Bio::Das - Interface to Distributed Annotation System River stage zero No dependents

Bio::Das provides access to genome sequencing and annotation databases that export their data in Distributed Annotation System (DAS) format version 1.5. This system is described at http://biodas.org. Both unencrypted (http:) and SSL-encrypted (https:...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::DSN - Object encapsulation of a DAS data source River stage zero No dependents

The Bio::Das::DSN object contains information pertaining to a Das data source. A set of these objects are returned by a call to Bio::Das->dsn(). METHODS Following is a complete list of methods implemented by Bio::Das::DSN. POD ERRORS Hey! The above d...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Map - Resolve map coordinates River stage zero No dependents

This module provides the infrastructure for handling relative coordinates in sequence annotations. You use it by creating a "map" that relates a set of sequence segment pairs. The segments are related in a parent/child relationship so that you can mo...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Util - Das Utilities River stage zero No dependents

This module contains yet another implementation of the rearrange() call, which is used to convert -name=>argument style argument passing into positional arguments....

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Type - A sequence annotation type River stage zero No dependents

The Bio::Das::Type class provides information about the type of an annotation. Each type has a category, which is a general description of the type, a unique ID, which names the type, and an optional method, which describes how the type was derived. ...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Feature - A genomic annotation River stage zero No dependents

A Bio::Das::Segment::Feature object contains information about a feature on the genome retrieve from a DAS server. Each feature -- also known as an "annotation" -- has a start and end position on the genome relative to a reference sequence, as well a...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Request - Base class for a request on a DAS server River stage zero No dependents

Each type of request on a DAS server (e.g. an entry_points request) is a subclass of Bio::Das::Request. The request encapsulates the essential information on the request: the server, the data source, and the command that will be executed. After the r...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Segment - Serial access to Bio::Das sequence "segments" River stage zero No dependents

The Bio::Das::Segment class is used to retrieve information about a genomic segment from a DAS server. You may retrieve a list of (optionally filtered) annotations on the segment, a summary of the feature types available across the segment, or the se...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Stylesheet - Access to DAS stylesheets River stage zero No dependents

The Bio::Das::Stylesheet class contains information about a remote DAS server's preferred visualization style for sequence features. Each server has zero or one stylesheets for each of the data sources it is responsible for. Stylesheets can provide s...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::TypeHandler - Utilities for handling types River stage zero No dependents

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::HTTP::Fetch - Manage the HTTP protocol for DAS transactions River stage zero No dependents

This is a low-level class that is used for managing multiplexed connections to DAS HTTP servers. It is used internally by Bio::Das and it is unlikely that application programs will ever interact with it directly. The exception is when writing custom ...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Request::Dsn - The DAS "dsn" request River stage zero No dependents

This is a subclass of Bio::Das::Request specialized for the "dsn" command. It is used to retrieve the data sources known to a set of DAS servers. The results() method returns a list of Bio::Das::DSN objects. All other methods are as described in Bio:...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Request::Dnas - The DAS "dna" request River stage zero No dependents

This is a subclass of Bio::Das::Request specialized for the "dna" command. It is used to retrieve the DNA corresponding to a set of segments on a set of DAS servers. METHODS All methods are the same as Bio::Das::Request with the exception of results(...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Request::Types - The DAS "types" request River stage zero No dependents

This is a subclass of Bio::Das::Request specialized for the "types" command. All methods are the same as Bio::Das::Request with the exception of results(), which has been modified to make it more useful. $types = $request->results In a scalar context...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::FeatureIterator - Iterate over a set of Bio::Das::Features River stage zero No dependents

When the Bio::Das->features() method is called with the -iterator argument, the method will return an iterator over the features returned from the various data sources. Each feature can be returned by calling next_seq() iteratively until the method r...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Request::Sequences - The DAS "sequence" request River stage zero No dependents

This is a subclass of Bio::Das::Request::Dnas specialized for the "sequence" command. It is used to retrieve the sequence corresponding to a set of segments on a set of DAS servers. POD ERRORS Hey! The above document had some coding errors, which are...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Request::Stylesheet - The DAS "stylesheet" request River stage zero No dependents

This is a subclass of Bio::Das::Request specialized for the "stylesheet" command. The results() method returns a series of Bio::Das::Stylesheet objects. All other methods are as described in Bio::Das::Request. ....

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Request::Entry_points - The DAS "entry_points" request River stage zero No dependents

This is a subclass of Bio::Das::Request specialized for the "entrypoints" command. It is used to retrieve the entry points (landmarks) known to a set of DAS servers. All methods are as described in Bio::Das::Request....

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Bio::Das::Request::Feature2Segments - Translate feature names into segments River stage zero No dependents

This is a subclass of Bio::Das::Request specialized for the "features" command with specialized arguments that allow it to translate a feature name into a segment of the genome. It works by issuing the DAS features command using a type of NULL (which...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

Das/AGPServer/Daemon.pm River stage zero No dependents

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC

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