[Bioperl-guts-l] bioperl-live/Bio/DB/Flat BinarySearch.pm, 1.28, 1.29

Senduran Balasubramaniam sendu at dev.open-bio.org
Thu Jun 14 10:16:13 EDT 2007


Update of /home/repository/bioperl/bioperl-live/Bio/DB/Flat
In directory dev.open-bio.org:/tmp/cvs-serv22328/Bio/DB/Flat

Modified Files:
	BinarySearch.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: BinarySearch.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/Flat/BinarySearch.pm,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** BinarySearch.pm	4 Oct 2006 05:52:06 -0000	1.28
--- BinarySearch.pm	14 Jun 2007 14:16:11 -0000	1.29
***************
*** 46,50 ****
  The index can now be created using 
  
!     my $index = new Bio::DB::Flat::BinarySearch(
               -directory         => "/home/max/",
               -dbname            => "mydb",
--- 46,50 ----
  The index can now be created using 
  
!     my $index = Bio::DB::Flat::BinarySearch->new(
               -directory         => "/home/max/",
               -dbname            => "mydb",
***************
*** 100,104 ****
      $secondary_patterns{"ID"} = '^ID   (\S+)';
  
!     my $index = new Bio::DB::Flat::BinarySearch(
                  -directory          => $index_directory,
  		          -dbname             => "ppp",
--- 100,104 ----
      $secondary_patterns{"ID"} = '^ID   (\S+)';
  
!     my $index = Bio::DB::Flat::BinarySearch->new(
                  -directory          => $index_directory,
  		          -dbname             => "ppp",
***************
*** 120,124 ****
  object 
  
!     my $index = new Bio::DB::Flat::BinarySearch(
                    -directory => $index_directory);
  
--- 120,124 ----
  object 
  
!     my $index = Bio::DB::Flat::BinarySearch->new(
                    -directory => $index_directory);
  
***************
*** 138,142 ****
  into objects.
  
!     my $seq = new Bio::SeqIO(-fh     => $fh,
  			                    -format => 'fasta');
  
--- 138,142 ----
  into objects.
  
!     my $seq = Bio::SeqIO->new(-fh     => $fh,
  			                    -format => 'fasta');
  
***************
*** 219,223 ****
   Title   : new
   Usage   : For reading 
!              my $index = new Bio::DB::Flat::BinarySearch(
                       -directory => '/Users/michele/indices/dbest',
  		     -dbname    => 'mydb',
--- 219,223 ----
   Title   : new
   Usage   : For reading 
!              my $index = Bio::DB::Flat::BinarySearch->new(
                       -directory => '/Users/michele/indices/dbest',
  		     -dbname    => 'mydb',
***************
*** 227,231 ****
  
               my %secondary_patterns = {"ACC" => "^>\\S+ +(\\S+)"}
!              my $index = new Bio::DB::Flat::BinarySearch(
  		     -directory          => '/Users/michele/indices',
                       -dbname             => 'mydb',
--- 227,231 ----
  
               my %secondary_patterns = {"ACC" => "^>\\S+ +(\\S+)"}
!              my $index = Bio::DB::Flat::BinarySearch->new(
  		     -directory          => '/Users/michele/indices',
                       -dbname             => 'mydb',
***************
*** 306,310 ****
      my $location = $config{'location'};
      
!     my $index =  new Bio::DB::Flat::BinarySearch(-dbname    => $dbname,
  						 -index_dir => $location,
  						 );
--- 306,310 ----
      my $location = $config{'location'};
      
!     my $index =  Bio::DB::Flat::BinarySearch->new(-dbname    => $dbname,
  						 -index_dir => $location,
  						 );
***************
*** 338,342 ****
      unless ( defined($self->{_seqio}) ) {
  
! 	$self->{_seqio} = new Bio::SeqIO(-fh => $fh,
  					 -format => $self->format);
      } else {
--- 338,342 ----
      unless ( defined($self->{_seqio}) ) {
  
! 	$self->{_seqio} = Bio::SeqIO->new(-fh => $fh,
  					 -format => $self->format);
      } else {
***************
*** 1661,1665 ****
      $secondary_patterns{"ID"} = $start_pattern;
  
!     my $index =  new Bio::DB::Flat::BinarySearch
  	(-index_dir          => $index_dir,
  	 -format             => 'swissprot',
--- 1661,1665 ----
      $secondary_patterns{"ID"} = $start_pattern;
  
!     my $index =  Bio::DB::Flat::BinarySearch->new
  	(-index_dir          => $index_dir,
  	 -format             => 'swissprot',
***************
*** 1683,1687 ****
     $secondary_patterns{"ID"} = $start_pattern;
  
!    my $index = new Bio::DB::Flat::BinarySearch
         (-index_dir          => $index_dir,
  	-format             => 'embl',
--- 1683,1687 ----
     $secondary_patterns{"ID"} = $start_pattern;
  
!    my $index = Bio::DB::Flat::BinarySearch->new
         (-index_dir          => $index_dir,
  	-format             => 'embl',
***************
*** 1707,1711 ****
     $secondary_patterns{"ID"} = "^>\\S+ +(\\S+)";
  
!    my $index =  new Bio::DB::Flat::BinarySearch
         (-index_dir          => $index_dir,
  	-format             => 'fasta',
--- 1707,1711 ----
     $secondary_patterns{"ID"} = "^>\\S+ +(\\S+)";
  
!    my $index =  Bio::DB::Flat::BinarySearch->new
         (-index_dir          => $index_dir,
  	-format             => 'fasta',



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