[Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI Iterator.pm, 1.1, 1.1.4.1 mysql.pm, 1.20.4.2, 1.20.4.3

Senduran Balasubramaniam sendu at dev.open-bio.org
Mon Oct 2 19:10:19 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/Store/DBI
In directory dev.open-bio.org:/tmp/cvs-serv28352/Bio/DB/SeqFeature/Store/DBI

Modified Files:
      Tag: branch-1-5-2
	Iterator.pm mysql.pm 
Log Message:
merge from HEAD

Index: Iterator.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/Store/DBI/Iterator.pm,v
retrieving revision 1.1
retrieving revision 1.1.4.1
diff -C2 -d -r1.1 -r1.1.4.1
*** Iterator.pm	2 Apr 2006 19:06:59 -0000	1.1
--- Iterator.pm	2 Oct 2006 23:10:17 -0000	1.1.4.1
***************
*** 1,4 ****
--- 1,12 ----
  package Bio::DB::SeqFeature::Store::DBI::Iterator;
  
+ # $Id$
+ 
+ =head1 NAME
+ 
+ Bio::DB::SeqFeature::Store::DBI::Iterator
+ 
+ =cut
+ 
  sub new {
    my $class          = shift;

Index: mysql.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/Store/DBI/mysql.pm,v
retrieving revision 1.20.4.2
retrieving revision 1.20.4.3
diff -C2 -d -r1.20.4.2 -r1.20.4.3
*** mysql.pm	17 Sep 2006 15:26:32 -0000	1.20.4.2
--- mysql.pm	2 Oct 2006 23:10:17 -0000	1.20.4.3
***************
*** 11,16 ****
  
    # Open the sequence database
!   my $db      = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql',
!                                                  -dsn     => 'dbi:mysql:test');
  
    # get a feature from somewhere
--- 11,16 ----
  
    # Open the sequence database
!   my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql',
!                                           -dsn     => 'dbi:mysql:test');
  
    # get a feature from somewhere
***************
*** 92,96 ****
  Bio::DB::SeqFeature::Store::mysql is the Mysql adaptor for
  Bio::DB::SeqFeature::Store. You will not create it directly, but
! instead use Bio::DB::SeqFeature::Store->new() to do so.
  
  See L<Bio::DB::SeqFeature::Store> for complete usage instructions.
--- 92,96 ----
  Bio::DB::SeqFeature::Store::mysql is the Mysql adaptor for
  Bio::DB::SeqFeature::Store. You will not create it directly, but
! instead use Bio::DB::SeqFeature::Store-E<gt>new() to do so.
  
  See L<Bio::DB::SeqFeature::Store> for complete usage instructions.
***************
*** 104,108 ****
  
  To establish a connection to the database, call
! Bio::DB::SeqFeature::Store->new(-adaptor=>'DBI::mysql', at more_args). The
  additional arguments are as follows:
  
--- 104,108 ----
  
  To establish a connection to the database, call
! Bio::DB::SeqFeature::Store-E<gt>new(-adaptor=E<gt>'DBI::mysql', at more_args). The
  additional arguments are as follows:
  
***************
*** 855,859 ****
    }
    $sth->finish;
!   return sort {$b->[2]<=>$a->[2]} @results;
  }
  
--- 855,860 ----
    }
    $sth->finish;
!   @results = sort {$b->[2]<=>$a->[2]} @results;
!   return @results;
  }
  
***************
*** 1239,1243 ****
    my $seqtable = $self->_sequence_table;
    my $sth = $self->_prepare(<<END);
! INSERT INTO $seqtable (id,offset,sequence) VALUES (?,?,?)
  END
    $sth->execute($id,$offset,$seq) or $self->throw($sth->errstr);
--- 1240,1244 ----
    my $seqtable = $self->_sequence_table;
    my $sth = $self->_prepare(<<END);
! REPLACE INTO $seqtable (id,offset,sequence) VALUES (?,?,?)
  END
    $sth->execute($id,$offset,$seq) or $self->throw($sth->errstr);



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