[Bioperl-guts-l] bioperl-live/Bio/Search/Hit GenericHit.pm, 1.45, 1.46

Christopher John Fields cjfields at dev.open-bio.org
Wed Nov 28 16:21:38 EST 2007


Update of /home/repository/bioperl/bioperl-live/Bio/Search/Hit
In directory dev.open-bio.org:/tmp/cvs-serv28569/Bio/Search/Hit

Modified Files:
	GenericHit.pm 
Log Message:
WUBLAST signif gets pvalue, NCBI BLAST signif gets evalue

Index: GenericHit.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Search/Hit/GenericHit.pm,v
retrieving revision 1.45
retrieving revision 1.46
diff -C2 -d -r1.45 -r1.46
*** GenericHit.pm	28 Nov 2007 06:29:03 -0000	1.45
--- GenericHit.pm	28 Nov 2007 21:21:36 -0000	1.46
***************
*** 341,345 ****
          # Set the bits of the Hit to that of the top HSP.
          unless( defined $self->{'_hsps'}->[0] ) {
!             $self->warn("No HSPs for this Hit (".$self->name.")");
              return;
          }   
--- 341,346 ----
          # Set the bits of the Hit to that of the top HSP.
          unless( defined $self->{'_hsps'}->[0] ) {
!             $self->warn("No HSPs for this minimal Hit (".$self->name.")\n".
!                     "If using NCBI BLAST, check bits() instead");
              return;
          }   
***************
*** 408,412 ****
          # Set the bits of the Hit to that of the top HSP.
  	unless( defined $self->{'_hsps'}->[0] ) {
! 	    $self->warn("No HSPs for this Hit (".$self->name.")");
  	    return;
  	}
--- 409,414 ----
          # Set the bits of the Hit to that of the top HSP.
  	unless( defined $self->{'_hsps'}->[0] ) {
! 	    $self->warn("No HSPs for this minimal Hit (".$self->name.")\n".
!                     "If using WU-BLAST, check raw_score() instead");
  	    return;
  	}
***************
*** 628,632 ****
  
      # $val can be zero.
!     if(not defined $val) {
          # P-value not defined, must be a NCBI Blast2 report.
          # Use expect instead.
--- 630,634 ----
  
      # $val can be zero.
!     if(!defined $val) {
          # P-value not defined, must be a NCBI Blast2 report.
          # Use expect instead.



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