Result:
found more than 465 distributions - search limited to the first 2001 files matching your query
( run in 1.224 )
Benchmark-Thread-Size
view release on metacpan or search on metacpan
lib/Benchmark/Thread/Size.pm view on Meta::CPAN
$size{$threads} = $size;
# Kill the process quickly (should work even on Windows)
# Close the pipe for good measure
# Remove the script
# Move cursor so the next number can be shown
kill 15,$pid;
close( $out ); # don't care whether successful
# unlink( $testfile );
print STDERR "\b\b\b\b";
BerkeleyDB-Easy
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lib/BerkeleyDB/Easy.pm view on Meta::CPAN
$db->put('foo', 'bar');
my $foo = $db->get('foo');
my $cur = $db->cursor;
while (my ($key, $val) = $cur->next) {
$db->del($key);
}
BerkeleyDB-Lite
view release on metacpan or search on metacpan
my $value = "" ;
my @values = () ;
# database locked
my $cursor = $self->db_cursor ;
if ( $cursor->c_get( $key, $value, DB_SET ) ) {
$cursor = undef ;
return @values ;
}
push @values, $value ;
while ( ! $cursor->c_get( $key, $value, DB_NEXT_DUP ) ) {
push @values, $value ;
}
$cursor = undef ;
return @values ;
}
## experimental to improve durability
sub sync {
my $self = tied %$ref ;
my $key = shift ;
my $value = shift ;
my $orig = $value ;
my $cursor = $self->db_cursor( DB_WRITECURSOR ) ;
my $status = $cursor->c_get( $key, $value, DB_GET_BOTH ) ;
## Warning: Ensure consistency between numbers with strings.
## See Storable documentation.
$cursor->c_del unless $status ;
$cursor = undef ;
return $status ;
}
sub DESTROY {
return [] unless $partkey ;
my $length = length $partkey ;
# database locked
my $cursor = $self->db_cursor ;
my $value = 0 ;
my $key = $partkey ;
my $status = $cursor->c_get( $key, $value, DB_SET_RANGE ) ;
while ( $key ) {
last if $status || substr( $key, 0, $length ) ne $partkey ;
if ( $isunique ) {
}
else {
push @each, [ $key, $value ] ;
}
$status = $cursor->c_get( $key, $value, DB_NEXT ) ;
}
$cursor = undef ;
@each = map { [ $_, $unique{$_} ] } keys %unique if $isunique ;
return \@each ;
}
sub matchingkeys {
my $ref = shift ;
my $self = tied %$ref ;
my $key = 0 ;
my $value = 0 ;
my $cursor = $self->db_cursor() ;
$cursor->c_get( $key, $value, DB_LAST ) ;
$ref->{ $key +1 } = {} ;
$cursor = undef ;
return $key +1 ;
}
package BerkeleyDB::Lite::Btree::Lexical ;
BerkeleyDB-Locks
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$db{test} = 'failed' ;
print stderr " attempting read lock...\n" ;
my ( $k, $v ) ;
my $c = $db->db_cursor ;
$c->c_get( $k, $v, DB_FIRST ) ;
alarm( 4 ) ;
while ( $flag ) {
sleep 1 ;
BerkeleyDB-Manager
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lib/BerkeleyDB/Manager.pm view on Meta::CPAN
if ( my $ret = $self->env->txn_checkpoint( $self->checkpoint_kbyte, $self->checkpoint_min, 0 ) ) {
die $ret;
}
}
sub dup_cursor_stream {
my ( $self, @args ) = @_;
my %args = @args;
my ( $init, $key, $first, $cb, $cursor, $db, $n ) = delete @args{qw(init key callback_first callback cursor db chunk_size)};
my ( $values, $keys ) = @args{qw(values keys)};
my $pairs = !$values && !$keys;
croak "'values' and 'keys' are mutually exclusive" if $values && $keys;
$key ||= '';
$cursor ||= ( $db || croak "either 'cursor' or 'db' is a required argument" )->db_cursor;
$first ||= sub {
my ( $c, $r ) = @_;
my $v;
lib/BerkeleyDB/Manager.pm view on Meta::CPAN
my $g = $init && $self->$init(%args);
my $ret = [];
my $bulk = Data::Stream::Bulk::Array->new( array => $ret );
if ( $cursor->$first($ret) ) {
$cursor->c_count(my $count);
if ( $count > 1 ) { # more entries for the same value
# fetch up to $n times
for ( 1 .. $n-1 ) {
unless ( $cursor->$cb($ret) ) {
return $bulk;
}
}
# and defer the rest
my $rest = $self->cursor_stream(@args, callback => $cb, cursor => $cursor);
return $bulk->cat($rest);
}
return $bulk;
} else {
return nil();
}
}
sub cursor_stream {
my ( $self, %args ) = @_;
my ( $init, $cb, $cursor, $db, $f, $n ) = delete @args{qw(init callback cursor db flag chunk_size)};
my ( $values, $keys ) = @args{qw(values keys)};
my $pairs = !$values && !$keys;
croak "'values' and 'keys' are mutually exclusive" if $values && $keys;
$cursor ||= ( $db || croak "either 'cursor' or 'db' is a required argument" )->db_cursor;
$f ||= DB_NEXT;
$cb ||= do {
my ( $k, $v ) = ( '', '' );
lib/BerkeleyDB/Manager.pm view on Meta::CPAN
$n ||= $self->chunk_size;
Data::Stream::Bulk::Callback->new(
callback => sub {
return unless $cursor;
my $g = $init && $self->$init(%args);
my $ret = [];
for ( 1 .. $n ) {
unless ( $cursor->$cb($ret) ) {
# we're done, this is the last block
undef $cursor;
return ( scalar(@$ret) && $ret );
}
}
return $ret;
lib/BerkeleyDB/Manager.pm view on Meta::CPAN
$db->db_put("foo", "bar");
die "error!"; # rolls back
});
# fetch all key/value pairs as a Data::Stream::Bulk
my $pairs = $m->cursor_stream( db => $db );
=head1 DESCRIPTION
This object provides a convenience wrapper for L<BerkeleyDB>
lib/BerkeleyDB/Manager.pm view on Meta::CPAN
The hash of currently open dbs.
=item chunk_size
See C<cursor_stream>.
Defaults to 500.
=back
lib/BerkeleyDB/Manager.pm view on Meta::CPAN
=item all_open_dbs
Returns a list of all the registered databases.
=item cursor_stream %args
Fetches data from a cursor, returning a L<Data::Stream::Bulk>.
If C<cursor> is not provided but C<db> is, a new cursor will be created.
If C<callback> is provided it will be invoked on the cursor with an accumilator
array repeatedly until it returns a false value. For example, to extract
triplets from a secondary index, you can use this callback:
my ( $sk, $pk, $v ) = ( '', '', '' ); # to avoid uninitialized warnings from BDB
$m->cursor_stream(
db => $db,
callback => {
my ( $cursor, $accumilator ) = @_;
if ( $cursor->c_pget( $sk, $pk, $v ) == 0 ) {
push @$accumilator, [ $sk, $pk, $v ];
return 1;
}
return; # nothing left
}
);
If it is not provided, C<c_get> will be used, returning C<[ $key, $value ]> for
each cursor position. C<flag> can be passed, and defaults to C<DB_NEXT>.
C<chunk_size> controls the number of pairs returned in each chunk. If it isn't
provided the attribute C<chunk_size> is used instead.
If C<values> or C<keys> is set to a true value then only values or keys will be
lib/BerkeleyDB/Manager.pm view on Meta::CPAN
Lastly, C<init> is an optional callback that is invoked once before each chunk,
that can be used to set up the database. The return value is retained until the
chunk is finished, so this callback can return a L<Scope::Guard> to perform
cleanup.
=item dup_cursor_stream %args
A specialization of C<cursor_stream> for fetching duplicate key entries.
Takes the same arguments as C<cursor_stream>, but adds a few more.
C<key> can be passed in to initialize the cursor with C<DB_SET>.
To do manual initialization C<callback_first> can be provided instead.
C<callback> is generated to use C<DB_NEXT_DUP> instead of C<DB_NEXT>, and
C<flag> is ignored.
BerkeleyDB
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BerkeleyDB.pm view on Meta::CPAN
sub CLEAR_old
{
my $self = shift ;
my ($key, $value) = (0, 0) ;
my $cursor = $self->_db_write_cursor() ;
while ($cursor->c_get($key, $value, BerkeleyDB::DB_PREV()) == 0)
{ $cursor->c_del() }
}
sub CLEAR_new
{
my $self = shift ;
BerkeleyDB.pm view on Meta::CPAN
sub SHIFT
{
my $self = shift;
my ($key, $value) = (0, 0) ;
my $cursor = $self->_db_write_cursor() ;
return undef if $cursor->c_get($key, $value, BerkeleyDB::DB_FIRST()) != 0 ;
return undef if $cursor->c_del() != 0 ;
return $value ;
}
BerkeleyDB.pm view on Meta::CPAN
{
my $self = shift;
if (@_)
{
my ($key, $value) = (0, 0) ;
my $cursor = $self->_db_write_cursor() ;
my $status = $cursor->c_get($key, $value, BerkeleyDB::DB_FIRST()) ;
if ($status == 0)
{
foreach $value (reverse @_)
{
$key = 0 ;
$cursor->c_put($key, $value, BerkeleyDB::DB_BEFORE()) ;
}
}
elsif ($status == BerkeleyDB::DB_NOTFOUND())
{
$key = 0 ;
BerkeleyDB.pm view on Meta::CPAN
{
my $self = shift;
if (@_)
{
my ($key, $value) = (-1, 0) ;
my $cursor = $self->_db_write_cursor() ;
my $status = $cursor->c_get($key, $value, BerkeleyDB::DB_LAST()) ;
if ($status == 0 || $status == BerkeleyDB::DB_NOTFOUND())
{
$key = -1 if $status != 0 and $self->type != BerkeleyDB::DB_RECNO() ;
foreach $value (@_)
{
BerkeleyDB.pm view on Meta::CPAN
}
# can use this when DB_APPEND is fixed.
# foreach $value (@_)
# {
# my $status = $cursor->c_put($key, $value, BerkeleyDB::DB_AFTER()) ;
#print "[$status]\n" ;
# }
}
}
sub POP
{
my $self = shift;
my ($key, $value) = (0, 0) ;
my $cursor = $self->_db_write_cursor() ;
return undef if $cursor->c_get($key, $value, BerkeleyDB::DB_LAST()) != 0 ;
return undef if $cursor->c_del() != 0 ;
return $value ;
}
sub SPLICE
BerkeleyDB.pm view on Meta::CPAN
my $wantarray = wantarray ;
my %values = () ;
my @values = () ;
my $counter = 0 ;
my $status = 0 ;
my $cursor = $db->db_cursor() ;
# iterate through the database until either EOF ($status == 0)
# or a different key is encountered ($key ne $origkey).
for ($status = $cursor->c_get($key, $value, BerkeleyDB::DB_SET()) ;
$status == 0 and $key eq $origkey ;
$status = $cursor->c_get($key, $value, BerkeleyDB::DB_NEXT()) ) {
# save the value or count number of matches
if ($wantarray) {
if ($flag)
{ ++ $values{$value} }
else
BerkeleyDB.pm view on Meta::CPAN
}
return ($wantarray ? ($flag ? %values : @values) : $counter) ;
}
sub db_cursor
{
my $db = shift ;
my ($addr) = $db->_db_cursor(@_) ;
my $obj ;
$obj = bless [$addr, $db] , "BerkeleyDB::Cursor" if $addr ;
return $obj ;
}
sub _db_write_cursor
{
my $db = shift ;
my ($addr) = $db->__db_write_cursor(@_) ;
my $obj ;
$obj = bless [$addr, $db] , "BerkeleyDB::Cursor" if $addr ;
return $obj ;
}
sub db_join
{
croak 'Usage: $db->BerkeleyDB::db_join([cursors], flags=0)'
if @_ < 2 || @_ > 3 ;
my $db = shift ;
croak 'db_join: first parameter is not an array reference'
if ! ref $_[0] || ref $_[0] ne 'ARRAY';
my ($addr) = $db->_db_join(@_) ;
BerkeleyDB.pm view on Meta::CPAN
package BerkeleyDB::Cursor ;
sub c_close
{
my $cursor = shift ;
$cursor->[1] = "" ;
return $cursor->_c_close() ;
}
sub c_dup
{
my $cursor = shift ;
my ($addr) = $cursor->_c_dup(@_) ;
my $obj ;
$obj = bless [$addr, $cursor->[1]] , "BerkeleyDB::Cursor" if $addr ;
return $obj ;
}
sub c_get_db_stream
{
my $cursor = shift ;
my $addr = $cursor->_c_get_db_stream(@_);
my $obj ;
$obj = bless [$addr, $cursor] , "BerkeleyDB::DbStream" if $addr ;
return $obj ;
}
sub db_stream
{
BerkeleyDB.pm view on Meta::CPAN
return $obj ;
}
#sub gdbs
#{
# my $cursor = shift ;
#
# my $k = '';
# my $v = '';
# $db->partial_set(0,0) ;
# ok $cursor->c_get($k, $v, DB_FIRST) == 0, "set cursor"
# or diag "Status is [" . $cursor->status() . "]";
# $db->partial_clear() ;
# is $k, "1";
#}
sub DESTROY
BerkeleyDB.pm view on Meta::CPAN
croak("CDS not enabled for this database\n")
if ! $db->cds_enabled();
if ( ! defined $Object{"$db"})
{
$Object{"$db"} = $db->_db_write_cursor()
|| return undef ;
}
++ $Count{"$db"} ;
BikePower
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BikePower/Tk.pm view on Meta::CPAN
my $d = $top->Dialog
(-title => $s{'Warning'},
-text => sprintf($s{'Overwrite existing file <%s>?'}, $file),
-default_button => $s{'No'},
-buttons => [$s{'Yes'}, $s{'No'}],
-popover => 'cursor');
return if $d->Show ne $s{'Yes'};
}
}
}
if (defined $file) {
Bio-ASN1-EntrezGene
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t/data/entrezgene.dat view on Meta::CPAN
gi 6226959 } ,
products {
{
type peptide ,
heading "Reference" ,
label "precursor" ,
accession "NP_000005" ,
version 1 ,
genomic-coords {
packed-int {
{
t/data/entrezgene.dat view on Meta::CPAN
gi 6226959 } ,
products {
{
type peptide ,
heading "Reference" ,
label "precursor" ,
accession "NP_000005" ,
version 1 ,
genomic-coords {
packed-int {
{
t/data/entrezgene.dat view on Meta::CPAN
gi 6226959 } ,
products {
{
type peptide ,
heading "Reference" ,
label "precursor" ,
accession "NP_000005" ,
version 1 ,
genomic-coords {
packed-int {
{
t/data/entrezgene.dat view on Meta::CPAN
src {
db "Protein" ,
tag
id 4557225 } ,
anchor "NP_000005" ,
post-text "alpha-2-macroglobulin precursor" } } ,
seqs {
whole
gi 4557225 } ,
comment {
{
t/data/entrezgene.dat view on Meta::CPAN
str "Jul 7 2004 1:36PM" } ,
{
type generif ,
text "There is a significant genetic association of the 5 bp deletion
and two novel polymorphisms in alpha-2-macroglobulin alpha-2-macroglobulin
precursor with AD" ,
version 0 ,
refs {
pmid 12966032 } ,
create-date
str "Jun 27 2004 5:41PM" ,
t/data/entrezgene.dat view on Meta::CPAN
comment {
{
type generif ,
text "Binding of HIV-1 Tat to LRP inhibits neuronal binding, uptake
and degradation of physiological ligands for LRP, including
alpha2-macroglobulin, apolipoprotein E4, amyloid precursor and amyloid
beta-protein" ,
version 0 ,
refs {
pmid 11100124 } ,
comment {
t/data/entrezgene.dat view on Meta::CPAN
gi 9665246 } ,
products {
{
type peptide ,
heading "Reference" ,
label "precursor" ,
accession "NP_001076" ,
version 1 ,
genomic-coords {
packed-int {
{
t/data/entrezgene.dat view on Meta::CPAN
gi 9665246 } ,
products {
{
type peptide ,
heading "Reference" ,
label "precursor" ,
accession "NP_001076" ,
version 1 ,
genomic-coords {
packed-int {
{
t/data/entrezgene.dat view on Meta::CPAN
gi 9665246 } ,
products {
{
type peptide ,
heading "Reference" ,
label "precursor" ,
accession "NP_001076" ,
version 1 ,
genomic-coords {
packed-int {
{
t/data/entrezgene.dat view on Meta::CPAN
db "Protein" ,
tag
id 50659080 } ,
anchor "NP_001076" ,
post-text "serine (or cysteine) proteinase inhibitor, clade
A, member 3 precursor" } } ,
seqs {
whole
gi 50659080 } ,
comment {
{
Bio-Biblio
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lib/Bio/DB/Biblio/eutils.pm view on Meta::CPAN
return $xml;
}
sub reset_retrieval {
shift->cursor(0);
return 1;
}
sub get_next {
my $self = shift;
return unless $self->has_next;
my $xml = $self->get_by_id( @{ $self->ids }[$self->cursor] );
$self->cursor( $self->cursor + 1 );
return $xml;
}
lib/Bio/DB/Biblio/eutils.pm view on Meta::CPAN
}
sub has_next {
my $self = shift;
return ($self->cursor < $self->count) ? 1 : undef;
}
lib/Bio/DB/Biblio/eutils.pm view on Meta::CPAN
my($webenv_element) = $self->twig->get_xpath('//WebEnv');
if (defined $webenv_element) {
$self->collection_id($webenv_element->text());
}
#initialize/reset cursor
$self->cursor(0);
return $self;
}
lib/Bio/DB/Biblio/eutils.pm view on Meta::CPAN
sub get_all_entries {
return;
}
sub cursor {
my $self = shift;
my $arg = shift;
return $self->{'cursor'} = $arg if defined($arg);
return $self->{'cursor'};
}
sub twig {
my $self = shift;
lib/Bio/DB/Biblio/eutils.pm view on Meta::CPAN
=head2 reset_retrieval
Title : reset_retrieval
Usage : $biblio->reset_retrieval();
Function: reset cursor in id list, see cursor()
Returns : 1
Args : none
=head2 get_next
lib/Bio/DB/Biblio/eutils.pm view on Meta::CPAN
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
=head2 cursor
Title : cursor
Usage : $obj->cursor($newval)
Function: holds position in reference collection
Returns : value of cursor (a scalar)
Args : on set, new value (a scalar or undef, optional)
=head2 twig
Title : twig
Bio-Chado-Schema
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doc/slides/dbic_intro/slides/ui/pretty.css view on Meta::CPAN
#footer>div#controls {position: fixed; bottom: 0; padding: 2em 0;
top: auto; height: auto;}
div#controls form {position: absolute; bottom: 0; right: 0; width: 100%;
margin: 0; padding: 0;}
div#controls a {font-size: 2em; padding: 0; margin: 0 0.5em; border: none; color: #f3f3f3;
cursor: pointer;}
div#controls a:hover {color: #f3f3f3;}
div#controls select {visibility: hidden; background: #f3f3f3; color: #333;}
div#controls div:hover select {visibility: visible;}
#toggle, #prev, #next {
Bio-Cluster
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t/data/sequencefamily.dat view on Meta::CPAN
ID ACON_CAEEL STANDARD; PRT; 788 AA.
AC P34455;
DT 01-FEB-1994 (Rel. 28, Created)
DT 01-FEB-1994 (Rel. 28, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE Probable aconitate hydratase, mitochondrial precursor (EC 4.2.1.3)
DE (Citrate hydro-lyase) (Aconitase).
GN F54H12.1.
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea;
OC Rhabditidae; Peloderinae; Caenorhabditis.
Bio-Community
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lib/Bio/Community/IO/FormatGuesser.pm view on Meta::CPAN
$format = (keys %ok_formats)[0];
}
# Cleanup
if ($in->noclose) {
# Reset filehandle cursor to original location
seek($self->fh, $original_pos, 0)
or $self->throw("Could not reset the cursor to its original position: $!");
}
$in->close;
return $format;
}
Bio-ConnectDots
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lib/Bio/ConnectDots/DB.pm view on Meta::CPAN
use Bio::ConnectDots::ConnectorSet;
@ISA = qw(Class::AutoClass);
@AUTO_ATTRIBUTES=qw(dsn dbh dbd database host port user password
read_only read_only_schema
_needs_disconnect _db_cursor _exists
load_name load_save load_chunksize load_cid_base
_ext_directory _load_fh _load_count _load_chunk sql_log
);
@OTHER_ATTRIBUTES=qw(ext_directory);
%SYNONYMS=(server=>'host');
Bio-DB-SeqFeature
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lib/Bio/DB/SeqFeature/Store/LoadHelper.pm view on Meta::CPAN
sub each_family {
my $self = shift;
my $db = tied(%{$self->{Parent2Child}});
if ($self->{_cursordone}) {
undef $self->{_cursordone};
undef $self->{_parent};
undef $self->{_child};
return;
}
# do a slightly tricky cursor search
unless (defined $self->{_parent}) {
return unless $db->seq($self->{_parent},$self->{_child},R_FIRST) == 0;
}
my $parent = $self->{_parent};
lib/Bio/DB/SeqFeature/Store/LoadHelper.pm view on Meta::CPAN
&& $self->{_parent} eq $parent
) {
push @children,$self->{_child};
}
$self->{_cursordone}++ if $status != 0;
return ($parent,\@children);
}
sub local_ids {
Bio-EnsEMBL
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lib/Bio/EnsEMBL/DBSQL/Driver/odbc.pm view on Meta::CPAN
attributes => {
'LongTruncOk' => 1,
'LongReadLen' => 2**16 - 8,
'RaiseError' => 1,
'PrintError' => 0,
'odbc_cursortype' => 2,
},
};
}
sub from_date_to_seconds {
Bio-FASTASequence
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lib/Bio/FASTASequence.pm view on Meta::CPAN
This module can parse the following formats:
=over 4
=item >P02656 APC3_HUMAN Apolipoprotein C-III precursor (Apo-CIII).
=item >IPI:IPI00166553|REFSEQ_XP:XP_290586|ENSEMBL:ENSP00000331094|TREMBL:Q8N3H0 T Hypothetical protein
=item >sp|P01815|HV2B_HUMAN Ig heavy chain V-II region COR - Homo sapiens (Human).
Bio-GFF3
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is_deeply( \%stuff,
$right_stuff,
'parsed the right stuff' )
or diag explain \%stuff;
# just do some cursory parsing of other files
for (
[ 1010, 'messy_protein_domains.gff3'],
[ 4, 'gff3_with_syncs.gff3' ],
[ 51, 'au9_scaffold_subset.gff3' ],
[ 14, 'tomato_chr4_head.gff3' ],
Bio-Gonzales
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t/data/uniprot_sprot.dat view on Meta::CPAN
AC Q6GZX2;
DT 28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2004, sequence version 1.
DT 21-SEP-2011, entry version 20.
DE RecName: Full=Uncharacterized protein 3R;
DE Flags: Precursor;
GN ORFNames=FV3-003R;
OS Frog virus 3 (isolate Goorha) (FV-3).
OC Viruses; dsDNA viruses, no RNA stage; Iridoviridae; Ranavirus.
OX NCBI_TaxID=654924;
OH NCBI_TaxID=8295; Ambystoma (mole salamanders).
t/data/uniprot_sprot.dat view on Meta::CPAN
AC Q197F5;
DT 16-JUN-2009, integrated into UniProtKB/Swiss-Prot.
DT 11-JUL-2006, sequence version 1.
DT 09-JAN-2013, entry version 19.
DE RecName: Full=Uncharacterized protein 005L;
DE Flags: Precursor;
GN ORFNames=IIV3-005L;
OS Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus).
OC Viruses; dsDNA viruses, no RNA stage; Iridoviridae; Chloriridovirus.
OX NCBI_TaxID=345201;
OH NCBI_TaxID=7163; Aedes vexans (Inland floodwater mosquito) (Culex vexans).
t/data/uniprot_sprot.dat view on Meta::CPAN
AC Q91G85;
DT 16-JUN-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-APR-2013, entry version 24.
DE RecName: Full=Uncharacterized protein 009R;
DE Flags: Precursor;
GN ORFNames=IIV6-009R;
OS Invertebrate iridescent virus 6 (IIV-6) (Chilo iridescent virus).
OC Viruses; dsDNA viruses, no RNA stage; Iridoviridae; Iridovirus.
OX NCBI_TaxID=176652;
OH NCBI_TaxID=6997; Acheta domesticus (House cricket).
Bio-Graphics
view release on metacpan or search on metacpan
lib/Bio/Graphics/FeatureFile.pm view on Meta::CPAN
format and a more human-friendly file format described below. Once a
FeatureFile object has been initialized, you can interrogate it for
its consistuent features and their settings, or render the entire file
onto a Bio::Graphics::Panel.
This module is a precursor of Jason Stajich's
Bio::Annotation::Collection class, and fulfills a similar function of
storing a collection of sequence features. However, it also stores
rendering information about the features, and does not currently
follow the CollectionI interface.
Bio-MAGETAB
view release on metacpan or search on metacpan
lib/Bio/MAGETAB/Util/Persistence.pm view on Meta::CPAN
update
erase
id
count
sum
cursor
remote )] );
has 'dbparams' => ( is => 'ro',
isa => ArrayRef,
required => 1,
lib/Bio/MAGETAB/Util/Persistence.pm view on Meta::CPAN
=item count
=item sum
=item cursor
=item remote
All these methods are delegated directly to the Tangram::Storage
object created by the C<connect> method, and contained within the
Bio-MUST-Core
view release on metacpan or search on metacpan
lib/Bio/MUST/Core/legacy.vim view on Meta::CPAN
setlocal cinwords=if,else,while,do,for,switch
setlocal colorcolumn=
setlocal comments=s1:/*,mb:*,ex:*/,://,b:#,:%,:XCOMM,n:>,fb:-
setlocal commentstring=/*%s*/
setlocal complete=.,w,b,u,t,i
setlocal concealcursor=
setlocal conceallevel=0
setlocal completefunc=
setlocal nocopyindent
setlocal cryptmethod=
setlocal nocursorbind
setlocal nocursorcolumn
setlocal cursorline
setlocal define=
setlocal dictionary=
setlocal nodiff
setlocal equalprg=
setlocal errorformat=
lib/Bio/MUST/Core/legacy.vim view on Meta::CPAN
setlocal cinwords=if,else,while,do,for,switch
setlocal colorcolumn=
setlocal comments=:#
setlocal commentstring=#%s
setlocal complete=.,w,b,u,t,i
setlocal concealcursor=
setlocal conceallevel=0
setlocal completefunc=
setlocal nocopyindent
setlocal cryptmethod=
setlocal nocursorbind
setlocal nocursorcolumn
setlocal nocursorline
setlocal define=[^A-Za-z_]
setlocal dictionary=~/.vim/perl-support/wordlists/perl.list
setlocal nodiff
setlocal equalprg=
setlocal errorformat=
lib/Bio/MUST/Core/legacy.vim view on Meta::CPAN
setlocal cinwords=if,else,while,do,for,switch
setlocal colorcolumn=
setlocal comments=:#
setlocal commentstring=#%s
setlocal complete=.,w,b,u,t,i
setlocal concealcursor=
setlocal conceallevel=0
setlocal completefunc=
setlocal nocopyindent
setlocal cryptmethod=
setlocal nocursorbind
setlocal nocursorcolumn
setlocal nocursorline
setlocal define=[^A-Za-z_]
setlocal dictionary=~/.vim/perl-support/wordlists/perl.list
setlocal nodiff
setlocal equalprg=
setlocal errorformat=
lib/Bio/MUST/Core/legacy.vim view on Meta::CPAN
setlocal cinwords=if,else,while,do,for,switch
setlocal colorcolumn=
setlocal comments=s1:/*,mb:*,ex:*/,://,b:#,:%,:XCOMM,n:>,fb:-
setlocal commentstring=/*%s*/
setlocal complete=.,w,b,u,t,i
setlocal concealcursor=
setlocal conceallevel=0
setlocal completefunc=
setlocal nocopyindent
setlocal cryptmethod=
setlocal nocursorbind
setlocal nocursorcolumn
setlocal nocursorline
setlocal define=
setlocal dictionary=
setlocal nodiff
setlocal equalprg=
setlocal errorformat=
Bio-Phylo
view release on metacpan or search on metacpan
t/32-tolweb.t view on Meta::CPAN
<NAMECOMMENT></NAMECOMMENT>
<COMBINATION_AUTHOR></COMBINATION_AUTHOR>
<AUTHDATE>1801</AUTHDATE>
<OTHERNAMES>
<OTHERNAME ISIMPORTANT="0" ISPREFERRED="0" SEQUENCE="0" DATE="1792" ITALICIZENAME="1">
<NAME><![CDATA[Bembidion cursor]]></NAME>
<AUTHORITY><![CDATA[Fabricius]]></AUTHORITY>
<COMMENTS></COMMENTS>
</OTHERNAME>
<OTHERNAME ISIMPORTANT="0" ISPREFERRED="0" SEQUENCE="1" DATE="1957" ITALICIZENAME="1">
<NAME><![CDATA[Bembidion pernigrum]]></NAME>
Bio-Roary
view release on metacpan or search on metacpan
contrib/roary_plots/roary.html view on Meta::CPAN
<style type="text/css">
/*!
*
* Twitter Bootstrap
*
*//*! normalize.css v3.0.2 | MIT License | git.io/normalize */html{font-family:sans-serif;-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,menu,nav,section,summary...
*
* Font Awesome
*
*//*!
* Font Awesome 4.3.0 by @davegandy - http://fontawesome.io - @fontawesome
contrib/roary_plots/roary.html view on Meta::CPAN
*
*/.ansibold{font-weight:bold}.ansiblack{color:black}.ansired{color:darkred}.ansigreen{color:darkgreen}.ansiyellow{color:#c4a000}.ansiblue{color:darkblue}.ansipurple{color:darkviolet}.ansicyan{color:steelblue}.ansigray{color:gray}.ansibgblack{backgrou...
*
* IPython notebook webapp
*
*/@media (max-width:767px){.notebook_app{padding-left:0;padding-right:0}}#ipython-main-app{box-sizing:border-box;-moz-box-sizing:border-box;-webkit-box-sizing:border-box;height:100%}div#notebook_panel{margin:0;padding:0;box-sizing:border-box;-moz-box...
</style>
<style type="text/css">
.highlight .hll { background-color: #ffffcc }
.highlight { background: #f8f8f8; }
.highlight .c { color: #408080; font-style: italic } /* Comment */
contrib/roary_plots/roary.html view on Meta::CPAN
} else {
window.onload = toggle;
}
}
</script><style type="text/css">.MathJax_Hover_Frame {border-radius: .25em; -webkit-border-radius: .25em; -moz-border-radius: .25em; -khtml-border-radius: .25em; box-shadow: 0px 0px 15px #83A; -webkit-box-shadow: 0px 0px 15px #83A; -moz-box-shadow: 0...
.MathJax_Hover_Arrow {position: absolute; width: 15px; height: 11px; cursor: pointer}
</style><style type="text/css">#MathJax_About {position: fixed; left: 50%; width: auto; text-align: center; border: 3px outset; padding: 1em 2em; background-color: #DDDDDD; color: black; cursor: default; font-family: message-box; font-size: 120%; fon...
.MathJax_Menu {position: absolute; background-color: white; color: black; width: auto; padding: 5px 0px; border: 1px solid #CCCCCC; margin: 0; cursor: default; font: menu; text-align: left; text-indent: 0; text-transform: none; line-height: normal; l...
.MathJax_MenuItem {padding: 1px 2em; background: transparent}
.MathJax_MenuArrow {position: absolute; right: .5em; color: #666666}
.MathJax_MenuActive .MathJax_MenuArrow {color: white}
.MathJax_MenuArrow.RTL {left: .5em; right: auto}
.MathJax_MenuCheck {position: absolute; left: .7em}
Bio-SearchIO-blastxml
view release on metacpan or search on metacpan
t/data/plague_yeast.bls.xml view on Meta::CPAN
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.1.3 [Apr-11-2001]</BlastOutput_version>
<BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~p...
<BlastOutput_db>yeast.aa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>gi|5763817|emb|CAB53170.1| coagulase/fibrinolysin precursor [Yersinia pestis]</BlastOutput_query-def>
<BlastOutput_query-len>312</BlastOutput_query-len>
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>0.1</Parameters_expect>
Bio-ViennaNGS
view release on metacpan or search on metacpan
# there is already a search function so this one should typically be disabled.
# For large projects the javascript based search engine can be slow, then
# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
# search using the keyboard; to jump to the search box use <access key> + S
# (what the <access key> is depends on the OS and browser, but it is typically
# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
# key> to jump into the search results window, the results can be navigated
# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
# the search. The filter options can be selected when the cursor is inside the
# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
# to select a filter and <Enter> or <escape> to activate or cancel the filter
# option.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
BioPerl-DB
view release on metacpan or search on metacpan
t/data/LL-sample.seq view on Meta::CPAN
ORGANISM: Homo sapiens
STATUS: REVIEWED
NM: NM_001091|4501850|na
NP: NP_001082|4501851
CDD: Copper amine oxidase|pfam01179|1775|na|6.883370e+02
PRODUCT: amiloride binding protein 1 precursor
ASSEMBLY: X78212
CONTIG: NT_007914.10|22047859|na|11083771|11092582|+|7|reference
EVID: supported by alignment with mRNA
XM: XM_032220|14745402|na
XP: XP_032220|14745403|na
t/data/LL-sample.seq view on Meta::CPAN
PROT: AAB60381|533538
OFFICIAL_SYMBOL: ABP1
OFFICIAL_GENE_NAME: amiloride binding protein 1 (amine oxidase (copper-containing))
ALIAS_SYMBOL: DAO
ALIAS_SYMBOL: AOC1
PREFERRED_PRODUCT: amiloride binding protein 1 precursor
SUMMARY: Summary: This gene encodes a membrane glycoprotein that binds amiloride, a diuretic that acts by closing epithelial sodium ion channels. Experimental evidence indicates, however, that the formation of an amiloride sensitive, sodium channel r...
CHR: 7
STS: RH71199|7|8014|na|seq_map|epcr
STS: ABP1|7|32801|ABP1|seq_map|epcr
COMP: 10090|Abp1|6|6 cM|76507|7|ABP1|ncbi_mgd
BioPerl-Network
view release on metacpan or search on metacpan
t/IO_psi10.t view on Meta::CPAN
# in Graph v. .86
@rts = $g1->articulation_points;
is scalar @rts, 1;
@proteins = $rts[0]->proteins;
$seq = $proteins[0];
is $seq->desc, "Erythropoietin receptor precursor";
#
# GO terms
#
$n = $g1->get_nodes_by_id("EBI-474016");
BioPerl
view release on metacpan or search on metacpan
Bio/DB/SeqFeature/Store/LoadHelper.pm view on Meta::CPAN
sub each_family {
my $self = shift;
my $db = tied(%{$self->{Parent2Child}});
if ($self->{_cursordone}) {
undef $self->{_cursordone};
undef $self->{_parent};
undef $self->{_child};
return;
}
# do a slightly tricky cursor search
unless (defined $self->{_parent}) {
return unless $db->seq($self->{_parent},$self->{_child},R_FIRST) == 0;
}
my $parent = $self->{_parent};
Bio/DB/SeqFeature/Store/LoadHelper.pm view on Meta::CPAN
&& $self->{_parent} eq $parent
) {
push @children,$self->{_child};
}
$self->{_cursordone}++ if $status != 0;
return ($parent,\@children);
}
sub local_ids {
( run in 1.224 second using v1.01-cache-2.11-cpan-39bf76dae61 )