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revision 1.39, Tue Mar 16 19:50:43 2010 UTC revision 1.40, Tue Mar 16 20:24:05 2010 UTC
# Line 613  Line 613 
613    
614  =head3 ReadGeneCorrespondenceFile  =head3 ReadGeneCorrespondenceFile
615    
616      my $list = ServerThing::ReadGeneCorrespondenceFile($fileName, $converse);      my $list = ServerThing::ReadGeneCorrespondenceFile($fileName, $converse, $all);
617    
618  Return the contents of the specified gene correspondence file in the form of  Return the contents of the specified gene correspondence file in the form of
619  a list of lists, with backward correspondences filtered out. If the file is  a list of lists, with backward correspondences filtered out. If the file is
# Line 633  Line 633 
633  If TRUE, the file columns will be reorderd automatically. The default is FALSE,  If TRUE, the file columns will be reorderd automatically. The default is FALSE,
634  meaning we want to use the file as it appears on disk.  meaning we want to use the file as it appears on disk.
635    
636    =item all (optional)
637    
638    TRUE if backward unidirectional correspondences should be included in the output.
639    The default is FALSE, in which case only forward and bidirectional correspondences
640    are included.
641    
642  =item RETURN  =item RETURN
643    
644  Returns a L</Gene Correspondence List> in the form of a reference to a list of lists.  Returns a L</Gene Correspondence List> in the form of a reference to a list of lists.
# Line 645  Line 651 
651    
652  sub ReadGeneCorrespondenceFile {  sub ReadGeneCorrespondenceFile {
653      # Get the parameters.      # Get the parameters.
654      my ($fileName, $converse) = @_;      my ($fileName, $converse, $all) = @_;
655      # Declare the return variable. We will only put something in here if we are      # Declare the return variable. We will only put something in here if we are
656      # completely successful.      # completely successful.
657      my $retVal;      my $retVal;
# Line 681  Line 687 
687              $error = 1;              $error = 1;
688          }          }
689          # If this row is in the correct direction, keep it.          # If this row is in the correct direction, keep it.
690          if ($row[8] ne '<-') {          if ($all || $row[8] ne '<-') {
691              push @corrList, \@row;              push @corrList, \@row;
692          }          }
693      }      }

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