ace::model(3pm) [debian man page]

Ace::Model(3pm) 					User Contributed Perl Documentation					   Ace::Model(3pm)

NAME

       Ace::Model - Get information about AceDB models

SYNOPSIS

	 use Ace;
	 my $db = Ace->connect(-path=>'/usr/local/acedb/elegans');
	 my $model = $db->model('Author');
	 print $model;
	 $name = $model->name;
	 @tags = $model->tags;
	 print "Paper is a valid tag" if $model->valid_tag('Paper');

DESCRIPTION

       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 to retrieve the model of a named class, or by
       calling an Ace::Object's model() method to retrieve the object's particular model.

METHODS

   new()
	 $model = Ace::Model->new($model_data);

       This is a constructor intended only for use by Ace and Ace::Object classes.  It constructs a new Ace::Model object from the raw string data
       in models.wrm.

   name()
	 $name = $model->name;

       This returns the class name for the model.

   tags()
	  @tags = $model->tags;

       This returns a list of all the valid tags in the model.

   valid_tag()
	  $boolean  = $model->valid_tag($tag);

       This returns true if the given tag is part of the model.

   path()
	  @path = $model->path($tag)

       Returns the path to the indicated tag, returning a list of intermediate tags.  For example, in the C elegans ?Locus model, the path for
       'Compelementation_data" will return the list ('Type','Gene').

   asString()
	  print $model->asString;

       asString() returns the human-readable representation of the model with comments stripped out.  Internally this method is called to
       automatically convert the model into a string when appropriate.	You need only to start performing string operations on the model object in
       order to convert it into a string automatically:

	  print "Paper is unique" if $model=~/Paper ?Paper UNIQUE/;

SEE ALSO

       Ace

AUTHOR

       Lincoln Stein <lstein@w3.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>

       Copyright (c) 1997-1998, Lincoln D. Stein

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

perl v5.14.2							    2003-06-01							   Ace::Model(3pm)

Ace::Sequence::Gene(3pm)				User Contributed Perl Documentation				  Ace::Sequence::Gene(3pm)

NAME

       Ace::Sequence::Gene - Simple "Gene" Object

SYNOPSIS

	   # open database connection and get an Ace::Object sequence
	   use Ace::Sequence;

	   # get a megabase from the middle of chromosome I
	   $seq = Ace::Sequence->new(-name   => 'CHROMOSOME_I,
				     -db     => $db,
				     -offset => 3_000_000,
				     -length => 1_000_000);

	   # get all the genes
	   @genes = $seq->genes;

	   # get the exons from the first one
	   @exons = $genes[0]->exons;

	   # get the introns
	   @introns = $genes[0]->introns

	   # get the CDSs (NOT IMPLEMENTED YET!)
	   @cds = $genes[0]->cds;

DESCRIPTION

       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.

OBJECT CREATION

       You will not ordinarily create an Ace::Sequence::Gene object directly.  Instead, objects will be created in response to a genes() call to
       an Ace::Sequence object.

OBJECT METHODS

       Most methods are inherited from Ace::Sequence::Feature.	The following methods are also supported:

       exons()
	     @exons = $gene->exons;

	   Return a list of Ace::Sequence::Feature objects corresponding to annotated exons.

       introns()
	     @introns = $gene->introns;

	   Return a list of Ace::Sequence::Feature objects corresponding to annotated introns.

       cds()
	     @cds = $gene->cds;

	   Return a list of Ace::Sequence::Feature objects corresponding to coding sequence.  THIS IS NOT YET IMPLEMENTED.

       relative()
	     $relative = $gene->relative;
	     $gene->relative(1);

	   This turns on and off relative coordinates.	By default, the exons and intron features will be returned in the coordinate system used
	   by the gene.  If relative() is set to a true value, then coordinates will be expressed as relative to the start of the gene.  The first
	   exon will (usually) be 1.

SEE ALSO

       Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF

AUTHOR

       Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>

       Copyright (c) 1999, Lincoln D. Stein

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.  See DISCLAIMER.txt for
       disclaimers of warranty.

POD ERRORS

       Hey! The above document had some coding errors, which are explained below:

       Around line 148:
	   You forgot a '=back' before '=head1'

perl v5.14.2							    2001-02-18						  Ace::Sequence::Gene(3pm)