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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

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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__} );

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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 ) = @_;

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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");

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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})

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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;

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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");

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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);
}

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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;

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

    return( $fitsP );
}

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

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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);

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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();

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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 ( $mark =~ /^\d+$/ );

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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";

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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.

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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}})
  {

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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;

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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);

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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';

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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);

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lib/Bio/RNA/Barriers/Results.pm  view on Meta::CPAN

# RateMatrix::keep_connected()), delete all other minima and update their
# ancesters' basin size information accordingly.
# Arguments:
#   ordered_connected_indices: ordered list of indices of (all???)
#       connected minima.
sub update_connected {
    my ($self, @ordered_connected_indices) = @_;

    # Go through all mins and check whether they're next in the connected
    # (==kept) index list. If not, add to removal list.
    my @connected_mins = $self->get_mins(@ordered_connected_indices);

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lib/Bio/ToolBox/Parser/ucsc/builder.pm  view on Meta::CPAN

	# transcript is complete
	return $transcript;
}

sub update_attributes {
	my ( $self, $seqf ) = @_;

	# add Note if possible
	if ( $self->note ) {
		$self->add_unique_attribute( $seqf, 'Note', $self->note );

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lib/Bio/VertRes/Config/MultipleTopLevelFiles.pm  view on Meta::CPAN

has 'database'         => ( is => 'ro', isa => 'Str',      required => 1 );
has 'pipeline_configs' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'config_base'  => ( is => 'ro', isa => 'Str',     required => 1 );

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

    my %short_name_to_configs;

    # split by short name

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lib/Bio/DB/BioSQL/BaseDriver.pm  view on Meta::CPAN

           then give the class name.


=cut

sub update_object{
    my ($self,$adp,$obj,$fkobjs) = @_;
    
    # obtain the object's slots to be serialized
    my @slots = $adp->get_persistent_slots($obj);
    # get the UPDATE statement 

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lib/Bio/Tools/Run/Phylo/Hyphy/Base.pm  view on Meta::CPAN

 Args    : boolean: keep existing parameter values


=cut

sub update_ordered_parameters {
   my ($self) = @_;
   for (my $i=0; $i < scalar(@{$self->{'_orderedparams'}}); $i++) {
      my ($param,$val) = each %{$self->{'_orderedparams'}[$i]};
      if (exists $self->{'_params'}{$param}) {
         $self->{'_orderedparams'}[$i] = {$param, $self->{'_params'}{$param}};

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Bio/Assembly/Scaffold.pm  view on Meta::CPAN

    Returns : 1 for success
    Args    : none 

=cut

sub update_seq_list {
    my $self = shift;
    
    $self->{'_seqs'} = {};

    # Put sequences in contigs in list of sequences belonging to the scaffold

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lib/BioX/Workflow/Command/run/Rules/Directives/Walk.pm  view on Meta::CPAN

Take the values from walk_directive and update the directive

=cut

sub update_directive {
    my $self = shift;
    my $text = shift;

    my ( $key, $container, $index );

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Bioinf.pl  view on Meta::CPAN

# Returns   :
# Argument  :
# Category  :
# Version   : 2.8
#--------------------------------------------------------------------
sub update_subroutines{
  #"""""""""""""""""< handle_arguments{ head Ver 4.1 >"""""""""""""""""""
  my(@A)=&handle_arguments(@_);my($num_opt)=${$A[7]};my($char_opt)=${$A[8]};
  my(@hash)=@{$A[0]};my(@file)=@{$A[4]};my(@dir)=@{$A[3]};my(@array)=@{$A[1]};
  my(@string)=@{$A[2]};my(@num_opt)=@{$A[5]};my(@char_opt)=@{$A[6]};
  my(@raw_string)=@{$A[9]};my(%vars)=%{$A[10]};my(@range)=@{$A[11]};

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lib/Bitcoin/Crypto/Transaction.pm  view on Meta::CPAN

	my $witness = $with_witness - $base;

	return $base * 4 + $witness;
}

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

	foreach my $input (@{$self->inputs}) {
		$input->utxo->unregister if $input->utxo_registered;