[Bioperl-guts-l] bioperl-live/Bio/SearchIO blast.pm,1.102,1.103

Christopher John Fields cjfields at dev.open-bio.org
Fri Sep 15 15:31:11 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/SearchIO
In directory dev.open-bio.org:/tmp/cvs-serv32573/Bio/SearchIO

Modified Files:
	blast.pm 
Log Message:
Bug 2091 (second bug)

Index: blast.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/blast.pm,v
retrieving revision 1.102
retrieving revision 1.103
diff -C2 -d -r1.102 -r1.103
*** blast.pm	25 Aug 2006 17:23:47 -0000	1.102
--- blast.pm	15 Sep 2006 19:31:09 -0000	1.103
***************
*** 493,496 ****
--- 493,497 ----
              next unless $1 =~ /Results from round/; 
              $self->debug("blast.pm: Possible psi blast iterations found...\n");
+             
              $self->in_element('hsp')
                && $self->end_element( { 'Name' => 'Hsp' } );
***************
*** 626,630 ****
                      # This to handle no-HSP case
                      my @line = split;
! 
                      # we want to throw away the score, evalue
                      pop @line, pop @line;
--- 627,631 ----
                      # This to handle no-HSP case
                      my @line = split;
!                     
                      # we want to throw away the score, evalue
                      pop @line, pop @line;
***************
*** 638,641 ****
--- 639,643 ----
                      push @hit_signifs,
                        [ $evalue, $score, shift @line, join( ' ', @line ) ];
+                     
                  }
                  elsif (/^CONVERGED/i) {
***************
*** 647,651 ****
                      );
                  }
! 
              }
          }
--- 649,653 ----
                      );
                  }
!                 @hit_signifs = sort {$a->[0] <=> $b->[0]} @hit_signifs;
              }
          }
***************
*** 673,676 ****
--- 675,679 ----
                    [ pop @line, pop @line, shift @line, join( ' ', @line ) ];
              }
+             
          }
          elsif (/^Database:\s*(.+)$/) {
***************
*** 760,764 ****
                  }
              );
! 
              my $v = shift @hit_signifs;
              if ( defined $v ) {
--- 763,768 ----
                  }
              );
!  
!             # add hit significance (from the hit table)
              my $v = shift @hit_signifs;
              if ( defined $v ) {
***************
*** 1421,1425 ****
                              else {
  
-                                 #print STDERR "fields are @fields\n";
                                  for my $type (
                                      qw(length
--- 1425,1428 ----
***************
*** 1973,1976 ****
--- 1976,1980 ----
  sub end_element {
      my ( $self, $data ) = @_;
+     
      my $nm   = $data->{'Name'};
      my $type = $MODEMAP{$nm};



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