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GBrowse-2.16
River stage zero No dependents
++

Changes for version 2.16

  • Added code to recognize and strip whitespace from search coordinates. This allows "chr1:2,000 .. 1,180,000" to work as a search term.
  • Added code that allows callbacks to invoke Bio::Graphics::Browser2::Render->request() in order to get a hash that contains various information about the current state. Interesting keys include: search_str, ref, start, end, flip, tracks, features, userid, uploadid, h_feat, width, grid. (NOTE: please update documentation WIKI with some explanation of how to use this).
  • Disable track filters when in summary mode, since the summary features generated when this mode is active rarely have the structure and attributes expected by the writer of the filter. The downside of this is that if you use track filters to distinguish one set of features from another, this will not be reflected in the summary density plots, which will show all features of the matching type regardless of the filter.
  • Basic support for Google federated login via openid.
  • "unit label" and "unit divider" should now work as advertised.
  • Add commas to coordinates more liberally.
  • Maybe fixed failing t/00.compile.t test.
  • Fixed problem with subtrack selection tables producing empty tracks under some conditions.
  • Fixed SequenceDumper plugin to not crash on BigWig tracks.
  • added # to the list of acceptable characters in feature IDs
  • uploaded files won't use the summary mode unless the number of lines loaded exceeds 10,000
  • Modified plugin base class to make it possible to get at the underlying renderer object by calling renderer() method.
  • Fixed regression in which database option wasn't propagating from base track to semantic zoom tracks.
  • Fixed SequenceDumper behavior on GFF dumping.
  • Removed brackets from list of naughty search characters to fix bug 3030462

Documentation

auto_install_databases.pl
Download and install GFF data sets
bp_load_gff.pl
Load a Bio::DB::GFF database from GFF files.
gbrowse_clean.pl
Clean up sessions and other temporary gbrowse2 files
gbrowse_netinstall.pl
gbrowse_netinstall.pl
load_genbank.pl
Load a Bio::DB::GFF database from GENBANK files.
make_das_conf.pl
Create GBrowse config files from DAS sources
process_gadfly.pl
Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
ncbi_2_gff.pl
Massage NCBI chromosome annotation into GFF-format suitable for Bio::DB::GFF
process_sgd.pl
Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
process_wormbase.pl
Massage WormBase GFF files into a version suitable for the Generic Genome Browser
ucsc_genes2gff.pl
Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse
wiggle2gff3.pl
axt2phy.pl
convert AXT pairwise alignment files to GFF, Fasta and wig files
ace2gff.pl
convert a phrap produced, ace file into a gff formatted file
blast2gff.pl
Convert a BLAST result file into a GFF file
import_ncbi_mv_hs.pl
make gff files from NCBI Map Viewer data files.
contrib::install_macosx::README
pod::BIOSQL_ADAPTER_HOWTO
pod::CONFIGURE_HOWTO
pod::CONTROLLER
pod::DAS_HOWTO
pod::FAQ
pod::GBROWSE_IMG
pod::GENBANK_HOWTO
pod::INSTALL.MacOSX
pod::INSTALL
pod::MAKE_IMAGES_HOWTO
pod::ORACLE_AND_POSTGRESQL
Bio::Graphics::Browser::Plugin
Base class for gbrowse plugins.
pod::README-berkeley-gadfly
pod::README-chado
pod::README-gff-files
pod::README-lucegene

Modules

b64_encoded_gif_renderer.pm
a renderer (HTML) for b64_encoded_gif type MOBY Objects
b64_encoded_jpeg_renderer.pm
a renderer (HTML) for b64_encoded_jpeg type MOBY Objects
text_formatted_renderer.pm
a renderer (HTML) for text-formatted type MOBY Objects
text_html_renderer.pm
a renderer (HTML) for text_html type MOBY Objects
text_plain_renderer.pm
a renderer (HTML) for text_plain type MOBY Objects
text_xml_renderer.pm
a renderer (HTML) for text_xml type MOBY Objects
Bio::Graphics::Browser2::Plugin::AlignTwoSequences
a plugin that executes NCBI's bl2seq on the current view
Bio::Graphics::Browser2::Plugin::Aligner
Dump multiple alignments from GBrowse
Bio::Graphics::Browser2::Plugin::AttributeHiliter
hilite features based on attributes
Bio::Graphics::Browser2::Plugin::Blat
plugin to map sequences against the genome
Bio::Graphics::Browser2::Plugin::CreateBlastDB
a plugin that creates a Blast-formatted database from a Bio::DB::GFF database
Bio::Graphics::Browser2::Plugin::PrimerDesigner
a plugin to design PCR primers with primer3
Bio::Graphics::Browser2::Plugin::ProteinDumper
A plugin for dumping translated protein sequences in various formats
Bio::Graphics::Browser2::Plugin::RestrictionAnnotator
Generate a restriction map track in GBrowse
Bio::Graphics::Browser2::Plugin::SequenceDumper
A plugin for dumping sequences in various formats
Bio::Graphics::Browser2::Plugin::SimpleTrackFinder
Limit list of tracks to those that match a name pattern
Bio::Graphics::Browser2::Plugin::SourceTrackFinder
Limit list of tracks to those that contain arbitrary fields
Bio::Graphics::Browser2::Plugin::Spectrogram
Bio::Graphics::Browser2::Plugin::TrackFinder
Limit list of tracks to those that mention keywords
contrib/Coverage/plugin/Coverage.pm
DAS::GUS
DAS-style accession to a gus database
DAS::GUS::Segment
DAS-style access to a GUS database
DAS::GUS::Segment::Feature
DAS::Util
A simple XML sql parser
contrib/install_macosx/BuildConfig.pm
install_util/GBrowseInstall.pm
Bio::DB::GFF::Aggregator::match_gap
GFF3 match aggregator
Bio::DB::GFF::Aggregator::reftranscript
Bio::DB::GFF::Aggregator::waba_alignment
A WABA alignment
Bio::DB::GFF::Aggregator::wormbase_gene
Wormbase gene aggregator
Bio::DB::Tagger
Simple object tagging system
Bio::DB::Tagger::Tag
Authored tags
Bio::Graphics::Browser2::AuthorizedFeatureFile
Add HTTP authorization features to FeatureFile
Bio::Graphics::Browser2::CAlign
Compiled helper for Bio::Graphics::Browser::Realign
Bio::Graphics::Browser2::DataBase
A simple cache for database handles
Bio::Graphics::Browser2::GFFhelper
Helps gbrowse plugins handle GFF
Bio::Graphics::Browser2::Markup
Markup routines for sequences in text form
Bio::Graphics::Browser2::OptionPick
Pick options
Bio::Graphics::Browser2::PadAlignment
Insert pads into a multiple alignment
Bio::Graphics::Browser2::Plugin
Base class for gbrowse plugins.
Bio::Graphics::Browser2::PluginSet
A set of plugins
Bio::Graphics::Browser2::Realign
Perl extension for Smith-Waterman alignments
Bio::Graphics::Browser2::RegionSearch
Search through multiple databases for feature matches.
Bio::Graphics::Browser2::RemoteSet
A set of plugins
Bio::Graphics::Browser2::Util
Exported utilities
CGI::Toggle
Utility methods for collapsible sections
Bio::Graphics::Browser::CAlign
Compiled helper for Bio::Graphics::Browser::Realign

Provides

Bio::DB::SeqFeature::Store::BedLoader
in lib/Bio/DB/SeqFeature/Store/BedLoader.pm
Bio::DB::Tagger::Iterator
in lib/Bio/DB/Tagger.pm
Bio::DB::Tagger::mysql
in lib/Bio/DB/Tagger/mysql.pm
Bio::Graphics::Browser2
in lib/Bio/Graphics/Browser2.pm
Bio::Graphics::Browser2::Action
in lib/Bio/Graphics/Browser2/Action.pm
Bio::Graphics::Browser2::AdminTracks
in lib/Bio/Graphics/Browser2/UserTracks.pm
Bio::Graphics::Browser2::CachedTrack
in lib/Bio/Graphics/Browser2/CachedTrack.pm
Bio::Graphics::Browser2::DataLoader
in lib/Bio/Graphics/Browser2/DataLoader.pm
Bio::Graphics::Browser2::DataLoader::bam
in lib/Bio/Graphics/Browser2/DataLoader/bam.pm
Bio::Graphics::Browser2::DataLoader::bed
in lib/Bio/Graphics/Browser2/DataLoader/bed.pm
Bio::Graphics::Browser2::DataLoader::bigwig
in lib/Bio/Graphics/Browser2/DataLoader/bigwig.pm
Bio::Graphics::Browser2::DataLoader::featurefile
in lib/Bio/Graphics/Browser2/DataLoader/featurefile.pm
Bio::Graphics::Browser2::DataLoader::generic
in lib/Bio/Graphics/Browser2/DataLoader/generic.pm
Bio::Graphics::Browser2::DataLoader::gff
in lib/Bio/Graphics/Browser2/DataLoader/gff.pm
Bio::Graphics::Browser2::DataLoader::gff3
in lib/Bio/Graphics/Browser2/DataLoader/gff3.pm
Bio::Graphics::Browser2::DataLoader::sam
in lib/Bio/Graphics/Browser2/DataLoader/sam.pm
Bio::Graphics::Browser2::DataLoader::wiggle
in lib/Bio/Graphics/Browser2/DataLoader/wiggle.pm
Bio::Graphics::Browser2::DataSource
in lib/Bio/Graphics/Browser2/DataSource.pm
Bio::Graphics::Browser2::ExternalData
in lib/Bio/Graphics/Browser2/ExternalData.pm
Bio::Graphics::Browser2::I18n
in lib/Bio/Graphics/Browser2/I18n.pm
Bio::Graphics::Browser2::MetaDB
in lib/Bio/Graphics/Browser2/RegionSearch.pm
Bio::Graphics::Browser2::MetaSegment
in lib/Bio/Graphics/Browser2/RegionSearch.pm
Bio::Graphics::Browser2::MetaSegment::Iterator
in lib/Bio/Graphics/Browser2/RegionSearch.pm
Bio::Graphics::Browser2::Region
in lib/Bio/Graphics/Browser2/Region.pm
Bio::Graphics::Browser2::Render
in lib/Bio/Graphics/Browser2/Render.pm
Bio::Graphics::Browser2::Render::HTML
in lib/Bio/Graphics/Browser2/Render/HTML.pm
Bio::Graphics::Browser2::Render::Slave
in lib/Bio/Graphics/Browser2/Render/Slave.pm
Bio::Graphics::Browser2::Render::Slave::Status
in lib/Bio/Graphics/Browser2/Render/Slave/Status.pm
Bio::Graphics::Browser2::RenderPanels
in lib/Bio/Graphics/Browser2/RenderPanels.pm
Bio::Graphics::Browser2::Session
in lib/Bio/Graphics/Browser2/Session.pm
Bio::Graphics::Browser2::Shellwords
in lib/Bio/Graphics/Browser2/Shellwords.pm
Bio::Graphics::Browser2::SubtrackTable
in lib/Bio/Graphics/Browser2/SubtrackTable.pm
Bio::Graphics::Browser2::TrackDumper
in lib/Bio/Graphics/Browser2/TrackDumper.pm
Bio::Graphics::Browser2::UserConf
in lib/Bio/Graphics/Browser2/UserTracks.pm
Bio::Graphics::Browser2::UserTracks
in lib/Bio/Graphics/Browser2/UserTracks.pm
Bio::Graphics::GBrowseFeature
in lib/Bio/Graphics/GBrowseFeature.pm
Bio::Graphics::Karyotype
in lib/Bio/Graphics/Karyotype.pm
Bio::Graphics::Wiggle::Loader::Nosample
in lib/Bio/Graphics/Browser2/DataLoader/wiggle.pm
FakeHomol
in lib/Bio/Graphics/Browser2/GFFhelper.pm
LRUCache
in lib/Bio/Graphics/Browser2/DataBase.pm
Legacy::DB::SyntenyBlock
in lib/Legacy/DB/SyntenyBlock.pm
Legacy::DB::SyntenyIO
in lib/Legacy/DB/SyntenyIO.pm
Legacy::Graphics::Browser
in lib/Legacy/Graphics/Browser.pm
Legacy::Graphics::Browser::I18n
in lib/Legacy/Graphics/Browser/I18n.pm
Legacy::Graphics::Browser::PageSettings
in lib/Legacy/Graphics/Browser/PageSettings.pm
Legacy::Graphics::Browser::Synteny
in lib/Legacy/Graphics/Browser/Synteny.pm
Legacy::Graphics::Browser::Util
in lib/Legacy/Graphics/Browser/Util.pm
Legacy::Graphics::BrowserConfig
in lib/Legacy/Graphics/Browser.pm
MyFeatureFileLoader
in lib/Bio/Graphics/Browser2/DataLoader/featurefile.pm

Other files