Ace - Object-Oriented Access to ACEDB Databases River stage one • 1 direct dependent • 2 total dependents

AcePerl provides an interface to the ACEDB object-oriented database. Both read and write access is provided, and ACE objects are returned as similarly-structured Perl objects. Multiple databases can be opened simultaneously. You will interact with se...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Model - Get information about AceDB models River stage one • 1 direct dependent • 2 total dependents

This class is provided for access to AceDB class models. It provides the model in human-readable form, and does some limited but useful parsing on your behalf. Ace::Model objects are obtained either by calling an Ace database handle's model() method ...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Local - use giface, tace or gifaceclient to open a local connection to an Ace database River stage one • 1 direct dependent • 2 total dependents

This class is provided for low-level access to local (non-networked) Ace databases via the *giface* program. You will generally not need to access it directly. Use Ace.pm instead. For the sake of completeness, the method can also use the *aceclient* ...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Graphics::Fk - A dummy feature object used for generating panel key tracks River stage one • 1 direct dependent • 2 total dependents

None. Used internally by Ace::Graphics::Panel....

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Iterator - Iterate Across an ACEDB Query River stage one • 1 direct dependent • 2 total dependents

The Ace::Iterator class implements a persistent query on an Ace database. You can create multiple simultaneous queries and retrieve objects from each one independently of the others. This is useful when a query is expected to return more objects than...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Object - Manipulate Ace Data Objects River stage one • 1 direct dependent • 2 total dependents

*Ace::Object* is the base class for objects returned from ACEDB databases. Currently there is only one type of *Ace::Object*, but this may change in the future to support more interesting object-specific behaviors. Using the *Ace::Object* interface, ...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Sequence - Examine ACeDB Sequence Objects River stage one • 1 direct dependent • 2 total dependents

*Ace::Sequence*, and its allied classes Ace::Sequence::Feature and Ace::Sequence::FeatureList, provide a convenient interface to the ACeDB Sequence classes and the GFF sequence feature file format. Using this class, you can define a region of the gen...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Sequence::Gene - Simple "Gene" Object River stage one • 1 direct dependent • 2 total dependents

Ace::Sequence::Gene is a subclass of Ace::Sequence::Feature. It inherits all the methods of Ace::Sequence::Feature, but adds the ability to retrieve the annotated introns and exons of the gene....

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Sequence::Homol - Temporary Sequence Homology Class River stage one • 1 direct dependent • 2 total dependents

*Ace::Sequence::Homol* is a subclass of Ace::Object (not Ace::Sequence) which is specialized for returning information about a DNA or protein homology. This is a temporary placeholder for a more sophisticated homology class which will include support...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Graphics::Track - PNG graphics of Ace::Sequence::Feature objects River stage one • 1 direct dependent • 2 total dependents

The Ace::Graphics::Track class is used by Ace::Graphics::Panel to lay out a set of sequence features using a uniform glyph type. You will ordinarily work with panels rather than directly with tracks....

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Sequence::Multi - Combine Feature Tables from Multiple Databases River stage one • 1 direct dependent • 2 total dependents

*Ace::Sequence::Multi* transparently combines information stored about a sequence in a reference database with features tables from any number of annotation databases. The resulting object can be used just like an Ace::Sequence object, except that th...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Graphics::Glyph - Base class for Ace::Graphics::Glyph objects River stage one • 1 direct dependent • 2 total dependents

Ace::Graphics::Glyph is the base class for all glyph objects. Each glyph is a wrapper around an Ace::Sequence::Feature object, knows how to render itself on an Ace::Graphics::Panel, and has a variety of configuration variables. End developers will no...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Graphics::Panel - PNG graphics of Ace::Sequence::Feature objects River stage one • 1 direct dependent • 2 total dependents

The Ace::Graphics::Panel class provides drawing and formatting services for Ace::Sequence::Feature objects or Das::Segment::Feature objects. Typically you will begin by creating a new Ace::Graphics::Panel object, passing it the width of the visual di...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Browser::SiteDefs - Access to AceBrowser configuration files River stage one • 1 direct dependent • 2 total dependents

Ace::Browser::SiteDefs evaluates an AceBrowser configuration file and returns a configuration object ("config object" for short). A config object is a bag of dynamically-generated methods, derived from the scalar variables, arrays, hashes and subrout...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Graphics::Glyph::ex - The "X" glyph River stage one • 1 direct dependent • 2 total dependents

This glyph draws an "X". OPTIONS In addition to the common options, the following glyph-specific options are recognized: Option Description Default ------ ----------- ------- -point Whether to draw an "X" the feature width scaled width of the feature...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Browser::AceSubs - Subroutines for AceBrowser River stage one • 1 direct dependent • 2 total dependents

Ace::Browser::AceSubs exports a set of routines that are useful for creating search pages and displays for AceBrowser CGI pages. See http://stein.cshl.org/AcePerl/AceBrowser. The following subroutines are exported by default: AceError AceMissing AceN...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Sequence::Feature - Examine Sequence Feature Tables River stage one • 1 direct dependent • 2 total dependents

*Ace::Sequence::Feature* is a subclass of Ace::Sequence::Feature specialized for returning information about particular features in a GFF format feature table....

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Graphics::Glyph::dot - The "ellipse" glyph River stage one • 1 direct dependent • 2 total dependents

This glyph draws an ellipse the width of the scaled feature passed, and height a possibly configured height (See Ace::Graphics::Glyph). OPTIONS In addition to the common options, the following glyph-specific options are recognized: Option Description...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Graphics::Glyph::span - The "span" glyph River stage one • 1 direct dependent • 2 total dependents

This draws the same thing as box....

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

Ace::Browser::SearchSubs - Subroutines for AceBrowser search scripts River stage one • 1 direct dependent • 2 total dependents

Ace::Browser::SearchSubs exports a set of constants and subroutines that are useful for creating AceBrowser search scripts. CONSTANTS This package exports the following constants: MAXOBJECTS The maximum number of objects that can be displayed per pag...

LDS/AcePerl-1.92 - 11 Nov 2008 16:47:31 GMT

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