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share/PerlCritic/Critic/Document.pm view on Meta::CPAN
## Then use the instance just like a PPI::Document
=head1 DESCRIPTION
Perl::Critic does a lot of iterations over the PPI document tree via
the C<PPI::Document::find()> method. To save some time, this class
pre-caches a lot of the common C<find()> calls in a single traversal.
Then, on subsequent requests we return the cached data.
This is implemented as a facade, where method calls are handed to the
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lib/Benchmark/Perl/Formance/Plugin/PerlStone2015/binarytrees.pm view on Meta::CPAN
my $long_lived_tree = bottom_up_tree($max_depth);
my $depth = $min_depth;
while ( $depth <= $max_depth ) {
my $iterations = 2 ** ($max_depth - $depth + $min_depth);
my $check = 0;
foreach my $i (1..$iterations) {
my $temp_tree = bottom_up_tree($depth);
$check += item_check($temp_tree);
$temp_tree = bottom_up_tree($depth);
$check += item_check($temp_tree);
}
#print $iterations * 2, "\t trees of depth $depth\t check: ", $check, "\n";
$depth += 2;
}
# print "long lived tree of depth $max_depth\t check: ",
# item_check($long_lived_tree), "\n";
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lib/Benchmark/Perl/Formance/Plugin/Shootout/binarytrees.pm view on Meta::CPAN
my $long_lived_tree = bottom_up_tree($max_depth);
my $depth = $min_depth;
while ( $depth <= $max_depth ) {
my $iterations = 2 ** ($max_depth - $depth + $min_depth);
my $check = 0;
foreach my $i (1..$iterations) {
my $temp_tree = bottom_up_tree($depth);
$check += item_check($temp_tree);
$temp_tree = bottom_up_tree($depth);
$check += item_check($temp_tree);
}
#print $iterations * 2, "\t trees of depth $depth\t check: ", $check, "\n";
$depth += 2;
}
# print "long lived tree of depth $max_depth\t check: ",
# item_check($long_lived_tree), "\n";
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lib/Benchmark/ProgressBar.pm view on Meta::CPAN
$n = $forn if defined $forn;
# A conservative warning to spot very silly tests.
# Don't assume that your benchmark is ok simply because
# you don't get this warning!
print " (warning: too few iterations for a reliable count)\n"
if $n < $Benchmark::Min_Count
|| ($t->real < 1 && $n < 1000)
|| $t->cpu_a < $Benchmark::Min_CPU;
$t;
}
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examples/serialize.pl view on Meta::CPAN
use Benchmark::Serialize::Library::ProtocolBuffers;
use Benchmark::Serialize::Library::ProtocolBuffers::XS;
use Benchmark::Serialize::Library::Data::Serializer;
my @benchmark = (); # package names of benchmarks to run
my $iterations = -1; # integer
my $structure = {
array => [ 'a' .. 'j' ],
hash => { 'a' .. 'z' },
string => 'x' x 200
};
examples/serialize.pl view on Meta::CPAN
Getopt::Long::GetOptions(
'b|benchmark=s@' => \@benchmark,
'deflate!' => \$Benchmark::Serialize::benchmark_deflate,
'inflate!' => \$Benchmark::Serialize::benchmark_inflate,
'roundtrip!' => \$Benchmark::Serialize::benchmark_roundtrip,
'i|iterations=i' => \$iterations,
'o|output=s' => \$Benchmark::Serialize::output,
'v|verbose!' => \$Benchmark::Serialize::verbose,
's|structure=s' => sub {
die "Structure option requires YAML.\n"
unless YAML->require;
examples/serialize.pl view on Meta::CPAN
Benchmark::Serialize::Library::ProtocolBuffers->register( ProtocolBuffers => ($protocolbuffers ? $protocolbuffers : $structure) );
}
@benchmark = ("all") unless @benchmark;
cmpthese($iterations, $structure, @benchmark);
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lib/Bigtop/Docs/TentTut.pod view on Meta::CPAN
If you need more details consult C<Bigtop::Docs::TentRef> or
C<Bigtop::Docs::Syntax> (or even C<Bigtop::Keywords>).
Here, I will walk you through using tentmaker to generate a bigtop file.
Then, I will show how to use bigtop to turn that into a web app. Finally,
I will return to expand the example in addtional iterations of feature
additions. There are a couple of screen shots here. If you don't see the
pictures in line, look for them in the docs directory of the Bigtop
distribution and/or on the web at http://www.usegantry.org/images/tenttut.
The example app I will build here is a contact database. It will initially
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lib/Bijection/XS.pm view on Meta::CPAN
Bijection::XS::inverse(Bijection::XS::biject($int));
}
});
Benchmark: timing 10000000 iterations of Bijection, XS...
Bijection: 8 wallclock secs ( 8.74 usr + 0.05 sys = 8.79 CPU) @ 1137656.43/s (n=10000000)
XS: 2 wallclock secs ( 2.48 usr + 0.01 sys = 2.49 CPU) @ 4016064.26/s (n=10000000)
=head1 AUTHOR
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lib/BingoX/Carbon.pm view on Meta::CPAN
return $self->error_handler("no bindings passed to format_conditions for type ($type)")
unless (@values);
$sql .= "$field " . uc($type) . ' ? AND ?';
push(@bindings, @values[0,1]);
} else { # LIST of conditions
splice (@valuelist, $x+1, 0, @$value); # appending will push to next iterations
}
} elsif ($value =~ /^\/(.+?)\/$/) { # regex
$sql .= "$field ~ ?";
push(@bindings, $1);
} elsif ($value =~ /^(\d+?)-(\d+?)$/) { # date or numeric range
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examples/full_example.pl view on Meta::CPAN
# There shouldn't be any simulation runs yet, but let's check
my $simulation_runs = Bio::Cellucidate::Model->simulation_runs($model->{id});
print "\nSimulation Runs for model:\n";
print Dumper $simulation_runs;
# Let's create a simulation run (2 iterations)!
my $simulation_run = Bio::Cellucidate::SimulationRun->create({ model_id => $model->{id}, num_iterations => 2 }); #, simulation_method => 'ODE' });
print "\nNewly created Simulation Run:\n";
print Dumper $simulation_run;
# Same pattern as import, poll and see when my run is complete...
while ($simulation_run->{state} ne 'succeeded') {
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lib/Bio/Community/Tools/Rarefier.pm view on Meta::CPAN
# Normalize communities in a metacommunity by repeatedly taking 1,000 random members
my $rarefier = Bio::Community::Tools::Rarefier->new(
-metacommunity => $meta,
-sample_size => 1000,
-threshold => 0.001, # stop bootstrap iterations when threshold is reached
);
# Rarefied results, with decimal counts
my $average_community = $rarefier->get_avg_meta->next_community;
lib/Bio/Community/Tools/Rarefier.pm view on Meta::CPAN
# Alternatively, specify a number of repetitions
my $rarefier = Bio::Community::Tools::Rarefier->new(
-metacommunity => $meta,
-sample_size => 1000,
-num_repetitions => 0.001, # stop after this number of bootstrap iterations
);
# ... or assume an infinite number of repetitions
my $rarefier = Bio::Community::Tools::Rarefier->new(
-metacommunity => $meta,
lib/Bio/Community/Tools/Rarefier.pm view on Meta::CPAN
=head2 verbose
Function: Get or set verbose mode. In verbose mode, the current number of
iterations (and beta diversity if a threshold is used) is displayed.
Usage : $rarefier->verbose(1);
Args : 0 (default) or 1
Returns : 0 or 1
=cut
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}
# The callback routine used below for authentication must accept three arguments:
# the fetcher object, the realm for authentication, and the iteration
# we are on. A return of undef means that we should stop trying this connection (e.g. cancel button
# pressed, or x number of iterations tried), otherwise a two element array (not a reference to an array)
# should be returned with the username and password in that order.
# I assume if you've called autheniticate, it's because you've gotten a 401 error.
# Otherwise this does not make sense.
# There is also no caching of authentication done. I suggest the callback do this, so
# the user isn't asked 20 times for the same name and password.
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lib/Bio/FastParsers/Blast/Xml.pm view on Meta::CPAN
extends 'Bio::FastParsers::Base';
use aliased 'Bio::FastParsers::Blast::Xml::BlastOutput';
# TODO: check behavior with single iterations, hits or hsps
# public attributes (some inherited)
lib/Bio/FastParsers/Blast/Xml.pm view on Meta::CPAN
# ...or equivalently
my $param = $bo->parameters;
say $param->expect; # 10
say $param->matrix; # BLOSUM62
# get the number of iterations (= queries)
say $bo->count_iterations; # 3
# loop through iterations (or queries), hits and hsps
# this is extremely fast because no data is moved around
for my $iter ($bo->all_iterations) {
say $iter->count_hits; # always available!
for my $hit ($iter->all_hits) {
for my $hsp ($hit->all_hsps) {
# ...
}
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examples/benchmark.pl view on Meta::CPAN
$query =~ tr{u}{t};
my $time;
my $VERBOSE=0;
my $filenameCDNA = 'TAIR8_cdna_20080412';
my $iterations = $DEBUG ? 1 : 20;
my $iterationsdb = $DEBUG ? 1: 2;
my $maxmm = $DEBUG ? 1 : 5;
#goto CREATETMP;
DB:
for $b (sort keys %be) {
my $sbe = $be{$b};
$time = [gettimeofday];
for my $i (1..$iterationsdb) {
system("rm -rf data$b/");
mkdir 'data' . $b;
$sbe->generate_database({
datapath => 'data' . $b,
file => "examples/$filenameCDNA",
prefix_length => 3,
});
}
$results{"${b}_dbgen"} = sprintf("%.2f",
(tv_interval($time)/$iterationsdb));
warn "$b took " . $results{"${b}_dbgen"} . " seconds\n";
}
MM:
for $b (sort keys %be) {
examples/benchmark.pl view on Meta::CPAN
$loop_counter = 1 if $b eq 'vmatch';
for my $online ( 0 .. $loop_counter) {
for my $mm (0..$maxmm) {
next MM if !defined $sbe->features->{MISMATCHES} && $mm > 0;
$time = [gettimeofday];
for my $i (1..$iterations) {
print "." if ($i % 5 == 0);
my %showdesc;
%showdesc = ( showdesc => 100) if $b eq 'vmatch';
my $gu = 1;
$gu = 0 if $b eq 'guugle';
examples/benchmark.pl view on Meta::CPAN
warn scalar(@ids). " results.\n" if $VERBOSE;
}
warn 'Is TRE? ' . $sbe->is_tre_agrep() if $b =~/agrep/;
$results{"${b}_mm_${mm}_$online"} = sprintf("%.2f",
tv_interval($time)/$iterations);
warn "$b (mm $mm) took " . $results{"${b}_mm_${mm}_$online"} . " seconds\n";
}
}
}
examples/benchmark.pl view on Meta::CPAN
$results{cpuinfo} = scalar $info->device('CPU')->identify;
$results{perl} = $info->perl_long();
$results{osname} = $info->os->name( long => 1 );
$results{filenameCDNA} = $filenameCDNA;
$results{biogrepv} = $Bio::Grep::VERSION;
$results{iterations} = $iterations;
$results{iterationsdb} = $iterationsdb;
$template->process('examples/Benchmarks.tt', \%results, 'lib/Bio/Grep/Benchmarks.pod') || die
$template->error(), "\n";
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lib/Bio/MUST/Apps/FortyTwo/OrgProcessor.pm view on Meta::CPAN
return unless $bo;
my %tol_score_for;
ORTHOLOGUE:
for my $orthologue ($bo->all_iterations) {
next ORTHOLOGUE unless $orthologue->count_hits;
# Note: this should never happen...
my $query_def = $orthologue->query_def;
my $transcript_acc = $orthologous_seqs->long_id_for($query_def);
lib/Bio/MUST/Apps/FortyTwo/OrgProcessor.pm view on Meta::CPAN
# abort if no hit
my $bo = $parser->blast_output;
return $aligned_seqs unless $bo;
ORTHOLOGUE:
for my $orthologue ($bo->all_iterations) {
unless ($orthologue->count_hits) {
###### [ORG] skipped orthologue due to lack of significant template
next ORTHOLOGUE;
} # TODO: investigate why this should happen at all...
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test/blastp.out view on Meta::CPAN
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_query-ID>Query_1</Iteration_query-ID>
<Iteration_query-def>Sulfurimonas_autotrophica_563040@ADN08900</Iteration_query-def>
<Iteration_query-len>675</Iteration_query-len>
test/blastp.out view on Meta::CPAN
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
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lib/Bio/MUST/Apps/TwoScalp/Seq2Seq.pm view on Meta::CPAN
return unless $bo;
my $sort_method = $self->single_hsp ? 'score' : 'hit_start';
QUERY:
for my $query ( $bo->all_iterations ) {
my $query_id = $query_seqs->long_id_for( $query->query_def );
##### [S2S] Aligning: $query_id
my @templates;
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-evalue => 1e-10,
-outfmt => 5,
} );
isa_ok($xml_parser, 'Bio::FastParsers::Blast::Xml');
cmp_ok $xml_parser->blast_output->count_iterations, '==', 7,
'got expected number of iterations';
$report_xml = $xml_parser->filename;
explain $report_xml;
compare_filter_ok $report_xml, file('test', 'report.blastp.xml'),
\&filter, 'wrote expected XML BLASTP report';
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lib/Bio/RNA/Treekin/Record.pm view on Meta::CPAN
info
init_population
rates_file
file_index
cmd
of_iterations
);
# Get number of population data rows stored.
sub population_data_count {
my ($self) = @_;
lib/Bio/RNA/Treekin/Record.pm view on Meta::CPAN
# Population data
my $population_str
= join "\n", map { "$_" } @{ $self->_population_data };
# Footer (new Treekin versions only).
my $footer_str = $self->has_of_iterations
? '# of iterations: ' . $self->of_iterations
: q{};
my $self_as_str = $header_str . "\n" . $population_str;
$self_as_str .= "\n" . $footer_str if $footer_str;
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lib/Bio/Roary/Output/NumberOfGroups.pm view on Meta::CPAN
use List::Util qw(shuffle);
use Bio::Roary::AnnotateGroups;
use Bio::Roary::GroupStatistics;
has 'group_statistics_obj' => ( is => 'ro', isa => 'Bio::Roary::GroupStatistics', required => 1 );
has 'number_of_iterations' => ( is => 'ro', isa => 'Int', default => 10);
has 'groups_to_contigs' => ( is => 'ro', isa => 'Maybe[HashRef]' );
has 'annotate_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnnotateGroups', required => 1 );
has 'core_definition' => ( is => 'ro', isa => 'Num', default => 1.0 );
has 'output_raw_filename_conserved_genes' => ( is => 'ro', isa => 'Str', default => 'number_of_conserved_genes.Rtab' );
lib/Bio/Roary/Output/NumberOfGroups.pm view on Meta::CPAN
has '_new_genes' => ( is => 'ro', isa => 'ArrayRef', default => sub { [] } );
sub create_output_files {
my ($self) = @_;
for ( my $i = 0 ; $i < $self->number_of_iterations ; $i++ ) {
$self->_single_iteration_gene_expansion;
}
$self->_create_raw_output_file( $self->output_raw_filename_conserved_genes, $self->_conserved_genes );
$self->_create_raw_output_file( $self->output_raw_filename_unique_genes, $self->_unique_genes );
lib/Bio/Roary/Output/NumberOfGroups.pm view on Meta::CPAN
}
sub _create_raw_output_file {
my ( $self, $filename, $output_data ) = @_;
open( my $fh, '>', $filename );
for my $iterations ( @{$output_data} ) {
print {$fh} join( "\t", @{$iterations} );
print {$fh} "\n";
}
close($fh);
}
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lib/Bio/SearchIO/XML/BlastHandler.pm view on Meta::CPAN
'BlastOutput_param' => 1,
'Iteration_hits' => 1,
'Statistics' => 1,
'Parameters' => 1,
'BlastOutput' => 1,
'BlastOutput_iterations' => 1,
);
sub start_document{
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scripts/testRNG_performance.pl view on Meta::CPAN
);
}
);
$benchmark->run_iterations($benchmark_reps);
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lib/Bio/Tools/Run/Alignment/MSAProbs.pm view on Meta::CPAN
Args : integer 0..5, [default 2] (optional)
=cut
=head2 iterations
Title : iterations
Usage : $prog->iterations($passes)
Function: get/set the number of iterative-refinement passes
Returns : integer
Args : integer 0..1000, [default 10] (optional)
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Bio/Align/DNAStatistics.pm view on Meta::CPAN
Title : calc_average_KaKs.
Useage : my $res= $stats->calc_average_KaKs($alnobj, 1000).
Function : calculates Nei_Gojobori stats for average of all
sequences in the alignment.
Args : A Bio::Align::AlignI compliant object such as a
Bio::SimpleAlign object, number of bootstrap iterations
(default 1000).
Returns : A reference to a hash of statistics as listed in Description.
=cut
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lib/Bio/AssemblyImprovement/Circlator/Main.pm view on Meta::CPAN
my @iterative_merge_files = sort {$self->_get_number_in_filename($a) <=> $self->_get_number_in_filename($b)} glob("$temp_dir/04.merge.merge.iter.*.reads.log"); #cannot rely on glob's lexical sorting
my @log_files = ("$temp_dir/02.bam2reads.log",
@iterative_merge_files,
"$temp_dir/04.merge.merge.iterations.log",
"$temp_dir/04.merge.merge.log",
"$temp_dir/04.merge.circularise_details.log",
"$temp_dir/04.merge.circularise.log",
"$temp_dir/05.clean.log",
"$temp_dir/06.fixstart.log",
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# Title : bla_to_msf (this is not used. Use convert_bla_to_msf)
# Usage : @msf_file_made=@{&bla_to_msf(\@bla_file)};
# Function : matched each query seq name and if the E value is lower than
# my arbitrary threshold, I put the subject and target pair
# alignment into a hash.
# In later iterations, the latest is replaced
# Example :
# Keywords : convert_bla_to_msf
# Options :
# Author :
# Category :
# Title : convert_bla_to_msf
# Usage : @msf_file_made=@{&convert_bla_to_msf(\@bla_file)};
# Function : matched each query seq name and if the E value is lower than
# my arbitrary threshold, I put the subject and target pair
# alignment into a hash.
# In later iterations, the latest is replaced
# Example :
# Keywords : convert_bla_to_msf
# Options :
# Author :
# Category :
# Title : convert_bla_multaln_to_msf
# Usage : @msf_file_made=@{&convert_bla_multaln_to_msf(\@bla_file, [i=2])};
# Function : matched each query seq name and if the E value is lower than
# my arbitrary threshold, I put the subject and target pair
# alignment into a hash.
# In later iterations, the latest is replaced,
# when you use m6 option for PSI blast
# this adds '00x' extensions to the repeatedly occurring seq names
#
# Example : @msf_file_made=@{&convert_bla_multaln_to_msf(\@bla_file,
# $verbose, "i=$iteration")};
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FlipFlop.pm view on Meta::CPAN
integer zero (0).
$r = set_test() ... reset_test();
# this same $r is present in the examples below
print 'the flip flop has been true for ', +$r, " iterations.\n";
=item lead_edge
The leading edge, when a flip flop changes from the false state to true
can be detected by testing the series for number 1.
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examples/xs_vs_pp.pl view on Meta::CPAN
Bit::Manip::PP::bit_set(65535, 0, 8, 0xFF);
}
__END__
Benchmark: timing 1000000 iterations of c, p...
c: 3 wallclock secs ( 3.35 usr + 0.00 sys = 3.35 CPU) @ 298507.46/s (n=1000000)
p: 17 wallclock secs (16.58 usr + 0.00 sys = 16.58 CPU) @ 60313.63/s (n=1000000)
Rate p c
p 60606/s -- -80%
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examples/xs_vs_pp.pl view on Meta::CPAN
Bit::Manip::PP::bit_set(65535, 0, 8, 0xFF);
}
__END__
Benchmark: timing 1000000 iterations of c, p...
c: 3 wallclock secs ( 3.35 usr + 0.00 sys = 3.35 CPU) @ 298507.46/s (n=1000000)
p: 17 wallclock secs (16.58 usr + 0.00 sys = 16.58 CPU) @ 60313.63/s (n=1000000)
Rate p c
p 60606/s -- -80%
c 299401/s 394% --