[Bioperl-guts-l] bioperl-live/Bio/SearchIO/Writer BSMLResultWriter.pm, 1.6, 1.7 GbrowseGFF.pm, 1.16, 1.17 HTMLResultWriter.pm, 1.41, 1.42 TextResultWriter.pm, 1.20, 1.21

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


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

Modified Files:
	BSMLResultWriter.pm GbrowseGFF.pm HTMLResultWriter.pm 
	TextResultWriter.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: BSMLResultWriter.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer/BSMLResultWriter.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** BSMLResultWriter.pm	26 Sep 2006 22:03:13 -0000	1.6
--- BSMLResultWriter.pm	14 Jun 2007 14:16:14 -0000	1.7
***************
*** 18,24 ****
  
    use Bio::SearchIO;
!   my $in = new Bio::SearchIO(-file   => 'result.blast',
                               -format => 'blast');
!   my $out = new Bio::SearchIO(-output_format  => 'BSMLResultWriter',
                                -file           => ">result.bsml");
    while( my $r = $in->next_result ) {
--- 18,24 ----
  
    use Bio::SearchIO;
!   my $in = Bio::SearchIO->new(-file   => 'result.blast',
                               -format => 'blast');
!   my $out = Bio::SearchIO->new(-output_format  => 'BSMLResultWriter',
                                -file           => ">result.bsml");
    while( my $r = $in->next_result ) {
***************
*** 76,80 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::SearchIO::Writer::BSMLResultWriter();
   Function: Builds a new Bio::SearchIO::Writer::BSMLResultWriter object 
   Returns : an instance of Bio::SearchIO::Writer::BSMLResultWriter
--- 76,80 ----
  
   Title   : new
!  Usage   : my $obj = Bio::SearchIO::Writer::BSMLResultWriter->new();
   Function: Builds a new Bio::SearchIO::Writer::BSMLResultWriter object 
   Returns : an instance of Bio::SearchIO::Writer::BSMLResultWriter

Index: TextResultWriter.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer/TextResultWriter.pm,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** TextResultWriter.pm	23 May 2007 05:52:27 -0000	1.20
--- TextResultWriter.pm	14 Jun 2007 14:16:14 -0000	1.21
***************
*** 21,29 ****
    use Bio::SearchIO::Writer::TextResultWriter;
  
!   my $in = new Bio::SearchIO(-format => 'blast',
  			     -file   => shift @ARGV);
  
!   my $writer = new Bio::SearchIO::Writer::TextResultWriter();
!   my $out = new Bio::SearchIO(-writer => $writer);
    $out->write_result($in->next_result);
  
--- 21,29 ----
    use Bio::SearchIO::Writer::TextResultWriter;
  
!   my $in = Bio::SearchIO->new(-format => 'blast',
  			     -file   => shift @ARGV);
  
!   my $writer = Bio::SearchIO::Writer::TextResultWriter->new();
!   my $out = Bio::SearchIO->new(-writer => $writer);
    $out->write_result($in->next_result);
  
***************
*** 53,57 ****
                                       # long enough    
    }
!   my $writer = new Bio::SearchIO::Writer::TextResultWriter(
         -filters => { 'HIT' =E<gt> \&hit_filter }  
        );
--- 53,57 ----
                                       # long enough    
    }
!   my $writer = Bio::SearchIO::Writer::TextResultWriter->new(
         -filters => { 'HIT' =E<gt> \&hit_filter }  
        );
***************
*** 64,68 ****
         return $hsp->percent_identity E<gt> 75;
     }
!    my $writer = new Bio::SearchIO::Writer::TextResultWriter(
         -filters => { 'HSP' =E<gt> \&hsp_filter }  
        );
--- 64,68 ----
         return $hsp->percent_identity E<gt> 75;
     }
!    my $writer = Bio::SearchIO::Writer::TextResultWriter->new(
         -filters => { 'HSP' =E<gt> \&hsp_filter }  
        );
***************
*** 135,139 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::SearchIO::Writer::TextResultWriter();
   Function: Builds a new Bio::SearchIO::Writer::TextResultWriter object 
   Returns : Bio::SearchIO::Writer::TextResultWriter
--- 135,139 ----
  
   Title   : new
!  Usage   : my $obj = Bio::SearchIO::Writer::TextResultWriter->new();
   Function: Builds a new Bio::SearchIO::Writer::TextResultWriter object 
   Returns : Bio::SearchIO::Writer::TextResultWriter

Index: GbrowseGFF.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer/GbrowseGFF.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** GbrowseGFF.pm	26 Sep 2006 22:03:13 -0000	1.16
--- GbrowseGFF.pm	14 Jun 2007 14:16:14 -0000	1.17
***************
*** 16,22 ****
  
    use Bio::SearchIO;
!   my $in = new Bio::SearchIO(-file   => 'result.blast',      
                               -format => 'blast');
!   my $out = new Bio::SearchIO(-output_format  => 'GbrowseGFF',
                                -output_cigar   => 1,
                                -output_signif  => 1,
--- 16,22 ----
  
    use Bio::SearchIO;
!   my $in = Bio::SearchIO->new(-file   => 'result.blast',      
                               -format => 'blast');
!   my $out = Bio::SearchIO->new(-output_format  => 'GbrowseGFF',
                                -output_cigar   => 1,
                                -output_signif  => 1,
***************
*** 80,84 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::SearchIO::Writer::GbrowseGFF(@args);
   Function: Builds a new Bio::SearchIO::Writer::GbrowseGFF object 
   Returns : an instance of Bio::SearchIO::Writer::GbrowseGFF
--- 80,84 ----
  
   Title   : new
!  Usage   : my $obj = Bio::SearchIO::Writer::GbrowseGFF->new(@args);
   Function: Builds a new Bio::SearchIO::Writer::GbrowseGFF object 
   Returns : an instance of Bio::SearchIO::Writer::GbrowseGFF

Index: HTMLResultWriter.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer/HTMLResultWriter.pm,v
retrieving revision 1.41
retrieving revision 1.42
diff -C2 -d -r1.41 -r1.42
*** HTMLResultWriter.pm	2 Oct 2006 04:45:37 -0000	1.41
--- HTMLResultWriter.pm	14 Jun 2007 14:16:14 -0000	1.42
***************
*** 23,31 ****
    use Bio::SearchIO::Writer::HTMLResultWriter;
  
!   my $in = new Bio::SearchIO(-format => 'blast',
  			     -file   => shift @ARGV);
  
!   my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
!   my $out = new Bio::SearchIO(-writer => $writer);
    $out->write_result($in->next_result);
  
--- 23,31 ----
    use Bio::SearchIO::Writer::HTMLResultWriter;
  
!   my $in = Bio::SearchIO->new(-format => 'blast',
  			     -file   => shift @ARGV);
  
!   my $writer = Bio::SearchIO::Writer::HTMLResultWriter->new();
!   my $out = Bio::SearchIO->new(-writer => $writer);
    $out->write_result($in->next_result);
  
***************
*** 42,48 ****
    }
  
!   my $writer = new Bio::SearchIO::Writer::HTMLResultWriter
                       (-filters => { 'HSP' => \&hsp_filter} );
!   my $out = new Bio::SearchIO(-writer => $writer);
    $out->write_result($in->next_result);
  
--- 42,48 ----
    }
  
!   my $writer = Bio::SearchIO::Writer::HTMLResultWriter->new
                       (-filters => { 'HSP' => \&hsp_filter} );
!   my $out = Bio::SearchIO->new(-writer => $writer);
    $out->write_result($in->next_result);
  
***************
*** 116,120 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::SearchIO::Writer::HTMLResultWriter();
   Function: Builds a new Bio::SearchIO::Writer::HTMLResultWriter object 
   Returns : Bio::SearchIO::Writer::HTMLResultWriter
--- 116,120 ----
  
   Title   : new
!  Usage   : my $obj = Bio::SearchIO::Writer::HTMLResultWriter->new();
   Function: Builds a new Bio::SearchIO::Writer::HTMLResultWriter object 
   Returns : Bio::SearchIO::Writer::HTMLResultWriter



More information about the Bioperl-guts-l mailing list