[Bioperl-guts-l] bioperl-live/t ProtPsm.t,1.3,1.4

Brian Osborne bosborne at pub.open-bio.org
Thu Oct 21 14:39:35 EDT 2004


Update of /home/repository/bioperl/bioperl-live/t
In directory pub.open-bio.org:/tmp/cvs-serv18197/t

Modified Files:
	ProtPsm.t 
Log Message:
Change number of tests


Index: ProtPsm.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/ProtPsm.t,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** ProtPsm.t	20 Oct 2004 20:25:04 -0000	1.3
--- ProtPsm.t	21 Oct 2004 18:39:33 -0000	1.4
***************
*** 17,21 ****
     use Test;
  
!    plan tests => 1;
  }
  
--- 17,21 ----
     use Test;
  
!    plan tests => 5;
  }
  
***************
*** 27,31 ****
  # Test psiblast reading functionality.
  my $psmIO =  new Bio::Matrix::PSM::IO(-format => 'psiblast', 
! 				      -file   => Bio::Root::IO->catfile(qw(t data atp1.matrix)));
  ok $psmIO;
  
--- 27,31 ----
  # Test psiblast reading functionality.
  my $psmIO =  new Bio::Matrix::PSM::IO(-format => 'psiblast', 
! 			      -file   => Bio::Root::IO->catfile(qw(t data atp1.matrix)));
  ok $psmIO;
  
***************
*** 37,46 ****
  ok $psm->IUPAC, $IUPAC;
  
! ##Lets try to compress and uncompress the log odds and the frequencies, see if there is no
! ##considerable loss of data.
  #my $fA=$psm->get_compressed_freq('A');
  #my @check=Bio::Matrix::PSM::SiteMatrix::_uncompress_string($fA,1,1);
  #my @A=$psm->get_array('A');
  #my ($var,$max) = (0,0);
  #for (my $i = 0; $i<@check;$i++) {
  #  my $diff=abs(abs($check[$i])-abs($A[$i]));
--- 37,48 ----
  ok $psm->IUPAC, $IUPAC;
  
! ## Lets try to compress and uncompress the log odds and the
! ## frequencies, see if there is no considerable loss of data.
! 
  #my $fA=$psm->get_compressed_freq('A');
  #my @check=Bio::Matrix::PSM::SiteMatrix::_uncompress_string($fA,1,1);
  #my @A=$psm->get_array('A');
  #my ($var,$max) = (0,0);
+ 
  #for (my $i = 0; $i<@check;$i++) {
  #  my $diff=abs(abs($check[$i])-abs($A[$i]));
***************
*** 69,73 ****
  #$psm2->matrix($matrix);
  #ok $psm,$psm2;
- 
  
  #ok $IUPAC,'CAGAAAAATWVAATYCCCACCHCCC';
--- 71,74 ----



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