bio/Gonzales/Domain/Identification/HMMER/SeqMarks.pm  view on Meta::CPAN

    } else {
        return $self->$orig;
    }
};

sub update_mark {
    my ( $self, $mark, $from, $to ) = @_;

    $mark = $self->mark_from_name($mark)
        unless ( $mark =~ /^\d+$/ );

 view release on metacpan or  search on metacpan

MAGE/XML/Handler/ObjectHandler/SQL.pm  view on Meta::CPAN

  my $indent = ' ' x $self->indent_level();
  my $fh = $self->fh();
  print $fh "$indent</$tag>\n";
}     

sub update_or_insert_row {
  my $self = shift || croak("parameter self not passed");
  my %args = @_;

  #### Decode the argument list
  my $table_name         = $args{'table_name'}         || die "ERROR: table_name not passed";

 view release on metacpan or  search on metacpan

lib/Bio/MAGETAB/Util/Builder.pm  view on Meta::CPAN

has 'relaxed_parser'      => ( is         => 'rw',
                               isa        => Bool,
                               default    => 0,
                               required   => 1 );

sub update {

    # Empty stub method; updates are not required when the objects are
    # all held in scope by the database hashref. This method is
    # overridden in persistence subclasses dealing with
    # e.g. relational databases.

 view release on metacpan or  search on metacpan

lib/Bio/MLST/Download/Database.pm  view on Meta::CPAN

has 'species'              => ( is => 'ro', isa => 'Str',     required => 1 );

has 'destination_directory' => ( is => 'ro', isa => 'Str',     lazy => 1, builder => '_build_destination_directory' );


sub update
{
  my ($self) = @_;

  for my $allele_file (@{$self->database_attributes->{alleles}})
  {

 view release on metacpan or  search on metacpan

lib/Bio/MUST/Apps/HmmCleaner.pm  view on Meta::CPAN

    }

    return \%matrix;
}

sub update_cleaners {
    my $self = shift;
    my $threshold = shift;
    $self->_set_threshold($threshold);
    my $costs = shift // $self->_get_default_cost;

 view release on metacpan or  search on metacpan

lib/Bio/MUST/Core/Taxonomy.pm  view on Meta::CPAN

    ### Done!
    return $tax;
}


sub update_cache {
    my $self = shift;

    my $cachefile = file($self->tax_dir, $CACHEDB);
    ### Updating binary cache file: $cachefile->stringify
    $self->store($cachefile);

 view release on metacpan or  search on metacpan

lib/Bio/Phylo/Beagle.pm  view on Meta::CPAN

           -deriv1 => Optional: List of indices of first derivative matrices to update
           -deriv2 => Optional: List of indices of second derivative matrices to update

=cut

sub update_transition_matrices {
    $logger->info("@_");
    my $self = shift;
    my %args = looks_like_hash @_;
        
    # create node and edge arrays

lib/Bio/Phylo/Beagle.pm  view on Meta::CPAN

           -count      => Number of operations (input)
           -index      => Index number of scaleBuffer to store accumulated factors (input)

=cut

sub update_partials {
    $logger->info("@_");
    my $self = shift;
    if ( my %args = looks_like_hash @_ ) {
        
        my $operations = $args{'-operations'} || throw 'BadArgs' => 'Need -operations argument';

 view release on metacpan or  search on metacpan

lib/Bio/PhyloNetwork/Factory.pm  view on Meta::CPAN

  $self->update();
  $self->{found}=[];
  bless($self,$pkg);
}

sub update {
  my ($self)=@_;

  my @candidates=$self->{oldnet}->edges();
  $self->{candidates}=\@candidates;
  $self->{numcandidates}=(scalar @candidates);