[Bioperl-guts-l] bioperl-live/Bio/Search/Result BlastPullResult.pm, 1.5, 1.6 BlastResult.pm, 1.26, 1.27 CrossMatchResult.pm, 1.1, 1.2 GenericResult.pm, 1.28, 1.29 HMMERResult.pm, 1.8, 1.9 HmmpfamResult.pm, 1.5, 1.6 PullResultI.pm, 1.5, 1.6 ResultFactory.pm, 1.8, 1.9 ResultI.pm, 1.24, 1.25 WABAResult.pm, 1.7, 1.8

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


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

Modified Files:
	BlastPullResult.pm BlastResult.pm CrossMatchResult.pm 
	GenericResult.pm HMMERResult.pm HmmpfamResult.pm 
	PullResultI.pm ResultFactory.pm ResultI.pm WABAResult.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: BlastPullResult.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Search/Result/BlastPullResult.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** BlastPullResult.pm	16 May 2007 07:49:57 -0000	1.5
--- BlastPullResult.pm	14 Jun 2007 14:16:14 -0000	1.6
***************
*** 20,24 ****
      # generally we use Bio::SearchIO to build these objects
      use Bio::SearchIO;
!     my $in = new Bio::SearchIO(-format => 'blast_pull',
  							   -file   => 'result.blast');
  
--- 20,24 ----
      # generally we use Bio::SearchIO to build these objects
      use Bio::SearchIO;
!     my $in = Bio::SearchIO->new(-format => 'blast_pull',
  							   -file   => 'result.blast');
  
***************
*** 78,82 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::SearchIO::Result::hmmpfam();
   Function: Builds a new Bio::SearchIO::Result::hmmpfam object 
   Returns : Bio::SearchIO::Result::hmmpfam
--- 78,82 ----
  
   Title   : new
!  Usage   : my $obj = Bio::SearchIO::Result::hmmpfam->new();
   Function: Builds a new Bio::SearchIO::Result::hmmpfam object 
   Returns : Bio::SearchIO::Result::hmmpfam
***************
*** 210,214 ****
  	#*** needs to inherit piped_behaviour, and we need to deal with _sequential
  	#    ourselves
! 	$self->_fields->{next_hit} = new Bio::Search::Hit::BlastPullHit(-parent => $self,
  																	-chunk => [$self->chunk, $start, $end],
  																	-hit_data => $hit_row);
--- 210,214 ----
  	#*** needs to inherit piped_behaviour, and we need to deal with _sequential
  	#    ourselves
! 	$self->_fields->{next_hit} = Bio::Search::Hit::BlastPullHit->new(-parent => $self,
  																	-chunk => [$self->chunk, $start, $end],
  																	-hit_data => $hit_row);

Index: BlastResult.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Search/Result/BlastResult.pm,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** BlastResult.pm	2 Oct 2006 04:06:16 -0000	1.26
--- BlastResult.pm	14 Jun 2007 14:16:14 -0000	1.27
***************
*** 87,91 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Search::Result::BlastResult();
   Function: Builds a new Bio::Search::Result::BlastResult object
   Returns : Bio::Search::Result::BlastResult
--- 87,91 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Search::Result::BlastResult->new();
   Function: Builds a new Bio::Search::Result::BlastResult object
   Returns : Bio::Search::Result::BlastResult

Index: CrossMatchResult.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Search/Result/CrossMatchResult.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** CrossMatchResult.pm	12 May 2007 04:20:26 -0000	1.1
--- CrossMatchResult.pm	14 Jun 2007 14:16:14 -0000	1.2
***************
*** 94,98 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Search::Result::CrossMatchResult();
   Function: Builds a new Bio::Search::Result::CrossMatchResult object
   Returns : Bio::Search::Result::CrossMatchResult
--- 94,98 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Search::Result::CrossMatchResult->new();
   Function: Builds a new Bio::Search::Result::CrossMatchResult object
   Returns : Bio::Search::Result::CrossMatchResult

Index: ResultFactory.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Search/Result/ResultFactory.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** ResultFactory.pm	26 Sep 2006 22:03:13 -0000	1.8
--- ResultFactory.pm	14 Jun 2007 14:16:14 -0000	1.9
***************
*** 18,22 ****
  
      use Bio::Search::Result::ResultFactory;
!     my $factory = new Bio::Search::Result::ResultFactory();
      my $resultobj = $factory->create(@args);
  
--- 18,22 ----
  
      use Bio::Search::Result::ResultFactory;
!     my $factory = Bio::Search::Result::ResultFactory->new();
      my $resultobj = $factory->create(@args);
  
***************
*** 77,81 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Search::Result::ResultFactory();
   Function: Builds a new Bio::Search::Result::ResultFactory object 
   Returns : Bio::Search::Result::ResultFactory
--- 77,81 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Search::Result::ResultFactory->new();
   Function: Builds a new Bio::Search::Result::ResultFactory object 
   Returns : Bio::Search::Result::ResultFactory

Index: GenericResult.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Search/Result/GenericResult.pm,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** GenericResult.pm	8 Mar 2007 16:12:09 -0000	1.28
--- GenericResult.pm	14 Jun 2007 14:16:14 -0000	1.29
***************
*** 22,26 ****
      # typically one gets Results from a SearchIO stream
      use Bio::SearchIO;
!     my $io = new Bio::SearchIO(-format => 'blast',
                                  -file   => 't/data/HUMBETGLOA.tblastx');
      while( my $result = $io->next_result ) {
--- 22,26 ----
      # typically one gets Results from a SearchIO stream
      use Bio::SearchIO;
!     my $io = Bio::SearchIO->new(-format => 'blast',
                                  -file   => 't/data/HUMBETGLOA.tblastx');
      while( my $result = $io->next_result ) {
***************
*** 34,38 ****
      my @hits = (); # would be a list of Bio::Search::Hit::HitI objects
      # typically these are created from a Bio::SearchIO stream
!     my $result = new Bio::Search::Result::GenericResult
          ( -query_name        => 'HUMBETGLOA',
            -query_accession   => ''
--- 34,38 ----
      my @hits = (); # would be a list of Bio::Search::Hit::HitI objects
      # typically these are created from a Bio::SearchIO stream
!     my $result = Bio::Search::Result::GenericResult->new
          ( -query_name        => 'HUMBETGLOA',
            -query_accession   => ''
***************
*** 139,143 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Search::Result::GenericResult();
   Function: Builds a new Bio::Search::Result::GenericResult object 
   Returns : Bio::Search::Result::GenericResult
--- 139,143 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Search::Result::GenericResult->new();
   Function: Builds a new Bio::Search::Result::GenericResult object 
   Returns : Bio::Search::Result::GenericResult
***************
*** 167,172 ****
    $self->{'_hits'} = [];
    $self->{'_hitindex'} = 0;
!   $self->{'_statistics'} = new Bio::Search::GenericStatistics;
!   $self->{'_parameters'} = new Bio::Tools::Run::GenericParameters;
  
    my ($qname,$qacc,$qdesc,$qlen,
--- 167,172 ----
    $self->{'_hits'} = [];
    $self->{'_hitindex'} = 0;
!   $self->{'_statistics'} = Bio::Search::GenericStatistics->new();
!   $self->{'_parameters'} = Bio::Tools::Run::GenericParameters->new();
  
    my ($qname,$qacc,$qdesc,$qlen,

Index: PullResultI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Search/Result/PullResultI.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** PullResultI.pm	14 May 2007 12:49:52 -0000	1.5
--- PullResultI.pm	14 Jun 2007 14:16:14 -0000	1.6
***************
*** 20,24 ****
      # typically one gets Results from a SearchIO stream
      use Bio::SearchIO;
!     my $io = new Bio::SearchIO(-format => 'hmmer_pull',
                                  -file   => 't/data/hmmpfam.out');
  
--- 20,24 ----
      # typically one gets Results from a SearchIO stream
      use Bio::SearchIO;
!     my $io = Bio::SearchIO->new(-format => 'hmmer_pull',
                                  -file   => 't/data/hmmpfam.out');
  
***************
*** 475,479 ****
      my ($self, $key, $value) = @_;
      unless (exists $self->{_parameters}) {
!         $self->{_parameters} = new Bio::Tools::Run::GenericParameters;
      }
      $self->{_parameters}->set_parameter($key => $value);
--- 475,479 ----
      my ($self, $key, $value) = @_;
      unless (exists $self->{_parameters}) {
!         $self->{_parameters} = Bio::Tools::Run::GenericParameters->new();
      }
      $self->{_parameters}->set_parameter($key => $value);
***************
*** 528,532 ****
      my ($self, $key, $value) = @_;
      unless (exists $self->{_statistics}) {
!         $self->{_statistics} = new Bio::Search::GenericStatistics;
      }
      $self->{_statistics}->set_statistic($key => $value);
--- 528,532 ----
      my ($self, $key, $value) = @_;
      unless (exists $self->{_statistics}) {
!         $self->{_statistics} = Bio::Search::GenericStatistics->new();
      }
      $self->{_statistics}->set_statistic($key => $value);

Index: ResultI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Search/Result/ResultI.pm,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** ResultI.pm	26 Sep 2006 22:03:13 -0000	1.24
--- ResultI.pm	14 Jun 2007 14:16:14 -0000	1.25
***************
*** 26,30 ****
  
      use Bio::SearchIO;
!     my $io = new Bio::SearchIO(-format => 'blast',
                                  -file   => 't/data/HUMBETGLOA.tblastx');
      my $result = $io->next_result;
--- 26,30 ----
  
      use Bio::SearchIO;
!     my $io = Bio::SearchIO->new(-format => 'blast',
                                  -file   => 't/data/HUMBETGLOA.tblastx');
      my $result = $io->next_result;

Index: HmmpfamResult.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Search/Result/HmmpfamResult.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** HmmpfamResult.pm	2 Oct 2006 04:06:16 -0000	1.5
--- HmmpfamResult.pm	14 Jun 2007 14:16:14 -0000	1.6
***************
*** 20,24 ****
      # generally we use Bio::SearchIO to build these objects
      use Bio::SearchIO;
!     my $in = new Bio::SearchIO(-format => 'hmmer_pull',
  							   -file   => 'result.hmmer');
  
--- 20,24 ----
      # generally we use Bio::SearchIO to build these objects
      use Bio::SearchIO;
!     my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
  							   -file   => 'result.hmmer');
  
***************
*** 75,79 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::SearchIO::Result::hmmpfam();
   Function: Builds a new Bio::SearchIO::Result::hmmpfam object 
   Returns : Bio::SearchIO::Result::hmmpfam
--- 75,79 ----
  
   Title   : new
!  Usage   : my $obj = Bio::SearchIO::Result::hmmpfam->new();
   Function: Builds a new Bio::SearchIO::Result::hmmpfam object 
   Returns : Bio::SearchIO::Result::hmmpfam
***************
*** 245,249 ****
  	my @hit_data = (@{$hit_table[$self->{_next_hit_index}++]}, $self->{_next_hit_index});
  	
! 	$self->_fields->{next_hit} = new Bio::Search::Hit::HmmpfamHit(-parent => $self,
  																  -hit_data => \@hit_data);
  	
--- 245,249 ----
  	my @hit_data = (@{$hit_table[$self->{_next_hit_index}++]}, $self->{_next_hit_index});
  	
! 	$self->_fields->{next_hit} = Bio::Search::Hit::HmmpfamHit->new(-parent => $self,
  																  -hit_data => \@hit_data);
  	

Index: HMMERResult.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Search/Result/HMMERResult.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** HMMERResult.pm	26 Sep 2006 22:03:13 -0000	1.8
--- HMMERResult.pm	14 Jun 2007 14:16:14 -0000	1.9
***************
*** 18,22 ****
  
      use Bio::Search::Result::HMMERResult;
!     my $result = new Bio::Search::Result::HMMERResult
      ( -hmm_name => 'pfam',
        -sequence_file => 'roa1.pep',
--- 18,22 ----
  
      use Bio::Search::Result::HMMERResult;
!     my $result = Bio::Search::Result::HMMERResult->new
      ( -hmm_name => 'pfam',
        -sequence_file => 'roa1.pep',
***************
*** 25,29 ****
      # generally we use Bio::SearchIO to build these objects
      use Bio::SearchIO;
!     my $in = new Bio::SearchIO(-format => 'hmmer',
  			       -file   => 'result.hmmer');
      while( my $result = $in->next_result ) {
--- 25,29 ----
      # generally we use Bio::SearchIO to build these objects
      use Bio::SearchIO;
!     my $in = Bio::SearchIO->new(-format => 'hmmer',
  			       -file   => 'result.hmmer');
      while( my $result = $in->next_result ) {
***************
*** 81,85 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Search::Result::HMMERResult();
   Function: Builds a new Bio::Search::Result::HMMERResult object 
   Returns : Bio::Search::Result::HMMERResult
--- 81,85 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Search::Result::HMMERResult->new();
   Function: Builds a new Bio::Search::Result::HMMERResult object 
   Returns : Bio::Search::Result::HMMERResult

Index: WABAResult.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Search/Result/WABAResult.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** WABAResult.pm	26 Sep 2006 22:03:13 -0000	1.7
--- WABAResult.pm	14 Jun 2007 14:16:14 -0000	1.8
***************
*** 72,76 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Search::Result::WABAResult();
   Function: Builds a new Bio::Search::Result::WABAResult object 
   Returns : Bio::Search::Result::WABAResult
--- 72,76 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Search::Result::WABAResult->new();
   Function: Builds a new Bio::Search::Result::WABAResult object 
   Returns : Bio::Search::Result::WABAResult



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