| Filename | /Users/ap13/perl5/perlbrew/perls/perl-5.16.2/lib/5.16.2/base.pm |
| Statements | Executed 2174 statements in 6.68ms |
| Calls | P | F | Exclusive Time |
Inclusive Time |
Subroutine |
|---|---|---|---|---|---|
| 61 | 61 | 60 | 25.8ms | 75.4ms | base::import (recurses: max depth 3, inclusive time 30.6ms) |
| 1 | 1 | 1 | 674µs | 1.36ms | base::BEGIN@4 |
| 88 | 1 | 1 | 315µs | 315µs | base::has_fields |
| 88 | 1 | 1 | 234µs | 234µs | base::has_attr |
| 1 | 1 | 1 | 20µs | 38µs | base::BEGIN@3 |
| 0 | 0 | 0 | 0s | 0s | base::__ANON__[:48] |
| 0 | 0 | 0 | 0s | 0s | base::__ANON__[:55] |
| 0 | 0 | 0 | 0s | 0s | base::get_attr |
| 0 | 0 | 0 | 0s | 0s | base::inherit_fields |
| Line | State ments |
Time on line |
Calls | Time in subs |
Code |
|---|---|---|---|---|---|
| 1 | package base; | ||||
| 2 | |||||
| 3 | 2 | 46µs | 2 | 57µs | # spent 38µs (20+18) within base::BEGIN@3 which was called:
# once (20µs+18µs) by Class::Load::BEGIN@7 at line 3 # spent 38µs making 1 call to base::BEGIN@3
# spent 18µs making 1 call to strict::import |
| 4 | 2 | 998µs | 2 | 1.39ms | # spent 1.36ms (674µs+684µs) within base::BEGIN@4 which was called:
# once (674µs+684µs) by Class::Load::BEGIN@7 at line 4 # spent 1.36ms making 1 call to base::BEGIN@4
# spent 35µs making 1 call to vars::import |
| 5 | 1 | 1µs | $VERSION = '2.18'; | ||
| 6 | 1 | 24µs | $VERSION = eval $VERSION; # spent 2µs executing statements in string eval | ||
| 7 | |||||
| 8 | # constant.pm is slow | ||||
| 9 | sub SUCCESS () { 1 } | ||||
| 10 | |||||
| 11 | sub PUBLIC () { 2**0 } | ||||
| 12 | sub PRIVATE () { 2**1 } | ||||
| 13 | sub INHERITED () { 2**2 } | ||||
| 14 | sub PROTECTED () { 2**3 } | ||||
| 15 | |||||
| 16 | |||||
| 17 | 1 | 800ns | my $Fattr = \%fields::attr; | ||
| 18 | |||||
| 19 | # spent 315µs within base::has_fields which was called 88 times, avg 4µs/call:
# 88 times (315µs+0s) by base::import at line 101, avg 4µs/call | ||||
| 20 | 264 | 419µs | my($base) = shift; | ||
| 21 | my $fglob = ${"$base\::"}{FIELDS}; | ||||
| 22 | return( ($fglob && 'GLOB' eq ref($fglob) && *$fglob{HASH}) ? 1 : 0 ); | ||||
| 23 | } | ||||
| 24 | |||||
| 25 | # spent 234µs within base::has_attr which was called 88 times, avg 3µs/call:
# 88 times (234µs+0s) by base::import at line 101, avg 3µs/call | ||||
| 26 | 264 | 271µs | my($proto) = shift; | ||
| 27 | my($class) = ref $proto || $proto; | ||||
| 28 | return exists $Fattr->{$class}; | ||||
| 29 | } | ||||
| 30 | |||||
| 31 | sub get_attr { | ||||
| 32 | $Fattr->{$_[0]} = [1] unless $Fattr->{$_[0]}; | ||||
| 33 | return $Fattr->{$_[0]}; | ||||
| 34 | } | ||||
| 35 | |||||
| 36 | 2 | 6µs | if ($] < 5.009) { | ||
| 37 | *get_fields = sub { | ||||
| 38 | # Shut up a possible typo warning. | ||||
| 39 | () = \%{$_[0].'::FIELDS'}; | ||||
| 40 | my $f = \%{$_[0].'::FIELDS'}; | ||||
| 41 | |||||
| 42 | # should be centralized in fields? perhaps | ||||
| 43 | # fields::mk_FIELDS_be_OK. Peh. As long as %{ $package . '::FIELDS' } | ||||
| 44 | # is used here anyway, it doesn't matter. | ||||
| 45 | bless $f, 'pseudohash' if (ref($f) ne 'pseudohash'); | ||||
| 46 | |||||
| 47 | return $f; | ||||
| 48 | } | ||||
| 49 | } | ||||
| 50 | else { | ||||
| 51 | *get_fields = sub { | ||||
| 52 | # Shut up a possible typo warning. | ||||
| 53 | () = \%{$_[0].'::FIELDS'}; | ||||
| 54 | return \%{$_[0].'::FIELDS'}; | ||||
| 55 | } | ||||
| 56 | } | ||||
| 57 | |||||
| 58 | # spent 75.4ms (25.8+49.6) within base::import which was called 61 times, avg 1.24ms/call:
# once (1.80ms+35.2ms) by Bio::Seq::SeqFactory::BEGIN@83 at line 83 of Bio/Seq/SeqFactory.pm
# once (3.71ms+15.9ms) by Bio::LocatableSeq::BEGIN@120 at line 120 of Bio/LocatableSeq.pm
# once (2.10ms+5.12ms) by Bio::SeqFeature::Generic::BEGIN@151 at line 151 of Bio/SeqFeature/Generic.pm
# once (1.62ms+4.59ms) by Bio::Location::Simple::BEGIN@87 at line 87 of Bio/Location/Simple.pm
# once (373µs+215µs) by Bio::Tools::GFF::BEGIN@154 at line 154 of Bio/Tools/GFF.pm
# once (391µs+182µs) by Bio::Location::Split::BEGIN@101 at line 101 of Bio/Location/Split.pm
# once (389µs+141µs) by Bio::Location::Fuzzy::BEGIN@84 at line 84 of Bio/Location/Fuzzy.pm
# once (400µs+124µs) by Bio::Annotation::Collection::BEGIN@96 at line 96 of Bio/Annotation/Collection.pm
# once (351µs+147µs) by Bio::Seq::SeqBuilder::BEGIN@133 at line 133 of Bio/Seq/SeqBuilder.pm
# once (304µs+168µs) by Bio::Factory::FTLocationFactory::BEGIN@102 at line 102 of Bio/Factory/FTLocationFactory.pm
# once (341µs+117µs) by Bio::Annotation::SimpleValue::BEGIN@82 at line 82 of Bio/Annotation/SimpleValue.pm
# once (114µs+17µs) by Graph::Traversal::DFS::BEGIN@6 at line 6 of Graph/Traversal/DFS.pm
# once (102µs+14µs) by Sub::Name::BEGIN@49 at line 49 of Sub/Name.pm
# once (96µs+14µs) by Graph::AdjacencyMatrix::BEGIN@8 at line 8 of Graph/AdjacencyMatrix.pm
# once (97µs+12µs) by Graph::SPTHeapElem::BEGIN@7 at line 7 of Graph/SPTHeapElem.pm
# once (94µs+14µs) by Graph::MSTHeapElem::BEGIN@7 at line 7 of Graph/MSTHeapElem.pm
# once (95µs+11µs) by Graph::Undirected::BEGIN@4 at line 4 of Graph/Undirected.pm
# once (90µs+10µs) by Bio::Factory::SequenceStreamI::BEGIN@80 at line 80 of Bio/Factory/SequenceStreamI.pm
# once (82µs+10µs) by Class::Load::BEGIN@7 at line 7 of Class/Load.pm
# once (69µs+13µs) by Moose::Meta::TypeConstraint::BEGIN@18 at line 18 of Moose/Meta/TypeConstraint.pm
# once (71µs+10µs) by Sub::Name::BEGIN@50 at line 50 of Sub/Name.pm
# once (64µs+11µs) by Bio::Roary::Exceptions::FileNotFound::BEGIN@3 at line 3 of (eval 180)[Exception/Class.pm:179]
# once (65µs+8µs) by Bio::Annotation::TypeManager::BEGIN@86 at line 86 of Bio/Annotation/TypeManager.pm
# once (62µs+10µs) by Exception::Class::Base::BEGIN@10 at line 10 of Exception/Class/Base.pm
# once (62µs+10µs) by Graph::AdjacencyMap::Heavy::BEGIN@13 at line 13 of Graph/AdjacencyMap/Heavy.pm
# once (56µs+7µs) by Bio::Tools::GuessSeqFormat::BEGIN@251 at line 251 of Bio/Tools/GuessSeqFormat.pm
# once (53µs+7µs) by Bio::Roary::Exceptions::CouldntWriteToFile::BEGIN@3 at line 3 of (eval 182)[Exception/Class.pm:179]
# once (53µs+6µs) by Graph::TransitiveClosure::BEGIN@9 at line 9 of Graph/TransitiveClosure.pm
# once (52µs+6µs) by Graph::AdjacencyMap::Light::BEGIN@10 at line 10 of Graph/AdjacencyMap/Light.pm
# once (46µs+6µs) by Graph::AdjacencyMap::Vertex::BEGIN@13 at line 13 of Graph/AdjacencyMap/Vertex.pm
# once (48µs+-48µs) by Bio::RangeI::BEGIN@96 at line 96 of Bio/RangeI.pm
# once (522µs+-522µs) by Bio::Seq::BEGIN@464 at line 464 of Bio/Seq.pm
# once (46µs+-46µs) by Bio::Factory::ObjectBuilderI::BEGIN@98 at line 98 of Bio/Factory/ObjectBuilderI.pm
# once (2.48ms+-2.48ms) by Bio::LocationI::BEGIN@79 at line 79 of Bio/LocationI.pm
# once (1.86ms+-1.86ms) by Bio::Root::Root::BEGIN@5 at line 5 of Bio/Root/Root.pm
# once (61µs+-61µs) by Bio::AnnotationI::BEGIN@120 at line 120 of Bio/AnnotationI.pm
# once (59µs+-59µs) by Bio::Factory::ObjectFactoryI::BEGIN@80 at line 80 of Bio/Factory/ObjectFactoryI.pm
# once (53µs+-53µs) by Bio::PrimarySeqI::BEGIN@126 at line 126 of Bio/PrimarySeqI.pm
# once (56µs+-56µs) by Bio::Location::SplitLocationI::BEGIN@84 at line 84 of Bio/Location/SplitLocationI.pm
# once (3.69ms+-3.69ms) by Bio::PrimarySeq::BEGIN@133 at line 134 of Bio/PrimarySeq.pm
# once (841µs+-841µs) by Bio::Location::Atomic::BEGIN@81 at line 81 of Bio/Location/Atomic.pm
# once (75µs+-75µs) by Bio::IdentifiableI::BEGIN@96 at line 96 of Bio/IdentifiableI.pm
# once (65µs+-65µs) by Bio::Tools::CodonTable::BEGIN@193 at line 193 of Bio/Tools/CodonTable.pm
# once (55µs+-55µs) by Bio::SeqAnalysisParserI::BEGIN@93 at line 93 of Bio/SeqAnalysisParserI.pm
# once (52µs+-52µs) by Bio::Location::CoordinatePolicyI::BEGIN@86 at line 86 of Bio/Location/CoordinatePolicyI.pm
# once (795µs+-795µs) by Bio::SeqI::BEGIN@116 at line 116 of Bio/SeqI.pm
# once (42µs+-42µs) by Bio::FeatureHolderI::BEGIN@98 at line 98 of Bio/FeatureHolderI.pm
# once (66µs+-66µs) by Bio::Root::IO::BEGIN@8 at line 8 of Bio/Root/IO.pm
# once (52µs+-52µs) by Bio::SeqFeatureI::BEGIN@109 at line 109 of Bio/SeqFeatureI.pm
# once (64µs+-64µs) by Bio::Location::FuzzyLocationI::BEGIN@78 at line 78 of Bio/Location/FuzzyLocationI.pm
# once (47µs+-47µs) by Bio::DB::RandomAccessI::BEGIN@68 at line 68 of Bio/DB/RandomAccessI.pm
# once (53µs+-53µs) by Bio::Factory::LocationFactoryI::BEGIN@94 at line 94 of Bio/Factory/LocationFactoryI.pm
# once (261µs+-261µs) by Bio::Factory::SequenceFactoryI::BEGIN@88 at line 88 of Bio/Factory/SequenceFactoryI.pm
# once (319µs+-319µs) by Bio::DB::InMemoryCache::BEGIN@77 at line 77 of Bio/DB/InMemoryCache.pm
# once (69µs+-69µs) by Bio::DescribableI::BEGIN@70 at line 70 of Bio/DescribableI.pm
# once (101µs+-101µs) by Bio::Range::BEGIN@94 at line 94 of Bio/Range.pm
# once (54µs+-54µs) by Bio::AnnotationCollectionI::BEGIN@137 at line 137 of Bio/AnnotationCollectionI.pm
# once (306µs+-306µs) by Bio::Location::WidestCoordPolicy::BEGIN@80 at line 80 of Bio/Location/WidestCoordPolicy.pm
# once (282µs+-282µs) by Bio::DB::SeqI::BEGIN@81 at line 81 of Bio/DB/SeqI.pm
# once (65µs+-65µs) by Bio::Tools::IUPAC::BEGIN@169 at line 169 of Bio/Tools/IUPAC.pm
# once (50µs+-50µs) by Bio::AnnotatableI::BEGIN@86 at line 86 of Bio/AnnotatableI.pm | ||||
| 59 | 488 | 1.21ms | my $class = shift; | ||
| 60 | |||||
| 61 | return SUCCESS unless @_; | ||||
| 62 | |||||
| 63 | # List of base classes from which we will inherit %FIELDS. | ||||
| 64 | my $fields_base; | ||||
| 65 | |||||
| 66 | my $inheritor = caller(0); | ||||
| 67 | |||||
| 68 | my @bases; | ||||
| 69 | foreach my $base (@_) { | ||||
| 70 | 444 | 1.48ms | if ( $inheritor eq $base ) { | ||
| 71 | warn "Class '$inheritor' tried to inherit from itself\n"; | ||||
| 72 | } | ||||
| 73 | |||||
| 74 | 140 | 224µs | next if grep $_->isa($base), ($inheritor, @bases); # spent 224µs making 140 calls to UNIVERSAL::isa, avg 2µs/call | ||
| 75 | |||||
| 76 | # Following blocks help isolate $SIG{__DIE__} changes | ||||
| 77 | { | ||||
| 78 | 264 | 47µs | my $sigdie; | ||
| 79 | { | ||||
| 80 | 440 | 2.16ms | local $SIG{__DIE__}; | ||
| 81 | eval "require $base"; # spent 205µs executing statements in 2 string evals (merged)
# spent 172µs executing statements in 2 string evals (merged)
# spent 158µs executing statements in string eval
# spent 145µs executing statements in string eval
# spent 141µs executing statements in 2 string evals (merged)
# spent 135µs executing statements in string eval
# spent 134µs executing statements in 19 string evals (merged)
# spent 131µs executing statements in 2 string evals (merged)
# spent 131µs executing statements in 2 string evals (merged)
# spent 130µs executing statements in 2 string evals (merged)
# spent 128µs executing statements in 15 string evals (merged)
# spent 122µs executing statements in 2 string evals (merged)
# spent 119µs executing statements in string eval
# spent 116µs executing statements in string eval
# spent 116µs executing statements in string eval
# spent 112µs executing statements in string eval
# spent 110µs executing statements in 4 string evals (merged)
# spent 109µs executing statements in string eval
# spent 101µs executing statements in string eval
# spent 101µs executing statements in 2 string evals (merged)
# spent 100µs executing statements in 3 string evals (merged)
# spent 98µs executing statements in 3 string evals (merged)
# spent 98µs executing statements in string eval
# spent 92µs executing statements in string eval
# spent 8µs executing statements in 2 string evals (merged)
# spent 7µs executing statements in 2 string evals (merged)
# spent 7µs executing statements in 3 string evals (merged)
# spent 6µs executing statements in 2 string evals (merged)
# spent 5µs executing statements in 2 string evals (merged)
# spent 4µs executing statements in string eval
# spent 4µs executing statements in string eval
# spent 4µs executing statements in string eval
# spent 3µs executing statements in string eval
# spent 2µs executing statements in string eval
# spent 2µs executing statements in string eval | ||||
| 82 | # Only ignore "Can't locate" errors from our eval require. | ||||
| 83 | # Other fatal errors (syntax etc) must be reported. | ||||
| 84 | die if $@ && $@ !~ /^Can't locate .*? at \(eval /; | ||||
| 85 | unless (%{"$base\::"}) { | ||||
| 86 | require Carp; | ||||
| 87 | local $" = " "; | ||||
| 88 | Carp::croak(<<ERROR); | ||||
| 89 | Base class package "$base" is empty. | ||||
| 90 | (Perhaps you need to 'use' the module which defines that package first, | ||||
| 91 | or make that module available in \@INC (\@INC contains: @INC). | ||||
| 92 | ERROR | ||||
| 93 | } | ||||
| 94 | $sigdie = $SIG{__DIE__} || undef; | ||||
| 95 | } | ||||
| 96 | # Make sure a global $SIG{__DIE__} makes it out of the localization. | ||||
| 97 | $SIG{__DIE__} = $sigdie if defined $sigdie; | ||||
| 98 | } | ||||
| 99 | push @bases, $base; | ||||
| 100 | |||||
| 101 | 176 | 549µs | if ( has_fields($base) || has_attr($base) ) { # spent 315µs making 88 calls to base::has_fields, avg 4µs/call
# spent 234µs making 88 calls to base::has_attr, avg 3µs/call | ||
| 102 | # No multiple fields inheritance *suck* | ||||
| 103 | if ($fields_base) { | ||||
| 104 | require Carp; | ||||
| 105 | Carp::croak("Can't multiply inherit fields"); | ||||
| 106 | } else { | ||||
| 107 | $fields_base = $base; | ||||
| 108 | } | ||||
| 109 | } | ||||
| 110 | } | ||||
| 111 | # Save this until the end so it's all or nothing if the above loop croaks. | ||||
| 112 | push @{"$inheritor\::ISA"}, @bases; | ||||
| 113 | |||||
| 114 | if( defined $fields_base ) { | ||||
| 115 | inherit_fields($inheritor, $fields_base); | ||||
| 116 | } | ||||
| 117 | } | ||||
| 118 | |||||
| 119 | |||||
| 120 | sub inherit_fields { | ||||
| 121 | my($derived, $base) = @_; | ||||
| 122 | |||||
| 123 | return SUCCESS unless $base; | ||||
| 124 | |||||
| 125 | my $battr = get_attr($base); | ||||
| 126 | my $dattr = get_attr($derived); | ||||
| 127 | my $dfields = get_fields($derived); | ||||
| 128 | my $bfields = get_fields($base); | ||||
| 129 | |||||
| 130 | $dattr->[0] = @$battr; | ||||
| 131 | |||||
| 132 | if( keys %$dfields ) { | ||||
| 133 | warn <<"END"; | ||||
| 134 | $derived is inheriting from $base but already has its own fields! | ||||
| 135 | This will cause problems. Be sure you use base BEFORE declaring fields. | ||||
| 136 | END | ||||
| 137 | |||||
| 138 | } | ||||
| 139 | |||||
| 140 | # Iterate through the base's fields adding all the non-private | ||||
| 141 | # ones to the derived class. Hang on to the original attribute | ||||
| 142 | # (Public, Private, etc...) and add Inherited. | ||||
| 143 | # This is all too complicated to do efficiently with add_fields(). | ||||
| 144 | while (my($k,$v) = each %$bfields) { | ||||
| 145 | my $fno; | ||||
| 146 | if ($fno = $dfields->{$k} and $fno != $v) { | ||||
| 147 | require Carp; | ||||
| 148 | Carp::croak ("Inherited fields can't override existing fields"); | ||||
| 149 | } | ||||
| 150 | |||||
| 151 | if( $battr->[$v] & PRIVATE ) { | ||||
| 152 | $dattr->[$v] = PRIVATE | INHERITED; | ||||
| 153 | } | ||||
| 154 | else { | ||||
| 155 | $dattr->[$v] = INHERITED | $battr->[$v]; | ||||
| 156 | $dfields->{$k} = $v; | ||||
| 157 | } | ||||
| 158 | } | ||||
| 159 | |||||
| 160 | foreach my $idx (1..$#{$battr}) { | ||||
| 161 | next if defined $dattr->[$idx]; | ||||
| 162 | $dattr->[$idx] = $battr->[$idx] & INHERITED; | ||||
| 163 | } | ||||
| 164 | } | ||||
| 165 | |||||
| 166 | |||||
| 167 | 1 | 11µs | 1; | ||
| 168 | |||||
| 169 | __END__ |