Bio::Das::ProServer::Authenticator - authenticates DAS requests

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This is a stub class intended to be extended....

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC

Bio::Das::ProServer::SourceHydra::sql - A database-backed implementation of B::D::P::SourceHydra

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Extension of the 'dbi' hydra to allow the use of custom SQL queries to determine the available source names....

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC

Bio::Das::ProServer::Authenticator::ip - authenticates DAS requests by IP address

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Authenticates requests according to a 'whitelist' of IP address ranges. Requests from clients not within one of these ranges are denied. The IP addresses that are checked against the whitelist are: 1) that of the socket connection 2) those listed in ...

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC

Bio::Das::ProServer::SourceAdaptor::sif

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Serves up interaction DAS responses from 'Simple Interaction Format' (SIF) files. See <http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_User_Manual/Network _Formats> http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_User_Manual/Network_ Formats ...

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC

Bio::Das::ProServer::SourceAdaptor::file - adaptor for file-based DAS sources

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This SourceAdaptor plugin allows for a full-featured DAS source (implementing the features command) to be created from one of a variety of simple text files. Fields that are not present in the data file may optionally be provided in the source's conf...

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC

Bio::Das::ProServer::Authenticator::http - authenticates DAS requests by issuing requests to a remote authority

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Authenticates DAS requests by connecting to a remote authentication HTTP server. An authentication token is parsed from the DAS request. By default this should be in an 'Authorization' header, but the authenticator can be configured to look in a cook...

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC

Bio::Das::ProServer::SourceAdaptor::bed12

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Serves up features DAS responses from BED files. See <http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED> http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED for details of the file format. The BED and DAS formats contain an intersec...

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC

Bio::Das::ProServer::SourceAdaptor::simple_volmap

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Serves up volume map DAS responses, using a file-based transport....

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC

Bio::Das::ProServer::SourceAdaptor::Transport::csv - Comma-separated-values transport layer

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RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC

Bio::Das::ProServer::SourceAdaptor::Transport::sif

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A data transport exposing interactions stored in a SIF file, along with attributes stored in Cytoscape attribute files. Access is via the 'query' method....

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC

Bio::Das::ProServer::SourceAdaptor::Transport::bed12 - DBI-like access to a BED file

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Transport helper class for BED file access, implemented as an extension to Bio::Das::ProServer::SourceAdaptor::Transport::csv. This transport is used by the Bio::Das::ProServer::SourceAdaptor::bed12 adaptor....

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC

Bio::Das::ProServer::SourceAdaptor::simple_interaction

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Serves up interaction DAS responses, using a file-based transport....

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC

Bio::Das::ProServer::SourceAdaptor::Transport::ensembl

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This class is a Transport that provides an interface to the Ensembl API. It uses the Ensembl Resistry to determine the location of the appropriate databases, and can be used in a species specific or cross-species manner. The main advantage of using t...

RPETTETT/Bio-Das-ProServer-2.20 - 02 Nov 2010 11:59:40 UTC