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.
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
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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.
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;}
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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;
}
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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>.
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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
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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>.
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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.
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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";
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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
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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++)
{
view release on metacpan or search on metacpan
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
view release on metacpan or search on metacpan
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 = $_->get_SeqFeatures;
# if (@cds_seg > 0) { push @result,@cds_seg } else { push @result,$_ }
view release on metacpan or search on metacpan
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
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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
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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.
view release on metacpan or search on metacpan
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.
view release on metacpan or search on metacpan
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) {
view release on metacpan or search on metacpan
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());
}
view release on metacpan or search on metacpan
bin/draw_bgc_maps.pl view on Meta::CPAN
# do not draw if no @genes or @domains
unless (@genes && @domains) {
return;
}
# make the background transparent and interlaced
my @sorted_ends = sort { $b <=> $a } map{ $_->{end} } @genes;
my $width = $sorted_ends[0];
my $height = $y_cluster + 600;
my $left_margin = 50;
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
*
*/.center-nav{display:inline-block;margin-bottom:-4px}/*!
*
* IPython tree view
*
*/.alternate_upload{background-color:none;display:inline}.alternate_upload.form{padding:0;margin:0}.alternate_upload input.fileinput{display:inline;opacity:0;z-index:2;width:12ex;margin-right:-12ex}.alternate_upload .input-overlay{display:inline-bloc...
*
* IPython text editor webapp
*
*/.selected-keymap i.fa{padding:0 5px}.selected-keymap i.fa:before{content:"\f00c"}#mode-menu{overflow:auto;max-height:20em}.edit_app #header{-webkit-box-shadow:0 0 12px 1px rgba(87,87,87,0.2);box-shadow:0 0 12px 1px rgba(87,87,87,0.2)}.edit_app #men...
*
* IPython notebook
*
*/.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>
contrib/roary_plots/roary.html view on Meta::CPAN
}
</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}
.MathJax_MenuCheck.RTL {right: .7em; left: auto}
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DNA to give the data actually read; cigar string is always in
canonical coordinates
Version 1.09
* Disabled checks for file readability when path is a remote BAM
index. This allows transparent access to BAM databases on
http/ftp servers.
Version 1.08
* Implemented a clone() method for use immediately before or after
a fork() attempt.
view release on metacpan or search on metacpan
lib/Bio/ToolBox.pm view on Meta::CPAN
=item load_file
Open a tab-delimited text file as a L<Bio::ToolBox::Data> object.
Simply pass the file path as a single argument. It assumes the first
row is the column headers, and comment lines begin with C<#>.
Compressed files are transparently handled. See the
L<Bio::ToolBox::Data> C<new> method for more details or options.
$Data = Bio::ToolBox->load_file('myfile.txt');
For advanced options, pass key =E<gt> value pairs as arguments as
lib/Bio/ToolBox.pm view on Meta::CPAN
$Data = Bio::ToolBox->new_bed(4);
=item read_file
Open a generic file handle for reading. It transparently handles
compression as necessary. Returns an L<IO::File> object. Pass the
file path as an argument.
$fh = Bio::ToolBox->read_file('mydata.txt.gz');
=item write_file
Open a generic file handle for writing. It transparently handles
compression as necessary based on filename extension or passed
options. It will use the C<pigz> multi-threaded, external, compression
utility if available. See the C<open_to_write_fh> method in
<Bio::ToolBox::Data::file> for more information.
lib/Bio/ToolBox.pm view on Meta::CPAN
=item open_database
Open a binary database file, including Bam, bigWig, bigBed, Fasta,
L<Bio::DB::SeqFeature::Store> SQLite file or named MySQL connection,
USeq file, or any other supported binary or indexed file formats.
Database type is transparently and automatically checked by looking for
common file extensions, if present. See the C<open_db_connection> in
L<Bio::ToolBox::db_helper> for more information.
$db = Bio::ToolBox->open_database($database);
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lib/Bio/ViennaNGS/Fasta.pm view on Meta::CPAN
=over 3
=item fasta (required)
Upcon object construction, this attribute expects an input fasta file,
which is transparently coerced into a L<Bio::DB::Fasta> object and
hitherto available via the C<fasta> attribute.
=item fastaids (auto-computed)
Arrary reference to the Fasta IDs found in the input file
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lib/Bio/DB/BioSQL/SeqFeatureAdaptor.pm view on Meta::CPAN
foreach $loc (@locs) {
$loc->rank(++$i) if $loc->can('rank');
$ok = $loc->store(-fkobjs => [$obj]) && $ok;
}
# store the annotation and associate ourselves with it; we use an adaptor
# to transparently access all annotation through the AnnotationCollectionI
# interface
my $ac = $self->_featann_adaptor();
$ac->feature($obj);
# we need to get an adaptor to store it (or make it persistent, which is
# unnecessary overhead since $ac will go out of scope at the end of this
lib/Bio/DB/BioSQL/SeqFeatureAdaptor.pm view on Meta::CPAN
$ok = @$locs > 0;
#
# look up annotation for this feature by association
#
my $annadp = $self->_anncoll_adaptor();
# we use an adaptor to transparently add all annotation through the
# AnnotationCollectionI interface
my $ac = $self->_featann_adaptor();
$ac->feature($obj);
# now have the adaptor find by association
$qres = $annadp->find_by_association(-objs => [$ac,$obj]);
# no need to attach the annotation collection to the feature - the
# annotation adaptor added everything to the feature transparently
$qres->next_object(); # remove it from the stack, just to be sure
# done
return $ok;
}
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lib/Bio/DB/SoapEUtilities.pm view on Meta::CPAN
=item * C<efetch>, Fetch Adaptors, and BioPerl object iterators
The C<FetchAdaptor> creates bona fide BioPerl objects. Currently,
there are FetchAdaptor subclasses for sequence data (both Genbank and
FASTA rettypes) and taxonomy data. The choice of FetchAdaptor is based
on information in the result message, and should be transparent to the
user.
$seqio = $fac->efetch( -db =>'nucleotide',
-id => \@ids,
-rettype => 'gb' )->run( -auto_adapt => 1 );
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Bio/DB/DBFetch.pm view on Meta::CPAN
Allows the dynamic retrieval of entries from databases using the
dbfetch script at EBI:
L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>cgi-binE<sol>dbfetch>.
In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out. This allows later
additions of more servers in different geographical locations.
This is a superclass which is called by instantiable subclasses with
correct parameters.
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lib/Bio/AssemblyImprovement/Util/FastqTools.pm view on Meta::CPAN
# title => 'Histogram of read lengths for '.$self->input_filename,
# x_labels_vertical => 1,
# bar_spacing => 0,
# shadow_depth => 1,
# shadowclr => 'dred',
# transparent => 0,
# )
# or warn $graph->error;
# #Draw the graph
# my $gd = $graph->plot($arrayref) or die $graph->error;
# #Store the graph