Result:
found more than 709 distributions - search limited to the first 2001 files matching your query
( run in 1.574 )
BeePack
view release on metacpan or search on metacpan
$ bee test.bee key
# sample complex key, no need for escaping
$ bee test.bee web#img/background.jpg#content
# get is transparent on string
$ bee test.bee gzipped_value | gunzip -c
# set key to nil
$ bee test.bee key n
Benchmark-CSV
view release on metacpan or search on metacpan
examples/math/aggregate_histogram.gnuplot view on Meta::CPAN
#set xrange [0.0006:0.001]
set datafile separator ','
set style fill transparent solid 0.05
set key autotitle columnheader
set grid ytics lc rgb "#777777" lt 0 back
Benchmark-DKbench
view release on metacpan or search on metacpan
data/wiki0.html view on Meta::CPAN
<div id="contentSub2"></div>
<div id="jump-to-nav"></div>
<a class="mw-jump-link" href="#mw-head">Jump to navigation</a>
<a class="mw-jump-link" href="#searchInput">Jump to search</a>
<div id="mw-content-text" class="mw-body-content mw-content-ltr" lang="en" dir="ltr"><div class="mw-parser-output"><style data-mw-deduplicate="TemplateStyles:r1049785579">.mw-parser-output #mp-topbanner{position:relative;box-sizing:border-box;min-w...
<div id="mp-topbanner" class="mp-bordered">
<div id="mp-welcomecount">
<div id="mp-welcome">Welcome to <a href="/wiki/Wikipedia" title="Wikipedia">Wikipedia</a>,</div>
<div id="mp-free">the <a href="/wiki/Free_content" title="Free content">free</a> <a href="/wiki/Encyclopedia" title="Encyclopedia">encyclopedia</a> that <a href="/wiki/Help:Introduction_to_Wikipedia" title="Help:Introduction to Wikipedia">anyone can ...
<div id="articlecount"><a href="/wiki/Special:Statistics" title="Special:Statistics">6,417,267</a> articles in <a href="/wiki/English_language" title="English language">English</a></div>
data/wiki0.html view on Meta::CPAN
<table role="presentation" id="mp-upper">
<tbody><tr>
<td id="mp-left" class="MainPageBG mp-bordered">
<h2 id="mp-tfa-h2" class="mp-h2"><span id="From_today.27s_featured_article"></span><span class="mw-headline" id="From_today's_featured_article">From today's featured article</span></h2>
<div id="mp-tfa"><div id="mp-tfa-img" style="float: left; margin: 0.5em 0.9em 0.4em 0em;">
<div class="thumbinner mp-thumb" style="background: transparent; border: none; padding: 0; max-width: 171px;">
<a href="/wiki/File:G%C3%A9iseres_del_Tatio,_Atacama,_Chile,_2016-02-01,_DD_01-02_HDR.JPG" class="image" title="Geysers of El Tatio"><img alt="Geysers of El Tatio" src="//upload.wikimedia.org/wikipedia/commons/thumb/5/5d/G%C3%A9iseres_del_Tatio%2C_At...
</div>
<p><b><a href="/wiki/El_Tatio" title="El Tatio">El Tatio</a></b> is a geothermal field with many <a href="/wiki/Geyser" title="Geyser">geysers</a> located in the <a href="/wiki/Andes" title="Andes">Andes</a> of <a href="/wiki/Norte_Grande" title="Nor...
</p>
<div class="tfa-recent" style="text-align: right;">
data/wiki0.html view on Meta::CPAN
<li><b><a href="/wiki/Wikipedia:Featured_articles" title="Wikipedia:Featured articles">More featured articles</a></b></li></ul>
</div></div>
<h2 id="mp-dyk-h2" class="mp-h2"><span class="mw-headline" id="Did_you_know_...">Did you know ...</span></h2>
<div id="mp-dyk">
<div class="dyk-img" style="float: right; margin-left: 0.5em;">
<div class="thumbinner mp-thumb" style="background: transparent; border: none; padding: 0; max-width: 178px;">
<a href="/wiki/File:Lampetra_fluviatilis.jpg" class="image" title="European river lamprey"><img alt="European river lamprey" src="//upload.wikimedia.org/wikipedia/commons/thumb/3/3f/Lampetra_fluviatilis.jpg/178px-Lampetra_fluviatilis.jpg" decoding="a...
</div>
<ul><li>... that on special occasions, the city of Gloucester supplies a <b><a href="/wiki/Lamprey_pie" title="Lamprey pie">pie made from lampreys</a></b> <i>(lamprey pictured)</i> to the British monarch?</li>
<li>... that in the board game <i><b><a href="/wiki/Sagrada_(board_game)" title="Sagrada (board game)">Sagrada</a></b></i>, players attempt to construct a <a href="/wiki/Stained_glass" title="Stained glass">stained-glass window</a> using dice?</li>
<li>... that economist <b><a href="/wiki/Nisvan_Erkal" title="Nisvan Erkal">Nisvan Erkal</a></b><span class="nowrap">'s</span> research showed that China's <a href="/wiki/One-child_policy" title="One-child policy">one-child policy</a> created chi...
data/wiki0.html view on Meta::CPAN
<td class="mp-bordered mid-table">
</td>
<td id="mp-right" class="MainPageBG mp-bordered">
<h2 id="mp-itn-h2" class="mp-h2"><span class="mw-headline" id="In_the_news">In the news</span></h2>
<div id="mp-itn"><style data-mw-deduplicate="TemplateStyles:r1053378754">.mw-parser-output .itn-img{float:right;margin-left:0.5em;margin-top:0.2em}</style><div role="figure" class="itn-img">
<div class="thumbinner mp-thumb" style="background: transparent; border: none; padding: 0; max-width: 171px;">
<a href="/wiki/File:2020_Indian_farmers%27_protest_-_sitting_protest.jpg" class="image" title="Indian farmers protesting on the March to Delhi in November 2020"><img alt="Indian farmers protesting on the March to Delhi in November 2020" src="//upload...
</div>
<ul><li>The <a href="/wiki/2020_Indian_agriculture_acts" title="2020 Indian agriculture acts">Indian agriculture acts</a> are repealed after <b><a href="/wiki/2020%E2%80%932021_Indian_farmers%27_protest" title="2020–2021 Indian farmers' protest...
<li><a href="/wiki/Xiomara_Castro" title="Xiomara Castro">Xiomara Castro</a> <b><a href="/wiki/2021_Honduran_general_election" title="2021 Honduran general election">is elected</a></b> as the first female <a href="/wiki/President_of_Honduras" title="...
<li><b><a href="/wiki/Magdalena_Andersson" title="Magdalena Andersson">Magdalena Andersson</a></b>, who resigned a week earlier after less than one day as <a href="/wiki/Prime_minister%E2%80%93designate" title="Prime minister–designate">prime minis...
data/wiki0.html view on Meta::CPAN
<h2 id="mp-otd-h2" class="mp-h2"><span class="mw-headline" id="On_this_day">On this day</span></h2>
<div id="mp-otd">
<p><b><a href="/wiki/December_3" title="December 3">December 3</a></b>
</p>
<div style="float:right;margin-left:0.5em;" id="mp-otd-img">
<div class="thumbinner mp-thumb" style="background: transparent; border: none; padding: 0; max-width: 120px;">
<a href="/wiki/File:Emmeline_Freda_du_Faur,_by_George_Edward_Mannering_(1862-1947).jpg" title="Freda Du Faur"><img alt="Freda Du Faur" src="//upload.wikimedia.org/wikipedia/commons/thumb/c/c8/Emmeline_Freda_du_Faur%2C_by_George_Edward_Mannering_%2818...
</div>
<ul><li><a href="/wiki/1800" title="1800">1800</a> – <a href="/wiki/War_of_the_Second_Coalition" title="War of the Second Coalition">War of the Second Coalition</a>: French forces defeated Austrian and Bavarian troops at the <b><a href="/wiki/Battl...
<li><a href="/wiki/1910" title="1910">1910</a> – <b><a href="/wiki/Freda_Du_Faur" title="Freda Du Faur">Freda Du Faur</a></b> <i>(pictured)</i> became the first woman to climb <a href="/wiki/Aoraki_/_Mount_Cook" title="Aoraki / Mount Cook">Mount Co...
<li><a href="/wiki/1968" title="1968">1968</a> – <a href="/wiki/Elvis_Presley" title="Elvis Presley">Elvis Presley</a>'s first television special and first live performance in seven years, <i><b><a href="/wiki/Elvis_(1968_TV_program)" title="Elvis ...
data/wiki0.html view on Meta::CPAN
</div></div>
</td></tr></tbody></table>
<div id="mp-middle" class="MainPageBG mp-bordered">
<div id="mp-center">
<h2 id="mp-tfl-h2" class="mp-h2"><span id="From_today.27s_featured_list"></span><span class="mw-headline" id="From_today's_featured_list">From today's featured list</span></h2>
<div id="mp-tfl"><div id="mp-tfl-img" style="float:right;margin:0.5em 0 0.4em 0.9em;"><div class="thumbinner mp-thumb" style="background: transparent; border: none; padding: 0; max-width: 140px;">
<a href="/wiki/File:British_2nd_Infantry_Division.svg" class="image" title="Divisional insignia used from c. 1940 until 2012"><img alt="Divisional insignia used from c. 1940 until 2012" src="//upload.wikimedia.org/wikipedia/commons/thumb/a/aa/Bri...
</div>
<p>The <a href="/wiki/2nd_Infantry_Division_(United_Kingdom)" title="2nd Infantry Division (United Kingdom)">2nd Division</a>, a <a href="/wiki/Division_(military)" title="Division (military)">division</a> of <a href="/wiki/Infantry" title="Infantry"...
</p>
<div class="tfl-recent" style="text-align: right;">
data/wiki0.html view on Meta::CPAN
</div>
<div id="mp-lower" class="MainPageBG mp-bordered">
<div id="mp-bottom">
<h2 id="mp-tfp-h2" class="mp-h2"><span id="Today.27s_featured_picture"></span><span class="mw-headline" id="Today's_featured_picture">Today's featured picture</span></h2>
<div id="mp-tfp">
<table role="presentation" style="margin:0 3px 3px; width:100%; box-sizing:border-box; text-align:center; background-color:transparent; border-collapse:collapse; padding:0.9em">
<tbody><tr>
<td><a href="/wiki/File:Russia_1771_Sestroretsk_Rouble.jpg" class="image" title="1771 Russian one-ruble coin"><img alt="1771 Russian one-ruble coin" src="//upload.wikimedia.org/wikipedia/commons/thumb/4/41/Russia_1771_Sestroretsk_Rouble.jpg/450px-Rus...
</td></tr>
<tr>
<td style="padding:0 0.9em; text-align:left;">
Benchmark-Harness-Graph
view release on metacpan or search on metacpan
'y2_label_skip' => 1,
'title' => undef, # as for the functions entry/exit lines, below.
'x_ticks' => 'true', 'x_tick_number' => 12,
'y1_ticks' => 'true', 'y1_tick_number' => 12,
'y2_ticks' => 'true', 'y2_tick_number' => 10,
'transparent' => 1, 'box_axis' => 0, 'line_width' => 3,
'x_max_value' => $self->{x_max_value}, 'x_min_value' => $self->{x_min_value},
'y1_max_value' => $self->{y1_max_value}, 'y1_min_value' => $self->{y1_min_value},
'y2_max_value' => $self->{y2_max_value}, 'y2_min_value' => $self->{y2_min_value},
);
'y2_label_skip' => 1,
'title' => undef,
'x_ticks' => 'true', 'x_tick_number' => 12,
'y1_ticks' => 'true', 'y1_tick_number' => 12,
'y2_ticks' => 'true', 'y2_tick_number' => 10,
'transparent' => 1, 'box_axis' => 0, 'line_width' => 2,
);
my @needsLegends = ( $x_axis, $y1_axis, $y2_axis ); # We'll build legends from this array later.
my @funcDataColors = ($y1_axis->{color}); # $graph->plot() needs this, below.
Benchmark-Perl-Formance-Cargo
view release on metacpan or search on metacpan
share/SpamAssassin/easy_ham/00166.8feace9f17d092d9532e62c35c37ce95 view on Meta::CPAN
<!-- Footer Styles -->
<style type='text/css'>
<!--
.a281108918593907-section_heading{color:#FFFFFF;background-color:#000000;font-family:arial;font-size:x-small;font-weight:bold;font-style:normal;text-decoration:none;text-align:left}
.a281108918593907-footer_publisher{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:normal;font-style:normal;text-decoration:none}
.a281108918593907-footer_publisher:hover{color:#FF0000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:normal;font-style:normal;text-decoration:underline}
.a281108918593907-footer_copyright{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:normal;font-style:normal;text-decoration:none}
.a281108918593907-footer_disclaimer{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:normal;font-style:normal;text-decoration:none}
.a281108918593907-footer_tellafriend{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:bold;font-style:normal;text-decoration:underline}
.a281108918593907-footer_tellafriend:hover{color:#FF0000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:bold;font-style:normal;text-decoration:underline}
.a281108918593907-footer_archive{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:bold;font-style:normal;text-decoration:none}
.a281108918593907-footer_archive:hover{color:#FF0000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:bold;font-style:normal;text-decoration:underline}
.a281108918593907-footer_pdf{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:bold;font-style:normal;text-decoration:none}
.a281108918593907-footer_pdf:hover{color:#FF0000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:bold;font-style:normal;text-decoration:underline}
-->
</style>
<!-- Article View Styles -->
<style type='text/css'>
<!--
.a281108918594507-section_heading{color:#FFFFFF;background-color:#000000;font-family:arial;font-size:x-small;font-weight:bold;font-style:normal;text-decoration:none;text-align:left}
.a281108918594507-contents_article_title{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:normal;font-style:normal;text-decoration:underline}
.a281108918594507-contents_article_title:hover{color:#FF0000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:normal;font-style:normal;text-decoration:underline}
-->
</style>
<!-- Article View Styles -->
<style type='text/css'>
<!--
.a281108918597543-section_heading{color:#FFFFFF;background-color:#000000;font-family:arial;font-size:x-small;font-weight:bold;font-style:normal;text-decoration:none;text-align:left}
.a281108918597543-contents_article_title{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:normal;font-style:normal;text-decoration:underline}
.a281108918597543-contents_article_title:hover{color:#FF0000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:normal;font-style:normal;text-decoration:underline}
-->
</style>
<!-- Footer Styles -->
<style type='text/css'>
<!--
.a281108918594847-section_heading{color:#FFFFFF;background-color:#000000;font-family:arial;font-size:x-small;font-weight:bold;font-style:normal;text-decoration:none;text-align:left}
.a281108918594847-footer_publisher{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:normal;font-style:normal;text-decoration:none}
.a281108918594847-footer_publisher:hover{color:#FF0000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:normal;font-style:normal;text-decoration:underline}
.a281108918594847-footer_copyright{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:normal;font-style:normal;text-decoration:none}
.a281108918594847-footer_disclaimer{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:normal;font-style:normal;text-decoration:none}
.a281108918594847-footer_tellafriend{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:bold;font-style:normal;text-decoration:underline}
.a281108918594847-footer_tellafriend:hover{color:#FF0000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:bold;font-style:normal;text-decoration:underline}
.a281108918594847-footer_archive{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:bold;font-style:normal;text-decoration:none}
.a281108918594847-footer_archive:hover{color:#FF0000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:bold;font-style:normal;text-decoration:underline}
.a281108918594847-footer_pdf{color:#000000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:bold;font-style:normal;text-decoration:none}
.a281108918594847-footer_pdf:hover{color:#FF0000;background-color:transparent;font-family:verdana;font-size:xx-small;font-weight:bold;font-style:normal;text-decoration:underline}
-->
</style>
</head>
Benchmark-Thread-Size
view release on metacpan or search on metacpan
being created. Even though they're created on the fly and removed
afterwards, they could use a little more documentation (looking back
at them about a year later).
Frank Tolstrup was so kind to send me the code to measure process size
under Windows. Now transparently included, which means this module
now also works under Windows! Updated the "HOW TO MEASURE SIZE?"
section. Added Win32::Process::Info as a conditional prerequisite
when making on a Windows system.
0.05 8 September 2003
BenchmarkAnything-Storage-Backend-SQL
view release on metacpan or search on metacpan
lib/BenchmarkAnything/Storage/Backend/SQL.pm view on Meta::CPAN
},
},
});
With such a config and an already set up Elasticsearch you can use the
lib as usual but it is handling all things transparently behind the
scenes to index and query the data with Elasticsearch. The relational
SQL storage is still used as the primary storage.
=head3 Index
Biblio-Isis
view release on metacpan or search on metacpan
lib/Biblio/Isis/Manual.pod view on Meta::CPAN
=back
For example the full name of the English version of the menu xXGEN is
C<AEXGEN.FMT>.
The page number is transparent to the CDS/ISIS user. Like the file
extension the page number is automatically provided by the system.
Therefore when a CDS/ISIS program prompts you to enter a menu or
worksheet name you must not include the page number. Furthermore as
file names are restricted to 6 characters, menus and worksheets names
may not be longer than 5 characters.
Biblio-Thesaurus-SQLite
view release on metacpan or search on metacpan
lib/Biblio/Thesaurus/SQLite.pm view on Meta::CPAN
changeTerm('term', 'oldrel', 'olddef', 'newrel', 'newdef', 'dbfile');
=head1 DESCRIPTION
This module provides transparent methods to maintain Thesaurus files
in a backend SQLite database. The module uses a subset from ISO 2788
which defines some standard
features to be found on thesaurus files. The module also supports
multilingual thesaurus and some extensions to the ISOs standard.
Biblio-Thesaurus
view release on metacpan or search on metacpan
lib/Biblio/Thesaurus.pm view on Meta::CPAN
$latex = $obj->toTex( ...)
$xml = $obj->toXml( ...)
=head1 ABSTRACT
This module provides transparent methods to maintain Thesaurus files.
The module uses a subset from ISO 2788 which defines some standard
features to be found on thesaurus files. The module also supports
multilingual thesaurus and some extensions to the ISOs standard.
=head1 DESCRIPTION
A Thesaurus is a classification structure. We can see it as a graph
where nodes are terms and the vertices are relations between terms.
This module provides transparent methods to maintain Thesaurus files.
The module uses a subset from ISO 2788 which defines some standard
features to be found on thesaurus files. This ISO includes a set of
relations that can be seen as standard but, this program can use user
defined ones. So, it can be used on ISO or not ISO thesaurus files.
Bigtop
view release on metacpan or search on metacpan
vim/syntax/bigtop.vim view on Meta::CPAN
hi def link bigtopJoinTableKeywords Identifier
hi def link bigtopMethodKeywords Identifier
hi def link bigtopTableKeywords Identifier
if exists("bigtop_fold")
syn region blockFold start="{" end ="}" transparent fold
syn sync fromstart
set foldmethod=syntax
endif
Bio-Affymetrix
view release on metacpan or search on metacpan
lib/Bio/Affymetrix/CHP.pm view on Meta::CPAN
for you :). This module parses CHP files.
This module requires a Bio::Affymetrix::CDF object before it can do
anything. This must be supplied to the constructor. See the perldoc
for that to see how to use that module. The module can parse various
types of CHP file transparently. You can find out what type you have
by using the original_version() method.
All of the Bio::Affymetrix modules parse a file entirely into
memory. You therefore need enough memory to hold these objects. For
some applications, parsing as a stream may be more appropriate-
lib/Bio/Affymetrix/CHP.pm view on Meta::CPAN
in theory. However the authors of this module have never actually
seen an actual GCOS v1.0 file, and so we rely on the specification
supplied by Affymetrix only. If you have GCOS v1.0 files, feedback
as to whether the code actually works is welcome.
Whatever file format you use the module should work transparently.
These modules are focused on GCOS v1.2 CHP files. The MAS5 CHP
files actually contain a lot of extra information that is not
displayed in MAS5 or GCOS. This information is thrown away by the
parser.
Bio-Chado-Schema
view release on metacpan or search on metacpan
doc/slides/dbic_intro/slides/ui/pretty.css view on Meta::CPAN
#currentSlide span {display: none;}
#slide0 {padding-top: 3.5em; font-size: 90%;}
#slide0 h1 {position: static; margin: 1em 0 1.33em; padding: 5px 0 5px 20px;
font: bold 2.2em Arial, Verdana, sans-serif; white-space: normal;
color: #000; background: transparent url(slide0h1.gif) no-repeat left bottom;
text-transform: none; }
#slide0 h3 {margin-top: 0.3em; font-size: 1.2em;}
#slide0 h4 {margin:0; font-size: 0.9em;}
ul.urls {list-style: none; display: inline; margin: 0;}
Bio-ConnectDots
view release on metacpan or search on metacpan
lib/Bio/ConnectDots/doc/cpan.css view on Meta::CPAN
color: #ff6600;
text-decoration: underline;
}
A:link, A:visited {
background: transparent;
color: #006699;
}
A[href="#POD_ERRORS"] {
background: transparent;
color: #FF0000;
}
TD {
margin: 0;
lib/Bio/ConnectDots/doc/cpan.css view on Meta::CPAN
padding: 0.4ex 1ex;
text-align: left;
}
TH A:link, TH A:visited {
background: transparent;
color: black;
}
.box {
border: 1px solid #006699;
lib/Bio/ConnectDots/doc/cpan.css view on Meta::CPAN
padding: 0.5ex 1ex;
vertical-align: baseline;
}
.path A {
background: transparent;
color: #006699;
font-weight: bold;
}
.pages {
lib/Bio/ConnectDots/doc/cpan.css view on Meta::CPAN
margin: 1ex 0;
padding: 1px;
}
.menubar .links {
background: transparent;
color: white;
padding: 0.2ex;
text-align: left;
}
lib/Bio/ConnectDots/doc/cpan.css view on Meta::CPAN
font: bold 10pt Arial,Helvetica,sans-serif;
text-decoration: none;
}
A.o:hover {
background: transparent;
color: #ff6600;
text-decoration: underline;
}
A.m:hover {
background: transparent;
color: #ff6600;
text-decoration: underline;
}
table.dlsip {
lib/Bio/ConnectDots/doc/cpan.css view on Meta::CPAN
padding: 1em;
white-space: pre;
}
.pod H1 {
background: transparent;
color: #006699;
font-size: large;
}
.pod H2 {
background: transparent;
color: #006699;
font-size: medium;
}
.pod IMG {
lib/Bio/ConnectDots/doc/cpan.css view on Meta::CPAN
.chmenu TD {
padding: 0.2ex 1ex;
}
.chmenu A:link, .chmenu A:visited {
background: transparent;
color: white;
text-decoration: none;
}
.chmenu A:hover {
background: transparent;
color: #ff6600;
text-decoration: underline;
}
.column {
lib/Bio/ConnectDots/doc/cpan.css view on Meta::CPAN
margin: auto;
width: 14em;
}
.date {
background: transparent;
color: #008000;
}
Bio-DB-EMBL
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lib/Bio/DB/EMBL.pm view on Meta::CPAN
Allows the dynamic retrieval of sequence objects L<Bio::Seq> from the
EMBL database using the dbfetch script at EBI:
L<http://www.ebi.ac.uk/Tools/dbfetch/dbfetch>.
In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out. This allows later
additions of more servers in different geographical locations.
The functionality of this module is inherited from L<Bio::DB::DBFetch>
which implements L<Bio::DB::WebDBSeqI>.
Bio-DB-GFF
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lib/Bio/DB/GFF.pm view on Meta::CPAN
=item *
a scalar corresponding to a GFF file on the system
A pathname to a local GFF file. Any files ending with the .gz, .Z, or
.bz2 suffixes will be transparently decompressed with the appropriate
command-line utility.
=item *
an array reference containing a list of GFF files on the system
lib/Bio/DB/GFF.pm view on Meta::CPAN
=item *
scalar corresponding to a FASTA file on the system
A pathname to a local FASTA file. Any files ending with the .gz, .Z, or
.bz2 suffixes will be transparently decompressed with the appropriate
command-line utility.
=item *
array reference containing a list of FASTA files on the
Bio-DB-RefSeq
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lib/Bio/DB/RefSeq.pm view on Meta::CPAN
http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
At this time the module specifically retrieves nucleotide sequences
only.
In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out. This allows later
additions of more servers in different geographical locations.
The functionality of this module is inherited from L<Bio::DB::DBFetch>
which implements L<Bio::DB::WebDBSeqI>.
Bio-DB-SwissProt
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lib/Bio/DB/SwissProt.pm view on Meta::CPAN
ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/.
Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the
SwissProt database via an Expasy retrieval.
In order to make changes transparent we have host type (currently only
expasy) and location (default to Switzerland) separated out. This
allows the user to pick the closest Expasy mirror for running their
queries.
Bio-DB-TFBS
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lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
# internal method which does the indexing
sub _build_index {
my ($self, $dat_dir, $force) = @_;
# MLDBM would give us transparent complex data structures with DB_File,
# allowing just one index file, but its yet another requirement and we
# don't strictly need it
my $index_dir = $self->index_directory;
my $gene_index = "$index_dir/gene.dat.index";
Bio-EnsEMBL
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lib/Bio/EnsEMBL/ChainedAssemblyMapper.pm view on Meta::CPAN
chromosome <-> contig
contig <-> clone
the ChainedAssemblyMapper would be able to perform implicit mapping
between the chromosome and clone coordinate systems. This should be
transparent to the user of this module, and users should not even
realise that they are using a chained assembly mapper as opposed to a
normal assembly mapper.
=head1 METHODS
Bio-GeneDesign
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lib/Bio/GeneDesign/Graph.pm view on Meta::CPAN
my $BitMap = GD::Image->new($Lseq1, $Lseq2);
my $white = $BitMap->colorAllocate(255,255,255);
my $black = $BitMap->colorAllocate(0,0,0);
$BitMap->transparent($white);
for (my $i = 0; $i < $Lseq1 - $winsize; $i++)
{
for (my $j = 0; $j < $Lseq2 - $winsize; $j++)
{
Bio-Genex
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AL_Spots/AL_Spots.pm view on Meta::CPAN
value from an object the built-in L<delayed fetch|/DELAYED_FETCH>
mechanism can be used. All objects are created without pre-fetching
any data from the DB. Whenever an attribute of the object is accessed
via a getter method, the data for that attribute will be fetched from
the DB if it has not already been. Delayed fetching happens
transparently without the user needing to enable or disable any
features.
Since data is not be fetched from the DB I<until> it is accessed by
the calling application, it could presumably save a lot of access time
for large complicated objects when only a few attribute values are
Bio-Graphics-Glyph-decorated_gene
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lib/Bio/Graphics/Glyph/decorated_gene.pm view on Meta::CPAN
else {
@subparts = $feature->get_SeqFeatures('exon');
}
# The CDS and UTRs may be represented as a single feature with subparts or as several features
# that have different IDs. We handle both cases transparently.
my @result;
foreach (@subparts) {
if ($_->primary_tag =~ /CDS|UTR/i) {
my @cds_seg = $_->get_SeqFeatures;
if (@cds_seg > 0) { push @result,@cds_seg } else { push @result,$_ }
lib/Bio/Graphics/Glyph/decorated_gene.pm view on Meta::CPAN
#
# @subparts = $feature->get_SeqFeatures(qw(CDS five_prime_UTR three_prime_UTR UTR));
# }
#
# # The CDS and UTRs may be represented as a single feature with subparts or as several features
# # that have different IDs. We handle both cases transparently.
# my @result;
# foreach (@subparts) {
# if ($_->primary_tag =~ /CDS|UTR/i) {
# my @cds_seg = $_->get_SeqFeatures;
# if (@cds_seg > 0) { push @result,@cds_seg } else { push @result,$_ }
Bio-Graphics
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lib/Bio/Graphics/Glyph.pm view on Meta::CPAN
'prior to rendering it.'],
opacity => [
'float',
'1.0',
'Default opacity to apply to glyph background and foreground colors.',
'This is a value between 0.0 (completely transparent) to 1.0 (completely opaque.',
'If the color contains an explicit opacity (alpha) value, the default value',
'will be ignored'],
linewidth => [
'integer',
1,
lib/Bio/Graphics/Glyph.pm view on Meta::CPAN
sub _translate_color {
my $self = shift;
my $color = shift;
my $opacity = $self->default_opacity;
return $opacity < 1 ? $self->factory->transparent_color($opacity,$color)
: $self->factory->translate_color($color);
}
# return value:
# 0 no bumping
Bio-Homology-InterologWalk
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lib/Bio/Homology/InterologWalk.pm view on Meta::CPAN
This is B<BETA> software. There will be bugs. The interface may change. Please be careful. Do not rely on it for anything mission-critical.
Please report any bugs you find, bug reports and any other feedback are most welcome.
-Currently only the EBI Intact DB is available for PPI retrieval. This will be expanded to account for all available PSICQUIC-compliant PPI dbs transparently.
This includes MINT, STRING, BioGrid and many more. For a full list of compliant DBs and for the status of the PSICQUIC service, check
http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS
Bio-MAGETAB
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lib/Bio/MAGETAB/Util/Reader/ADF.pm view on Meta::CPAN
=head1 DESCRIPTION
This class is used to parse ADF files. It can be used on its own, but
more often you will want to use the main Bio::MAGETAB::Util::Reader
class which handles extended parsing options more transparently.
=head1 ATTRIBUTES
See the L<TagValueFile|Bio::MAGETAB::Util::Reader::TagValueFile> class for superclass attributes.
Bio-MUST-Apps-FortyTwo
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lib/Bio/MUST/Apps/FortyTwo/Manual.pod view on Meta::CPAN
sequences must appear on a single (long) line; (2) gaps are encoded as asterisk
characters (C<*>) instead of dashes (C<->) and any whitespace is interpreted as
missing character states; (3) sequence identifiers accept a single whitespace
between genus and species (more on this just below); and (4) comment lines
(starting with the hashtag character C<#>) are allowed. Although C<42> can read
and write C<FASTA> files transparently, its C<ALI> roots sometimes play tricks
to the user.
This is especially true for sequence identifiers. Basically, each identifier has
to hold the organism name (C<org>) followed by a separator (C<@>) and by a
protein/gene accession number. The organism name is usually the binomial name.
Bio-MUST-Core
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bin/ali2phylip.pl view on Meta::CPAN
my $args = { clean => 1, $ARGV_p80 ? (short => 0, chunk => -1) : () };
$ali->$method($outfile, $args);
}
}
# wrapper to native methods to transparently handle codon_mask
sub _apply_mask {
my $ali = shift;
my $mask = shift;
if ($ARGV_keep_codons) {
Bio-NEXUS
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lib/Bio/NEXUS/Tools/NexPlotter.pm view on Meta::CPAN
$my_data_obj->set_image_handler($p);
$my_data_obj->set_font($font);
}
else {
my $im = new GD::Simple($nexusG->get_xsize,$nexusG->get_ysize);
# make the background transparent and interlaced
#$im->transparent($white);
$im->interlaced('true');
$my_data_obj->set_image_handler($im);
$my_data_obj->allocate_colors;
$my_data_obj->set_font(gdSmallFont());
}
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