# $Id: SeqPattern.pm 16139 2009-09-18 21:11:23Z cjfields $ # # bioperl module for Bio::Tools::SeqPattern # # Please direct questions and support issues to # # Cared for by Steve Chervitz (sac-at-bioperl.org) # # Copyright Steve Chervitz # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::SeqPattern - represent a sequence pattern or motif =head1 SYNOPSIS use Bio::Tools::SeqPattern; my $pat1 = 'T[GA]AA...TAAT'; my $pattern1 = Bio::Tools::SeqPattern->new(-SEQ =>$pat1, -TYPE =>'Dna'); my $pat2 = '[VILM]R(GXX){3,2}...[^PG]'; my $pattern2 = Bio::Tools::SeqPattern->new(-SEQ =>$pat2, -TYPE =>'Amino'); =head1 DESCRIPTION L module encapsulates generic data and methods for manipulating regular expressions describing nucleic or amino acid sequence patterns (a.k.a, "motifs"). L is a concrete class that inherits from L. This class grew out of a need to have a standard module for doing routine tasks with sequence patterns such as: -- Forming a reverse-complement version of a nucleotide sequence pattern -- Expanding patterns containing ambiguity codes -- Checking for invalid regexp characters -- Untainting yet preserving special characters in the pattern Other features to look for in the future: -- Full pattern syntax checking -- Conversion between expanded and condensed forms of the pattern =head1 MOTIVATIONS A key motivation for L is to have a way to generate a reverse complement of a nucleotide sequence pattern. This makes possible simultaneous pattern matching on both sense and anti-sense strands of a query sequence. In principle, one could do such a search more inefficiently by testing against both sense and anti-sense versions of a sequence. It is entirely equivalent to test a regexp containing both sense and anti-sense versions of the *pattern* against one copy of the sequence. The latter approach is much more efficient since: 1) You need only one copy of the sequence. 2) Only one regexp is executed. 3) Regexp patterns are typically much smaller than sequences. Patterns can be quite complex and it is often difficult to generate the reverse complement pattern. The Bioperl SeqPattern.pm addresses this problem, providing a convenient set of tools for working with biological sequence regular expressions. Not all patterns have been tested. If you discover a pattern that is not handled properly by Bio::Tools::SeqPattern.pm, please send me some email (sac@bioperl.org). Thanks. =head1 OTHER FEATURES =head2 Extended Alphabet Support This module supports the same set of ambiguity codes for nucleotide sequences as supported by L. These ambiguity codes define the behavior or the L method. ------------------------------------------ Symbol Meaning Nucleic Acid ------------------------------------------ A A (A)denine C C (C)ytosine G G (G)uanine T T (T)hymine U U (U)racil M A or C a(M)ino group R A or G pu(R)ine W A or T (W)eak bond S C or G (S)trong bond Y C or T p(Y)rimidine K G or T (K)eto group V A or C or G H A or C or T D A or G or T B C or G or T X G or A or T or C N G or A or T or C . G or A or T or C ------------------------------------------ Symbol Meaning ------------------------------------------ A Alanine C Cysteine D Aspartic Acid E Glutamic Acid F Phenylalanine G Glycine H Histidine I Isoleucine K Lysine L Leucine M Methionine N Asparagine P Proline Q Glutamine R Arginine S Serine T Threonine V Valine W Tryptophan Y Tyrosine B Aspartic Acid, Asparagine Z Glutamic Acid, Glutamine X Any amino acid . Any amino acid =head2 Multiple Format Support Ultimately, this module should be able to build SeqPattern.pm objects using a variety of pattern formats such as ProSite, Blocks, Prints, GCG, etc. Currently, this module only supports patterns using a grep-like syntax. =head1 USAGE A simple demo script called seq_pattern.pl is included in the examples/ directory of the central Bioperl distribution. =head1 SEE ALSO L - Lightweight sequence object. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.open-bio.org/ =head1 AUTHOR Steve Chervitz, sac-at-bioperl.org =head1 COPYRIGHT Copyright (c) 1997-8 Steve Chervitz. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =cut # ## ### #### END of main POD documentation. ### ## #' # CREATED : 28 Aug 1997 package Bio::Tools::SeqPattern; use base qw(Bio::Root::Root); use strict; use vars qw ($ID); $ID = 'Bio::Tools::SeqPattern'; ## These constants may be more appropriate in a Bio::Dictionary.pm ## type of class. my $PURINES = 'AG'; my $PYRIMIDINES = 'CT'; my $BEE = 'DN'; my $ZED = 'EQ'; my $Regexp_chars = '\w,.\*()\[\]<>\{\}^\$'; # quoted for use in regexps ## Package variables used in reverse complementing. my (%Processed_braces, %Processed_asterics); ##################################################################################### ## CONSTRUCTOR ## ##################################################################################### =head1 new Title : new Usage : my $seqpat = Bio::Tools::SeqPattern->new(); Purpose : Verifies that the type is correct for superclass (Bio::Seq.pm) : and calls superclass constructor last. Returns : n/a Argument : Parameters passed to new() Throws : Exception if the pattern string (seq) is empty. Comments : The process of creating a new SeqPattern.pm object : ensures that the pattern string is untained. See Also : L, L =cut #---------------- sub new { #---------------- my($class, %param) = @_; my $self = $class->SUPER::new(%param); my ($seq,$type) = $self->_rearrange([qw(SEQ TYPE)], %param); $seq || $self->throw("Empty pattern."); my $t; # Get the type ready for Bio::Seq.pm if ($type =~ /nuc|[dr]na/i) { $t = 'Dna'; } elsif ($type =~ /amino|pep|prot/i) { $t = 'Amino'; } $seq =~ tr/a-z/A-Z/; #ps 8/8/00 Canonicalize to upper case $self->str($seq); $self->type($t); return $self; } =head1 alphabet_ok Title : alphabet_ok Usage : $mypat->alphabet_ok; Purpose : Checks for invalid regexp characters. : Overrides Bio::Seq::alphabet_ok() to allow : additional regexp characters ,.*()[]<>{}^$ : in addition to the standard genetic alphabet. : Also untaints the pattern and sets the sequence : object's sequence to the untained string. Returns : Boolean (1 | 0) Argument : n/a Throws : Exception if the pattern contains invalid characters. Comments : Does not call the superclass method. : Actually permits any alphanumeric, not just the : standard genetic alphabet. =cut #----------------' sub alphabet_ok { #---------------- my( $self) = @_; return 1 if $self->{'_alphabet_checked'}; $self->{'_alphabet_checked'} = 1; my $pat = $self->seq(); if($pat =~ /[^$Regexp_chars]/io) { $self->throw("Pattern contains invalid characters: $pat", 'Legal characters: a-z,A-Z,0-9,,.*()[]<>{}^$ '); } # Untaint pattern (makes code taint-safe). $pat =~ /([$Regexp_chars]+)/io; $self->setseq(uc($1)); # print STDERR "\npattern ok: $pat\n"; 1; } =head1 expand Title : expand Usage : $seqpat_object->expand(); Purpose : Expands the sequence pattern using special ambiguity codes. Example : $pat = $seq_pat->expand(); Returns : String containing fully expanded sequence pattern Argument : n/a Throws : Exception if sequence type is not recognized : (i.e., is not one of [DR]NA, Amino) See Also : L, L<_expand_pep>(), L<_expand_nuc>() =cut #---------- sub expand { #---------- my $self = shift; if($self->type =~ /[DR]na/i) { $self->_expand_nuc(); } elsif($self->type =~ /Amino/i) { $self->_expand_pep(); } else{ $self->throw("Don't know how to expand ${\$self->type} patterns.\n"); } } =head1 _expand_pep Title : _expand_pep Usage : n/a; automatically called by expand() Purpose : Expands peptide patterns Returns : String (the expanded pattern) Argument : String (the unexpanded pattern) Throws : n/a See Also : L(), L<_expand_nuc>() =cut #---------------- sub _expand_pep { #---------------- my ($self,$pat) = @_; $pat ||= $self->str; $pat =~ s/X/./g; $pat =~ s/^$/\$/; ## Avoid nested situations: [bmnq] --/--> [[$ZED]mnq] ## Yet correctly deal with: fze[bmnq] ---> f[$BEE]e[$ZEDmnq] if($pat =~ /\[\w*[BZ]\w*\]/) { $pat =~ s/\[(\w*)B(\w*)\]/\[$1$ZED$2\]/g; $pat =~ s/\[(\w*)Z(\w*)\]/\[$1$BEE$2\]/g; $pat =~ s/B/\[$ZED\]/g; $pat =~ s/Z/\[$BEE\]/g; } else { $pat =~ s/B/\[$ZED\]/g; $pat =~ s/Z/\[$BEE\]/g; } $pat =~ s/\((.)\)/$1/g; ## Doing these last since: $pat =~ s/\[(.)\]/$1/g; ## Pattern could contain [B] (for example) return $pat; } =head1 _expand_nuc Title : _expand_nuc Purpose : Expands nucleotide patterns Returns : String (the expanded pattern) Argument : String (the unexpanded pattern) Throws : n/a See Also : L(), L<_expand_pep>() =cut #--------------- sub _expand_nuc { #--------------- my ($self,$pat) = @_; $pat ||= $self->str; $pat =~ s/N|X/./g; $pat =~ s/pu/R/ig; $pat =~ s/py/Y/ig; $pat =~ s/U/T/g; $pat =~ s/^$/\$/; ## Avoid nested situations: [ya] --/--> [[ct]a] ## Yet correctly deal with: sg[ya] ---> [gc]g[cta] if($pat =~ /\[\w*[RYSWMK]\w*\]/) { $pat =~ s/\[(\w*)R(\w*)\]/\[$1$PURINES$2\]/g; $pat =~ s/\[(\w*)Y(\w*)\]/\[$1$PYRIMIDINES$2\]/g; $pat =~ s/\[(\w*)S(\w*)\]/\[$1GC$2\]/g; $pat =~ s/\[(\w*)W(\w*)\]/\[$1AT$2\]/g; $pat =~ s/\[(\w*)M(\w*)\]/\[$1AC$2\]/g; $pat =~ s/\[(\w*)K(\w*)\]/\[$1GT$2\]/g; $pat =~ s/\[(\w*)V(\w*)\]/\[$1ACG$2\]/g; $pat =~ s/\[(\w*)H(\w*)\]/\[$1ACT$2\]/g; $pat =~ s/\[(\w*)D(\w*)\]/\[$1AGT$2\]/g; $pat =~ s/\[(\w*)B(\w*)\]/\[$1CGT$2\]/g; $pat =~ s/R/\[$PURINES\]/g; $pat =~ s/Y/\[$PYRIMIDINES\]/g; $pat =~ s/S/\[GC\]/g; $pat =~ s/W/\[AT\]/g; $pat =~ s/M/\[AC\]/g; $pat =~ s/K/\[GT\]/g; $pat =~ s/V/\[ACG\]/g; $pat =~ s/H/\[ACT\]/g; $pat =~ s/D/\[AGT\]/g; $pat =~ s/B/\[CGT\]/g; } else { $pat =~ s/R/\[$PURINES\]/g; $pat =~ s/Y/\[$PYRIMIDINES\]/g; $pat =~ s/S/\[GC\]/g; $pat =~ s/W/\[AT\]/g; $pat =~ s/M/\[AC\]/g; $pat =~ s/K/\[GT\]/g; $pat =~ s/V/\[ACG\]/g; $pat =~ s/H/\[ACT\]/g; $pat =~ s/D/\[AGT\]/g; $pat =~ s/B/\[CGT\]/g; } $pat =~ s/\((.)\)/$1/g; ## Doing thses last since: $pat =~ s/\[(.)\]/$1/g; ## Pattern could contain [y] (for example) return $pat; } =head1 revcom Title : revcom Usage : revcom([1]); Purpose : Forms a pattern capable of recognizing the reverse complement : version of a nucleotide sequence pattern. Example : $pattern_object->revcom(); : $pattern_object->revcom(1); ## returns expanded rev complement pattern. Returns : Object reference for a new Bio::Tools::SeqPattern containing : the revcom of the current pattern as its sequence. Argument : (1) boolean (optional) (default= false) : true : expand the pattern before rev-complementing. : false: don't expand pattern before or after rev-complementing. Throws : Exception if called for amino acid sequence pattern. Comments : This method permits the simultaneous searching of both : sense and anti-sense versions of a nucleotide pattern : by means of a grep-type of functionality in which any : number of patterns may be or-ed into the recognition : pattern. : Overrides Bio::Seq::revcom() and calls it first thing. : The order of _fixpat() calls is critical. See Also : L, L, L, L, L, L =cut #-----------' sub revcom { #----------- my($self,$expand) = @_; if ($self->type !~ /Dna|Rna/i) { $self->throw("Can't get revcom for ${\$self->type} sequence types.\n"); } # return $self->{'_rev'} if defined $self->{'_rev'}; $expand ||= 0; my $str = $self->str; $str =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; my $rev = CORE::reverse $str; $rev =~ tr/[](){}<>/][)(}{>_expand_nuc($rev); # print "\nExpanded: $rev\n"; } %Processed_braces = (); %Processed_asterics = (); my $fixrev = _fixpat_1($rev); # print "FIX 1: $fixrev";; $fixrev = _fixpat_2($fixrev); # print "FIX 2: $fixrev";; $fixrev = _fixpat_3($fixrev); # print "FIX 3: $fixrev";; $fixrev = _fixpat_4($fixrev); # print "FIX 4: $fixrev";; $fixrev = _fixpat_5($fixrev); # print "FIX 5: $fixrev";; ##### Added by ps 8/7/00 to allow non-greedy matching $fixrev = _fixpat_6($fixrev); # print "FIX 6: $fixrev";; # $self->{'_rev'} = $fixrev; return new Bio::Tools::SeqPattern(-seq =>$fixrev, -type =>$self->type); } =head1 backtranslate Title : backtranslate Usage : backtranslate(); Purpose : Produce a degenerate oligonucleotide whose translation would produce : the original protein motif. Example : $pattern_object->backtranslate(); Returns : Object reference for a new Bio::Tools::SeqPattern containing : the reverse translation of the current pattern as its sequence. Throws : Exception if called for nucleotide sequence pattern. =cut sub backtranslate { my $self = shift; # _load_module loads dynamically, caches call if successful $self->_load_module('Bio::Tools::SeqPattern::Backtranslate'); Bio::Tools::SeqPattern::Backtranslate->import("_reverse_translate_motif"); if ($self->type ne 'Amino') { $self->throw( "Can't get backtranslate for ${\$self->type} sequence types.\n" ); } return __PACKAGE__->new( -SEQ => _reverse_translate_motif($self->str), -TYPE => 'Dna', ); } =head1 _fixpat_1 Title : _fixpat_1 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all {7,5} --> {5,7} (Part I) : and [T^] --> [^T] (Part II) : and *N --> N* (Part III) Returns : String (the new, partially reversed pattern) Argument : String (the expanded pattern) Throws : n/a See Also : L() =cut #-------------- sub _fixpat_1 { #-------------- my $pat = shift; ## Part I: my (@done,@parts); while(1) { $pat =~ /(.*)\{(\S+?)\}(.*)/ or do{ push @done, $pat; last; }; $pat = $1.'#{'.reverse($2).'}'.$3; # print "1: $1\n2: $2\n3: $3\n"; # print "modified pat: $pat";; @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";; last if not $pat; } $pat = join('', reverse @done); ## Part II: @done = (); while(1) { $pat =~ /(.*)\[(\S+?)\](.*)/ or do{ push @done, $pat; last; }; $pat = $1.'#['.reverse($2).']'.$3; # print "1: $1\n2: $2\n3: $3\n"; # print "modified pat: $pat";; @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";; last if not $pat; } $pat = join('', reverse @done); ## Part III: @done = (); while(1) { $pat =~ /(.*)\*([\w.])(.*)/ or do{ push @done, $pat; last; }; $pat = $1.'#'.$2.'*'.$3; $Processed_asterics{$2}++; # print "1: $1\n2: $2\n3: $3\n"; # print "modified pat: $pat";; @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";; last if not $pat; } return join('', reverse @done); } =head1 _fixpat_2 Title : _fixpat_2 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all {5,7}Y ---> Y{5,7} : and {10,}. ---> .{10,} Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : L() =cut #-------------- sub _fixpat_2 { #-------------- my $pat = shift; local($^W) = 0; my (@done,@parts,$braces); while(1) { # $pat =~ s/(.*)([^])])(\{\S+?\})([\w.])(.*)/$1$2#$4$3$5/ or do{ push @done, $pat; last; }; $pat =~ s/(.*)(\{\S+?\})([\w.])(.*)/$1#$3$2$4/ or do{ push @done, $pat; last; }; $braces = $2; $braces =~ s/[{}]//g; $Processed_braces{"$3$braces"}++; # print "modified pat: $pat";; @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";; last if not $pat; } return join('', reverse @done); } =head1 _fixpat_3 Title : _fixpat_3 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all {5,7}(XXX) ---> (XXX){5,7} Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : L() =cut #------------- sub _fixpat_3 { #------------- my $pat = shift; my (@done,@parts,$braces,$newpat,$oldpat); while(1) { # $pat =~ s/(.+)(\{\S+\})(\(\w+\))(.*)/$1#$3$2$4/ or do{ push @done, $pat; last; }; if( $pat =~ /(.*)(.)(\{\S+\})(\(\w+\))(.*)/) { $newpat = "$1#$2$4$3$5"; ##ps $oldpat = "$1#$2$3$4$5"; # print "1: $1\n2: $2\n3: $3\n4: $4\n5: $5\n"; ##ps $braces = $3; ##ps $braces =~ s/[{}]//g; ##ps if( exists $Processed_braces{"$2$braces"} || exists $Processed_asterics{$2}) { ##ps $pat = $oldpat; # Don't change it. Already processed. # print "saved pat: $pat";; ##ps } else { # print "new pat: $newpat";; $pat = $newpat; # Change it. ##ps } } elsif( $pat =~ /^(\{\S+\})(\(\w+\))(.*)/) { $pat = "#$2$1$3"; } else { push @done, $pat; last; } @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";; last if not $pat; } return join('', reverse @done); } =head1 _fixpat_4 Title : _fixpat_4 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all {5,7}[XXX] ---> [XXX]{5,7} Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : L() =cut #--------------- sub _fixpat_4 { #--------------- my $pat = shift; my (@done,@parts,$braces,$newpat,$oldpat); while(1) { # $pat =~ s/(.*)(\{\S+\})(\[\w+\])(.*)/$1#$3$2$4/ or do{ push @done, $pat; last; }; # $pat =~ s/(.*)([^\w.])(\{\S+\})(\[\w+\])(.*)/$1$2#$4$3$5/ or do{ push @done, $pat; last; }; if( $pat =~ /(.*)(.)(\{\S+\})(\[\w+\])(.*)/) { $newpat = "$1#$2$4$3$5"; $oldpat = "$1#$2$3$4$5"; # print "1: $1\n2: $2\n3: $3\n4: $4\n5: $5\n"; $braces = $3; $braces =~ s/[{}]//g; if( (defined $braces and defined $2) and exists $Processed_braces{"$2$braces"} || exists $Processed_asterics{$2}) { $pat = $oldpat; # Don't change it. Already processed. # print "saved pat: $pat";; } else { $pat = $newpat; # Change it. # print "new pat: $pat";; } } elsif( $pat =~ /^(\{\S+\})(\[\w+\])(.*)/) { $pat = "#$2$1$3"; } else { push @done, $pat; last; } @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";; last if not $pat; } return join('', reverse @done); } =head1 _fixpat_5 Title : _fixpat_5 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all *[XXX] ---> [XXX]* : and *(XXX) ---> (XXX)* Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : L() =cut #-------------- sub _fixpat_5 { #-------------- my $pat = shift; my (@done,@parts,$newpat,$oldpat); while(1) { # $pat =~ s/(.*)(\{\S+\})(\[\w+\])(.*)/$1#$3$2$4/ or do{ push @done, $pat; last; }; # $pat =~ s/(.*)([^\w.])(\{\S+\})(\[\w+\])(.*)/$1$2#$4$3$5/ or do{ push @done, $pat; last; }; if( $pat =~ /(.*)(.)\*(\[\w+\]|\(\w+\))(.*)/) { $newpat = "$1#$2$3*$4"; $oldpat = "$1#$2*$3$4"; # print "1: $1\n2: $2\n3: $3\n4: $4\n"; if( exists $Processed_asterics{$2}) { $pat = $oldpat; # Don't change it. Already processed. # print "saved pat: $pat";; } else { $pat = $newpat; # Change it. # print "new pat: $pat";; } } elsif( $pat =~ /^\*(\[\w+\]|\(\w+\))(.*)/) { $pat = "#$1*$3"; } else { push @done, $pat; last; } @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";; last if not $pat; } return join('', reverse @done); } ############################ # # PS: Added 8/7/00 to allow non-greedy matching patterns # ###################################### =head1 _fixpat_6 Title : _fixpat_6 Usage : n/a; called automatically by revcom() Purpose : Utility method for revcom() : Converts all ?Y{5,7} ---> Y{5,7}? : and ?(XXX){5,7} ---> (XXX){5,7}? : and ?[XYZ]{5,7} ---> [XYZ]{5,7}? Returns : String (the new, partially reversed pattern) Argument : String (the expanded, partially reversed pattern) Throws : n/a See Also : L() =cut #-------------- sub _fixpat_6 { #-------------- my $pat = shift; my (@done,@parts); @done = (); while(1) { $pat =~ /(.*)\?(\[\w+\]|\(\w+\)|\w)(\{\S+?\})?(.*)/ or do{ push @done, $pat; last; }; my $quantifier = $3 ? $3 : ""; # Shut up warning if no explicit quantifier $pat = $1.'#'.$2.$quantifier.'?'.$4; # $pat = $1.'#'.$2.$3.'?'.$4; # print "1: $1\n2: $2\n3: $3\n"; # print "modified pat: $pat";; @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";; last if not $pat; } return join('', reverse @done); } =head2 str Title : str Usage : $obj->str($newval) Function: Returns : value of str Args : newvalue (optional) =cut sub str{ my $obj = shift; if( @_ ) { my $value = shift; $obj->{'str'} = $value; } return $obj->{'str'}; } =head2 type Title : type Usage : $obj->type($newval) Function: Returns : value of type Args : newvalue (optional) =cut sub type{ my $obj = shift; if( @_ ) { my $value = shift; $obj->{'type'} = $value; } return $obj->{'type'}; } 1; __END__ ######################################################################### # End of class ######################################################################### =head1 FOR DEVELOPERS ONLY =head2 Data Members Information about the various data members of this module is provided for those wishing to modify or understand the code. Two things to bear in mind: =over 2 =item 1 Do NOT rely on these in any code outside of this module. All data members are prefixed with an underscore to signify that they are private. Always use accessor methods. If the accessor doesn't exist or is inadequate, create or modify an accessor (and let me know, too!). =item 2 This documentation may be incomplete and out of date. It is easy for this documentation to become obsolete as this module is still evolving. Always double check this info and search for members not described here. =back An instance of Bio::Tools::RestrictionEnzyme.pm is a blessed reference to a hash containing all or some of the following fields: FIELD VALUE ------------------------------------------------------------------------ _rev : The corrected reverse complement of the fully expanded pattern. INHERITED DATA MEMBERS: _seq : (From Bio::Seq.pm) The original, unexpanded input sequence after untainting. _type : (From Bio::Seq.pm) 'Dna' or 'Amino' =cut