[Bioperl-guts-l] bioperl-run/t Consense.t, 1.5, 1.6 DrawGram.t, 1.2, 1.3 DrawTree.t, 1.2, 1.3 EMBOSS.t, 1.16, 1.17 Molphy.t, 1.7, 1.8 PAML.t, 1.14, 1.15 Probcons.t, 1.5, 1.6

Thu Jun 14 11:23:11 EDT 2007

Update of /home/repository/bioperl/bioperl-run/t
In directory dev.open-bio.org:/tmp/cvs-serv24084/t

Modified Files:
	Consense.t DrawGram.t DrawTree.t EMBOSS.t Molphy.t PAML.t 
	Probcons.t 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: Consense.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/t/Consense.t,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Consense.t	25 Oct 2006 09:22:17 -0000	1.5
--- Consense.t	14 Jun 2007 15:23:09 -0000	1.6
***************
*** 36,40 ****
  ok(1);
  my $verbose = $DEBUG;
! my $sb_factory = new Bio::Tools::Run::Phylo::Phylip::Consense
      (-verbose => $verbose);
  unless($sb_factory->executable){
--- 36,40 ----
  ok(1);
  my $verbose = $DEBUG;
! my $sb_factory = Bio::Tools::Run::Phylo::Phylip::Consense->new
      (-verbose => $verbose);
  unless($sb_factory->executable){

Index: Probcons.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/t/Probcons.t,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Probcons.t	6 Nov 2006 18:04:23 -0000	1.5
--- Probcons.t	14 Jun 2007 15:23:09 -0000	1.6
***************
*** 67,71 ****
  my ($tfhannot,$annotfilename) = $factory->io->tempfile(-dir=>$factory->tempdir);
  my ($tfhdummy,$dummyfilename) = $factory->io->tempfile(-dir=>$factory->tempdir);
! my $factory2 = new Bio::Tools::Run::Alignment::Probcons
      (
       'iterative-refinement'  => '1000',
--- 67,71 ----
  my ($tfhannot,$annotfilename) = $factory->io->tempfile(-dir=>$factory->tempdir);
  my ($tfhdummy,$dummyfilename) = $factory->io->tempfile(-dir=>$factory->tempdir);
! my $factory2 = Bio::Tools::Run::Alignment::Probcons->new
      (
       'iterative-refinement'  => '1000',
***************
*** 87,91 ****
  $factory2 = '';

! $factory2 = new Bio::Tools::Run::Alignment::Probcons
      (
       'iterative-refinement'  => '1000',
--- 87,91 ----
  $factory2 = '';

! $factory2 = Bio::Tools::Run::Alignment::Probcons->new
      (
       'iterative-refinement'  => '1000',

Index: DrawGram.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/t/DrawGram.t,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** DrawGram.t	8 Oct 2005 21:42:46 -0000	1.2
--- DrawGram.t	14 Jun 2007 15:23:09 -0000	1.3
***************
*** 51,55 ****

! my $intree = new Bio::TreeIO(-file => 
  			     Bio::Root::IO->catfile(qw(t data
  						       treefile.example)));
--- 51,55 ----

! my $intree = Bio::TreeIO->new(-file => 
  			     Bio::Root::IO->catfile(qw(t data
  						       treefile.example)));

Index: Molphy.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/t/Molphy.t,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** Molphy.t	2 May 2003 16:24:10 -0000	1.7
--- Molphy.t	14 Jun 2007 15:23:09 -0000	1.8
***************
*** 58,62 ****
  	     'search' => 'quick', 
  	     "other" => [ '-information', '-w']); 
! my $protml = new Bio::Tools::Run::Phylo::Molphy::ProtML(-verbose => $verbose,
  							-flags => \%args);
  unless ($protml->executable){
--- 58,62 ----
  	     'search' => 'quick', 
  	     "other" => [ '-information', '-w']); 
! my $protml = Bio::Tools::Run::Phylo::Molphy::ProtML->new(-verbose => $verbose,
  							-flags => \%args);
  unless ($protml->executable){
***************
*** 65,69 ****
  }

! my $in = new Bio::AlignIO(-format => 'clustalw',
  			  -file   => Bio::Root::IO->catfile('t','data',
  							    'cel-cbr-fam.aln'));
--- 65,69 ----
  }

! my $in = Bio::AlignIO->new(-format => 'clustalw',
  			  -file   => Bio::Root::IO->catfile('t','data',
  							    'cel-cbr-fam.aln'));

Index: DrawTree.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/t/DrawTree.t,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** DrawTree.t	8 Oct 2005 21:42:46 -0000	1.2
--- DrawTree.t	14 Jun 2007 15:23:09 -0000	1.3
***************
*** 46,50 ****
  }

! my $intree = new Bio::TreeIO(-file => Bio::Root::IO->catfile(qw(t data treefile.example)));

  $file = $treedraw->draw_tree(Bio::Root::IO->catfile(qw(t data 
--- 46,50 ----
  }

! my $intree = Bio::TreeIO->new(-file => Bio::Root::IO->catfile(qw(t data treefile.example)));

  $file = $treedraw->draw_tree(Bio::Root::IO->catfile(qw(t data 

Index: PAML.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/t/PAML.t,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** PAML.t	1 Oct 2004 14:00:05 -0000	1.14
--- PAML.t	14 Jun 2007 15:23:09 -0000	1.15
***************
*** 55,59 ****
  use Bio::Root::IO;

! my $inpaml = new Bio::Tools::Phylo::PAML(-file => 
  					 Bio::Root::IO->catfile(qw(t data 
  								   codeml.mlc)));
--- 55,59 ----
  use Bio::Root::IO;

! my $inpaml = Bio::Tools::Phylo::PAML->new(-file => 
  					 Bio::Root::IO->catfile(qw(t data 
  								   codeml.mlc)));
***************
*** 64,68 ****
  use Bio::Tools::Run::Phylo::PAML::Yn00;
  use Bio::AlignIO;
! my $codeml = new Bio::Tools::Run::Phylo::PAML::Codeml(-verbose => $verbose);
  unless ($codeml->executable) {
    warn("PAML not is installed. skipping tests $Test::ntest to $NUMTESTS\n");
--- 64,68 ----
  use Bio::Tools::Run::Phylo::PAML::Yn00;
  use Bio::AlignIO;
! my $codeml = Bio::Tools::Run::Phylo::PAML::Codeml->new(-verbose => $verbose);
  unless ($codeml->executable) {
    warn("PAML not is installed. skipping tests $Test::ntest to $NUMTESTS\n");
***************
*** 70,74 ****
  }

! my $in = new Bio::AlignIO(-format => 'phylip',
  			  -file   => Bio::Root::IO->catfile(qw(t data 
  							       gf-s85.phylip)));
--- 70,74 ----
  }

! my $in = Bio::AlignIO->new(-format => 'phylip',
  			  -file   => Bio::Root::IO->catfile(qw(t data 
  							       gf-s85.phylip)));
***************
*** 130,134 ****

! $codeml = new Bio::Tools::Run::Phylo::PAML::Codeml
      (-params => { 'alpha' => 1.53 },
       -verbose => $verbose);
--- 130,134 ----

! $codeml = Bio::Tools::Run::Phylo::PAML::Codeml->new
      (-params => { 'alpha' => 1.53 },
       -verbose => $verbose);

Index: EMBOSS.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/t/EMBOSS.t,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** EMBOSS.t	25 Oct 2006 14:48:22 -0000	1.16
--- EMBOSS.t	14 Jun 2007 15:23:09 -0000	1.17
***************
*** 53,57 ****
  ## total number of tests that will be run.

! my $factory = new Bio::Factory::EMBOSS(-verbose => $verbose);
  ok($factory);
  my $compseqapp = $factory->program('compseq');
--- 53,57 ----
  ## total number of tests that will be run.

! my $factory = Bio::Factory::EMBOSS->new(-verbose => $verbose);
  ok($factory);
  my $compseqapp = $factory->program('compseq');
***************
*** 78,82 ****

  # testing in-memory use of 
! my $in = new Bio::SeqIO(-format => 'fasta',
  			-file =>  Bio::Root::IO->catfile('t',
  							 'data',
--- 78,82 ----

  # testing in-memory use of 
! my $in = Bio::SeqIO->new(-format => 'fasta',
  			-file =>  Bio::Root::IO->catfile('t',
  							 'data',
***************
*** 85,89 ****
  ok($seq);
  my @amino;
! $in = new Bio::SeqIO(-format => 'fasta',
  		     -file =>  Bio::Root::IO->catfile('t',
  						      'data',
--- 85,89 ----
  ok($seq);
  my @amino;
! $in = Bio::SeqIO->new(-format => 'fasta',
  		     -file =>  Bio::Root::IO->catfile('t',
  						      'data',
***************
*** 117,121 ****
  ok(-e $wateroutfile);

! my $alnin = new Bio::AlignIO(-format => 'emboss',
  			    -file   => $wateroutfile);

--- 117,121 ----
  ok(-e $wateroutfile);

! my $alnin = Bio::AlignIO->new(-format => 'emboss',
  			    -file   => $wateroutfile);

***************
*** 139,143 ****
  my $cons = $factory->program('cons');
  $cons->verbose(0);
! $in = new Bio::AlignIO(-format => 'msf',
  		       -file   => Bio::Root::IO->catfile('t',
  							 'data',
--- 139,143 ----
  my $cons = $factory->program('cons');
  $cons->verbose(0);
! $in = Bio::AlignIO->new(-format => 'msf',
  		       -file   => Bio::Root::IO->catfile('t',
  							 'data',