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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

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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

signature_for update_utxos => (
	method => Object,
	positional => [],
);

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

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

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lib/BlankOnDev/Repo.pm  view on Meta::CPAN

    # Read Sources list :

}
# Subroutine for update database repository on local system :
# ------------------------------------------------------------------------
sub update {
    # repo update :
    system('sudo apt-get update');
}
# Subroutine for install packages before build :
# ------------------------------------------------------------------------

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lib/BmltClient/ApiClient.pm  view on Meta::CPAN

# update header and query param based on authentication setting
#
# @param array $headerParams header parameters (by ref)
# @param array $queryParams query parameters (by ref)
# @param array $authSettings array of authentication scheme (e.g ['api_key'])
sub update_params_for_auth {
    my ($self, $header_params, $query_params, $auth_settings) = @_;

    return $self->_global_auth_setup($header_params, $query_params)
        unless $auth_settings && @$auth_settings;

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lib/Bootylicious/Document.pm  view on Meta::CPAN

    print $file $self->content || '';

    return $self;
}

sub update {
    my $self = shift;
    my $hash = shift;

    $hash ||= {};
    foreach my $key (keys %$hash) {

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lib/Bot/Backbone/Service/OFun/Karma.pm  view on Meta::CPAN

    # OK!
    return 1;
}


sub update_scores {
    my ($self, $message) = @_;

    my @args = $message->all_args;
    THING: for my $i (0 .. $#args) {
        my $arg  = $args[$i];

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lib/Bot/BasicBot/Pluggable/Module/Seen.pm  view on Meta::CPAN

    my $what = 'joining the channel';
    $self->update_seen( $mess->{who}, $mess->{channel}, $what );
    return;
}

sub update_seen {
    my ( $self, $who, $channel, $what ) = @_;
    my $nick = lc $who;
    $channel = lc $channel;
    my $ignore_channels = $self->get('user_ignore_channels') || {};
    return if exists $ignore_channels->{$channel};

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JabberBot.pm  view on Meta::CPAN

	}
	$self->roster(\@roster);
    }
} 

sub update_session {
    my ($self,$said) = @_;
    my $session = $self->session;
    my $dialogue = $session->{$said->{who}} || [ ];
    my $session_length = $self->session_length || '8';
    if (scalar(@{$dialogue}) > 8) {

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examples/UberBot/Seen.pm  view on Meta::CPAN

    else {
        return "I haven't seen $user, $nick";
    }
}

sub update_seen {
    my ($self, $nick, $channel, $msg) = @_;
    $self->{seen}{$nick} = {
        'time' => time(),
        'msg' => $msg,
        'channel' => $channel,

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t/lib/Bot/Telegram/Test.pm  view on Meta::CPAN

sub loop_for_a_second {
  timer { Mojo::IOLoop -> stop } 1;
  Mojo::IOLoop -> start;
}

sub update {
  my ($type, $id) = @_;

  return {
    $type => {
      foo => 'bar',