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revision 1.68, Fri Nov 16 14:19:38 2007 UTC revision 1.69, Thu Dec 6 13:48:31 2007 UTC
# Line 36  Line 36 
36  =head3 new  =head3 new
37    
38  usage:  usage:
39  C<< my $figfam_obj = FigFam->new($fig, $fam_id, $fam_dir); >>      my $figfam_obj = FigFam->new($fig, $fam_id, $fam_dir);
40    
41  This is the constructor.  Presumably, C<$class> is 'FigFam'.  This is the constructor.  Presumably, C<$class> is 'FigFam'.
42    
# Line 520  Line 520 
520  =head3 reset_function  =head3 reset_function
521    
522  usage:  usage:
523  C<< $figfam_obj->reset_function(); >>      $figfam_obj->reset_function();
524    
525  Resets the function of a FIGfam to its "consensus function,"  Resets the function of a FIGfam to its "consensus function,"
526  where the weight of a vote toward the "consensus" is doubled  where the weight of a vote toward the "consensus" is doubled
# Line 554  Line 554 
554  =head3 display  =head3 display
555    
556  usage:  usage:
557  C<< print $figfam_obj->display(); >>      print $figfam_obj->display();
558    
559  Returns a list-formatted table describing a family and its members.  Returns a list-formatted table describing a family and its members.
560    
# Line 586  Line 586 
586  =head3 pegs_of  =head3 pegs_of
587    
588  usage:  usage:
589  C<< print $figfam_obj->pegs_of(); >>      print $figfam_obj->pegs_of();
590    
591  Returns a list of just pegs.  Returns a list of just pegs.
592    
# Line 603  Line 603 
603    
604  usage:  usage:
605    
606  C<< $seqs_of_members = $figfam_obj->fasta_of(); >>      $seqs_of_members = $figfam_obj->fasta_of();
607    
608  or  or
609    
610  C<< $figfam_obj->fasta_of($filehandle_glob); >>      $figfam_obj->fasta_of($filehandle_glob);
611    
612  Returns a ptr to a hash containing the sequences for all members of a FIGfam,  Returns a ptr to a hash containing the sequences for all members of a FIGfam,
613  keyed by FIG feature ID (FID).  keyed by FIG feature ID (FID).
# Line 648  Line 648 
648  =head3 ok_func  =head3 ok_func
649    
650  usage:  usage:
651  C<< if ( &FigFam::ok_func( $fig, $func, $func2, $id2, $fam) ) { #...do something... } >>      if ( &FigFam::ok_func( $fig, $func, $func2, $id2, $fam) ) { #...do something... }
652    
653  C<$fig> is an object constriucted by C<FIG->new()>.  C<$fig> is an object constriucted by C<FIG->new()>.
654    
# Line 709  Line 709 
709  =head3 member  =head3 member
710    
711  usage:  usage:
712  C<< if ( &FigFam::member($x, \@y)) { #...do something... } >>      if ( &FigFam::member($x, \@y)) { #...do something... }
713    
714  C<$x> is a scalar.  C<$x> is a scalar.
715    
# Line 732  Line 732 
732  =head3 list_members  =head3 list_members
733    
734  usage:  usage:
735  C<< @ids = $figfam_obj->list_members(); >>      @ids = $figfam_obj->list_members();
736    
737  Returns a list of the PEG FIDs in a family.  Returns a list of the PEG FIDs in a family.
738    
# Line 756  Line 756 
756    
757  usage:  usage:
758    
759  C<< if ( &FigFam::loose_same_func($f1, $f2) ) { #...do something... } >>      if ( &FigFam::loose_same_func($f1, $f2) ) { #...do something... }
760    
761  C<$f1> and C<$f2> are function strings.  C<$f1> and C<$f2> are function strings.
762    
# Line 806  Line 806 
806  =head3 should_be_member  =head3 should_be_member
807    
808  usage:  usage:
809  C<< if ( $figfam_obj->should_be_member( $seq ) ) { #...do something... } >>      if ( $figfam_obj->should_be_member( $seq ) ) { #...do something... }
810    
811  Returns ($placed,$sims).  $placed will be  Returns ($placed,$sims).  $placed will be
812  C<TRUE> if the protein sequence in C<$seq> is judged to be  C<TRUE> if the protein sequence in C<$seq> is judged to be
# Line 814  Line 814 
814    
815  I have added the "loose" argument as an optional last argument.  This means that  I have added the "loose" argument as an optional last argument.  This means that
816    
817  C<< if ( $figfam_obj->should_be_member( $seq,0,1 ) ) { #...do something... } >>      if ( $figfam_obj->should_be_member( $seq,0,1 ) ) { #...do something... }
818    
819  will return true, even if the input sequence is truncated (i.e., we do not force the  will return true, even if the input sequence is truncated (i.e., we do not force the
820  similarity to go across 80% of matched sequences in the family).  similarity to go across 80% of matched sequences in the family).
# Line 830  Line 830 
830  =head3 family_function  =head3 family_function
831    
832  usage:  usage:
833  C<< $func = $figfam_obj->family_function(); >>      $func = $figfam_obj->family_function();
834    
835  Returns the "consensus function" assigned to a FIGfam object.  Returns the "consensus function" assigned to a FIGfam object.
836    
# Line 847  Line 847 
847  =head3 family_id  =head3 family_id
848    
849  usage:  usage:
850  C<< $fam_id = $figfam_obj->family_id(); >>      $fam_id = $figfam_obj->family_id();
851    
852  Returns the FIGfam ID of a FIGfam object.  Returns the FIGfam ID of a FIGfam object.
853    
# Line 863  Line 863 
863    
864  usage:  usage:
865    
866  C<< $dir = &FigFam::family_dir( $fam_data, $fam_id ); >>      $dir = &FigFam::family_dir( $fam_data, $fam_id );
867    
868  Returns the path to the subdirectory of C<$fam_data>  Returns the path to the subdirectory of C<$fam_data>
869  that the FIGfam data for a FIGfam with ID C<$fam_id>  that the FIGfam data for a FIGfam with ID C<$fam_id>

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