Download Shareware and Freeware Software for Windows, Linux, Macintosh, PDA

line Home  |  About Us  |  Link To Us  |  FAQ  |  Contact

Serving Software Downloads in 976 Categories, Downloaded 30.066.651 Times

Bio::AnnotationCollectionI 1.4

  Date Added: April 10, 2010  |  Visits: 571

Bio::AnnotationCollectionI

Report Broken Link
Printer Friendly Version


Product Homepage
Download (72 downloads)

Bio::AnnotationCollectionI is a Perl interface for annotation collections. SYNOPSIS # get an AnnotationCollectionI somehow, eg $ac = $seq->annotation(); foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an Bio::AnnotationI, and defines a "as_text" method print "Annotation ",$key," stringified value ",$value->as_text,"n"; # also defined hash_tree method, which allows data orientated # access into this object $hash = $value->hash_tree(); } } Annotation Collections are a way of storing a series of "interesting facts" about something. We call an "interesting fact" in Bioperl an Annotation (this differs from a Sequence Feature, which is called a Sequence Feature and may or may not have an Annotation Collection). The trouble about this is we are not that sure what "interesting facts" someone might want to store: the possibility is endless. Bioperls approach is that the "interesting facts" are represented by Bio::AnnotationI objects. The interface Bio::AnnotationI guarentees two methods $obj->as_text(); # string formated to display to users and $obj->hash_tree(); # hash with defined rules for data-orientated discovery The hash_tree method is designed to play well with XML output and other "nested-tag-of-data-values" think BoulderIO and/or Ace stuff. For more info read Bio::AnnotationI docs Annotations are stored in AnnotationCollections, each Annotation under a different "tag". The tags allow simple discovery of the available annotations, and in some cases (like the tag "gene_name") indicate how to interpret the data underneath the tag. The tag is only one tag deep and each tag can have an array of values. In addition, AnnotationCollectionIs are guarentee to maintain a consistent set object values under each tag - at least that each object complies to one interface. The "standard" AnnotationCollection insists the following rules are set up Tag Object --- ------ comment Bio::Annotation::Comment dblink Bio::Annotation::DBLink description Bio::Annotation::SimpleValue gene_name Bio::Annotation::SimpleValue ontology_term Bio::Annotation::OntologyTerm reference Bio::Annotation::Reference These tags are the implict tags that the SeqIO system needs to round-trip GenBank/EMBL/Swissprot. However, you as a user and us collectively as a community can grow the "standard" tag mapping over time and specifically for a particular area. Whats New in This Release: - Perl.

Requirements: No special requirements
Platforms: Linux
Keyword: Annotation Annotationcollectioni Annotationi Bioannotationcollectioni Hash Interface Libraries Perl Programming Tag Values
Users rating: 0/10

License: Freeware Size: 4.7 MB
BIO::ANNOTATIONCOLLECTIONI RELATED
Libraries  -  Class::Method::hash 2.08
Class::Method::hash is a Perl module that helps you create methods for handling a hash value. SYNOPSIS use Class::MethodMaker [ hash => [qw/ x /] ]; $instance->x; # empty $instance->x(a => 1, b => 2, c => 3); $instance->x_count == 3; #...
89.09 KB  
Libraries  -  Template::Plugin::MP3::Tag 0.01
Template::Plugin::MP3::Tag is a Perl interface to the MP3::Tag Module. SYNOPSIS [% USE tag = MP3("path_to_mp3_file") %] [% tag.title %] [% tag.album %] # perldoc MP3::Tag for more ideas Template::Plugin::MP3::Tag provides a simple...
4.1 KB  
Network & Internet  -  mod_perl 2.0.3
mod_perl project brings together the full power of the Perl programming language and the Apache HTTP server. You can use Perl to manage Apache, respond to requests for web pages and much more. mod_perl gives you a persistent Perl interpreter...
3.5 MB  
Libraries  -  Set::Hash 0.01
Set::Hash is a Perl module with hashes as objects with lots of handy methods (including set comparisons) and support for method chaining. SYNOPSIS use Set::Hash; my $sh1 = Set::Hash->new(name=>"dan",age=>33); my $sh2 =...
7.17 KB  
Libraries  -  Tie::Proxy::Hash 1.01
Tie::Proxy::Hash is a Perl module created to efficiently merge & translate hashes. SYNOPSIS my (%hash, $ref); $ref = tie %hash, Tie::Proxy::Hash, (bart => +{a => 1, b => 2}, maggie => +{a => 5, c => 6, e => 10}, ); $hash{a} == 1; # true...
19.46 KB  
Libraries  -  Db::Documentum 1.63
Db::Documentum is a Documentum API interface for Perl. SYNOPSIS use Db::Documentum qw(:all); scalar = dmAPIGet( ); $sessionID = dmAPIGet("connect,docbase,username,password"); scalar = dmAPIExec( ); $rv =...
296.96 KB  
Libraries  -  CGI::Ex::Conf 2.06
CGI::Ex::Conf is a Perl module with Conf Reader/Writer for many different data format types. SYNOPSIS use CGI::Ex::Conf qw(conf_read conf_write); my $hash = conf_read("/tmp/foo.yaml"); conf_write("/tmp/foo.yaml", {key1 => $val1, key2 =>...
215.04 KB  
Libraries  -  Lufs::C 0.21
Lufs::C is a C interface to perl. ABSTRACT This interface is used by the C code to call the perl subs. SEE ALSO perlfs.c.
24.58 KB  
Libraries  -  DBI 1.57
DBI is a database independent interface for Perl. SYNOPSIS use DBI; @driver_names = DBI->available_drivers; %drivers = DBI->installed_drivers; @data_sources = DBI->data_sources($driver_name, %attr); $dbh = DBI->connect($data_source,...
481.28 KB  
Utilities  -  Perl OS 4
Perl OS is a program written in the Perl programming language combined with the Perl module Tk. Perl OS was created to make an easy interface to run Perl/Tk programs. It was also created to be an easy working environment complete with a text...
143.36 KB  
NEW DOWNLOADS IN PROGRAMMING, LIBRARIES
Programming  -  FLEX-db Digital Asset Manager 3.0.9
FLEX-db - an enterprise Digital Asset Manager (DAM). It ingests and links metadata with files, creates thumbnails, and processes files using business rules. FLEX-db has a JSP client, Java app server for file input and output and an EJB metadata...
21.57 MB  
Programming  -  Libicom 0.9.0
The libicom library is a character based dynamicly linked library for Linux. It is used to remotely control the Icom IC-R8500 wide band receiver via an RS232 link. All call and return parameters to the control functions are character string based....
20.48 KB  
Programming  -  dotdesktop 0.3
Dotdesktop library provides ability to parse desktop entry file and access the information in a convenient way. Desktop entry file format is defined by freedesktop.org, it is used to describe information about an application such as the name and...
327.68 KB  
Programming  -  Cedalion for Linux 0.2.6
Cedalion is a programming language that allows its users to add new abstractions and define (and use) internal DSLs. Its innovation is in the fact that it uses projectional editing to allow the new abstractions to have no syntactic limitations.
471.04 KB  
Programming  -  libyasl 0.2
Libyasl is a C++ class library to easily realize TCP/UDP/Multicast clientsand servers in IPv4 and IPv6 environments under GNU/Linux systems.
143.36 KB  
Libraries  -  wolfSSL 3.12.0
The wolfSSL embedded SSL/TLS library is a lightweight SSL library written in ANSI standard C and targeted for embedded and RTOS environments - primarily because of its small size, speed, and feature set. It is commonly used in standard operating...
2.73 MB  
Libraries  -  EuGTK 4.8.9
Makes it easy to develop good- looking, fast, cross-platform programs that run on Linux, OS X, and Windows. Euphoria is a very fast interpreted/compiled language with straight-forward syntax. EuGTK allows programming in a clean, object-oriented...
10.68 MB  
Libraries  -  Linux User Group Library Manager 1.0
The LUG Library Manager is a project to help Linux User Groups start their own library. A LUG library is helpful to the community at large because it increases access to information, and gives everyone the opportunity to become more knowledgeable.
5.35 KB  
Libraries  -  Module::MakefilePL::Parse 0.12
Module::MakefilePL::Parse is a Perl module to parse required modules from Makefile.PL. SYNOPSIS use Module::MakefilePL::Parse; open $fh, Makefile.PL; $parser = Module::MakefilePL::Parse->new( join("", ) ); $info = $parser->required;...
8.19 KB  
Libraries  -  sqlpp 0.06
sqlpp Perl package is a SQL preprocessor. sqlpp is a conventional cpp-alike preprocessor taught to understand SQL ( PgSQL, in particular) syntax specificities. In addition to the standard #define/#ifdef/#else/#endif cohort, provides also...
10.24 KB