Rose Mcgowan Bio

Bio::Map::MappableI is an object that can be placed in a map. SYNOPSIS # get a Bio::Map::MappableI somehow my $position = $element->map_position(); # these methods will be important for building sorted lists if( $position->equals($p2) ) { # do something } elsif( $position->less_tha($p2)...

Bio::Tree::Tree is an implementation of TreeI interface. SYNOPSIS # like from a TreeIO my $treeio = new Bio::TreeIO(-format => newick, -file => treefile.dnd); my $tree = $treeio->next_tree; my @nodes = $tree->get_nodes; my $root = $tree->get_root_node; This object holds handles to Nodes...

Bio::Factory::SequenceFactoryI is a Perl interface that allows for generic building of sequences in factories which create sequences (like SeqIO). SYNOPSIS # do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like use Bio::Seq::SeqFactory; my...


Platforms: *nix

Rose::Object::MakeMethods::Generic is a Perl module that can create simple object methods. SYNOPSIS package MyObject; use Rose::Object::MakeMethods::Generic ( scalar => [ power, error, ], scalar --get_set_init => name, boolean --get_set_init => is_tall, boolean => [ is_red,...


Platforms: *nix

Rose::DB::Object::Tutorial is a guided tour of the basics of Rose::DB::Object. INTRODUCTION This document provides a step-by-step introduction to the Rose::DB::Object module distribution. It demonstrates all of the important features using a semi-realistic example database. This tutorial does...


Platforms: *nix

Rose::DateTime::Util Perl module contains some simple DateTime wrapper functions. SYNOPSIS use Rose::DateTime::Util qw(:all); $now = parse_date(now); $then = parse_date(12/25/2001 11pm); print $now->day_of_week; # e.g., "Monday" # "December 25th 2001 at 11:00:00 PM" $date_text =...


Platforms: *nix

Rose::DB::Object::Helpers is a mix-in class containing convenience methods for Rose::DB::Object. SYNOPSIS package MyDBObject; use Rose::DB::Object; our @ISA = qw(Rose::DB::Object); use Rose::DB::Object::Helpers clone, { load_or_insert => find_or_create }; ... $obj =...


Platforms: *nix

Rose::DB::Object::QueryBuilder is a Perl module that can build SQL queries on behalf of Rose::DB::Object::Manager. SYNOPSIS use Rose::DB::Object::QueryBuilder qw(build_select); # Build simple query $sql = build_select ( dbh => $dbh, select => COUNT(*), tables => [ articles ], columns...


Platforms: *nix

Rose::Class::MakeMethods::Set is a Perl module to create class methods to manage sets. SYNOPSIS package MyClass; use Rose::Class::MakeMethods::Set ( inheritable_set => [ required_name => { add_implies => add_valid_name, test_method => name_is_required, }, ], inherited_set => [...


Platforms: *nix

Rose::Object is a simple object base class. SYNOPSIS package MyObject; use Rose::Object; our @ISA = qw(Rose::Object); sub foo { ... } sub bar { ... } ... my $o = MyObject->new(foo => abc, bar => 5); ... Rose::Object is a generic object base class. It provides very little...


Platforms: *nix

Rose::DateTime is a Perl module with DateTime helper functions and objects. SYNOPSIS use Rose::DateTime::Util qw(:all); $now = parse_date(now); $then = parse_date(12/25/2001 6pm); $date_text = format_date($then, "%D at %T %p"); ... use Rose::DateTime::Parser; $parser =...


Platforms: *nix

Rose::URI is a standalone URI class allowing easy and efficient manipulation of query parameters and other URI components. SYNOPSIS use Rose::URI; $uri = Rose::URI->new(http://un:pw@foo.com/bar/baz?a=1&b=two+3); $scheme = $uri->scheme; $user = $uri->username; $pass = $uri->password;...


Platforms: *nix

Rose::HTML::Objects is a Perl object-oriented interfaces for HTML. SYNOPSIS use Rose::HTML::Form; $form = Rose::HTML::Form->new(action => /foo, method => post); $form->add_fields ( name => { type => text, size => 20, required => 1 }, height => { type => text, size => 5, maxlength => 5...


Platforms: *nix

Rose::HTML::Form is a HTML form base class. SYNOPSIS package PersonForm; use Rose::HTML::Form; our @ISA = qw(Rose::HTML::Form); use Person; sub build_form { my($self) = shift; $self->add_fields ( name => { type => text, size => 25, required => 1 }, email => { type => email, size...


Platforms: *nix

Bio::LiveSeq::Translation is a translation class for LiveSeq. This stores informations about aminoacids translations of transcripts. The implementation is that a Translation object is the translation of a Transcript object, with different possibilities of manipulation, different coordinate...


Platforms: *nix

Bio::Tools::Run::JavaRunner is a Perl module that can run java programs. SYNOPSIS my $runner = Bio::Tools::Run::JavaRunner->new(-jar => $jar); $runner->run(); This module is probably incomplete. It is intended to be a wrapper for running java programs..


Platforms: *nix

Bio::Graphics::Glyph::cds module contains the "cds" glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This glyph draws features that are associated with a protein coding region. At high magnifications, draws a series of boxes that are color-coded to indicate the...


Platforms: *nix

Bio::Graphics::Panel is a Perl module to generate GD images of Bio::Seq objects. SYNOPSIS # This script parses a GenBank or EMBL file named on the command # line and produces a PNG rendering of it. Call it like this: # render.pl my_file.embl | display - use strict; use Bio::Graphics;...


Platforms: *nix

Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel. SYNOPSIS use Bio::Graphics::Feature; # create a simple feature with no internal structure $f = Bio::Graphics::Feature->new(-start => 1000, -stop => 2000, -type => transcript, -name => alpha-1...


Platforms: *nix

Bio::DB::Flat::BDB::swissprot is a swissprot adaptor for Open-bio standard BDB-indexed flat file. SYNOPSIS See Bio::DB::Flat. This module allows swissprot files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this...


Platforms: *nix