[Bioperl-guts-l] bioperl-live/Bio/DB GFF.pm,1.127,1.128

Lincoln Stein lstein at pub.open-bio.org
Fri Jul 29 12:23:46 EDT 2005


Update of /home/repository/bioperl/bioperl-live/Bio/DB
In directory pub.open-bio.org:/tmp/cvs-serv9971/Bio/DB

Modified Files:
	GFF.pm 
Log Message:
documentation enhancements


Index: GFF.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/GFF.pm,v
retrieving revision 1.127
retrieving revision 1.128
diff -C2 -d -r1.127 -r1.128
*** GFF.pm	29 Jul 2005 16:21:16 -0000	1.127
--- GFF.pm	29 Jul 2005 16:23:44 -0000	1.128
***************
*** 11,17 ****
    # Open the sequence database
    my $db      = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt',
!                                    -dsn     => 'dbi:mysql:elegans',
! 				   -fasta   => '/usr/local/fasta_files'
! 				 );
  
    # fetch a 1 megabase segment of sequence starting at landmark "ZK909"
--- 11,15 ----
    # Open the sequence database
    my $db      = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt',
!                                    -dsn     => 'dbi:mysql:elegans);
  
    # fetch a 1 megabase segment of sequence starting at landmark "ZK909"
***************
*** 421,429 ****
  and access methods.
  
! Currently there are two adaptors: 'dbi::mysql' and 'dbi::mysqlopt'.
! The former is an interface to a simple Mysql schema.  The latter is an
! optimized version of dbi::mysql which uses a binning scheme to
! accelerate range queries and the Bio::DB::Fasta module for rapid
! retrieval of sequences.  Note the double-colon between the words.
  
  =item Aggregators
--- 419,444 ----
  and access methods.
  
! There are currently five adaptors recommended for general use:
! 
!   Adaptor Name             Description
!   ------------             -----------
! 
!   memory                   A simple in-memory database suitable for testing
!                             and small data sets.
! 
!   berkeleydb               An indexed file database based on the DB_File module,
!                             suitable for medium-sized read-only data sets.
! 
!   dbi::mysql               An interface to a schema implemented in the Mysql
!                             relational database management system.
! 
!   dbi::oracle              An interface to a schema implemented in the Oracle
!                             relational database management system.
! 
!   dbi::pg                  An interface to a schema implemented in the PostgreSQL
!                             relational database management system.
! 
! Check the Bio/DB/GFF/Adaptor directory and subdirectories for other,
! more specialized adaptors, as well as experimental ones.
  
  =item Aggregators
***************
*** 3624,3627 ****
--- 3639,3643 ----
  L<Bio::DB::GFF::Adaptor::dbi::oracle>,
  L<Bio::DB::GFF::Adaptor::memory>
+ L<Bio::DB::GFF::Adaptor::berkeleydb>
  
  =head1 AUTHOR



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