use Bio::Type::Sequence;

class Bio::Tools::IUPAC {
 our %IUB = ( 'A' => [< A >],
 'C' => [< C >],
 'G' => [< G >],
 'T' => [< T >],
 'U' => [],
 'M' => [<A C>],
 'R' => [<A G>],
 'W' => [<A T>],
 'S' => [<C G>],
 'Y' => [<C T>],
 'K' => [<G T>],
 'V' => [<A C G>],
 'H' => [<A C T>],
 'D' => [<A G T>],
 'B' => [<C G T>],
 'X' => [<G A T C>],
 'N' => [<G A T C>]
 ); 

 our %REV_IUB =
 ('A' => 'A',
 'T' => 'T',
 'C' => 'C',
 'G' => 'G',
 'AC' => 'M',
 'AG' => 'R',
 'AT' => 'W',
 'CG' => 'S',
 'CT' => 'Y',
 'GT' => 'K',
 'ACG' => 'V',
 'ACT' => 'H',
 'AGT' => 'D',
 'CGT' => 'B',
 'ACGT' => 'N',
 'N' => 'N'
 );


 our %IUP = ('A' => [<A>],
 'B' => [<D N>],
 'C' => [<C>],
 'D' => [<D>],
 'E' => [<E>],
 'F'=> [<F>],
 'G' => [<G>],
 'H' => [<H>],
 'I' => [],
 'J' => [],
 'K' => [<K>],
 'L' => [<L>],
 'M' => [<M>],
 'N' => [<N>],
 'O' => [<O>],
 'P' => [],
 'Q' => [<Q>],
 'R' => [<R>],
 'S' => [<S>],
 'T' => [<T>],
 'U' => [],
 'V' => [<V>],
 'W' => [<W>],
 'X' => [<X>],
 'Y' => [<Y>],
 'Z' => [<E Q>],
 '*' => ['*']
 );

 has $.seq;
 has @.alpha;
 has @.string;

 # should be BUILD? 
 submethod BUILD($self: :$!seq, :$alphabet ) {
 
 my @alpha;
 my @string;
 
 given $!seq.alphabet {
 when ( dna | rna ) {
 @!alpha = map { %IUB{uc($_)} } , comb(/\S/, $!seq.seq); 
 }
 
 when (protein) {
 @!alpha = map { %IUP{uc($_)} } , comb(/\S/, $!seq.seq); 
 }
 
 default {
 die "No alphabet can be determine from seq object";
 }
 }
 @!string = 0 xx $!seq.seq.chars;
 
 @!string.elems == 0 && die "Sequence is length 0";
 @!string[0] = -1;
 
 }
 
 # NOTE: Not really sure of the utility here, this class seems to be more a
 # factory than anything else
 
 #being next_seq
 
 # Title : next_seq
 # Usage : $iupac.next_seq()
 # Function: returns the next unique Seq object
 # Returns : a Seq.pm object
 # Args : none.
 
 
 #end
 
 method next_seq() {
 
 for 0..@!string.end() -> $i {
 next unless @!string[$i] || @!alpha[$i] > 1;
 if ( @!string[$i] == @!alpha[$i].end ) { # rollover
 if ( $i == @!string.end ) { # end of possibilities
 return;
 } else {
 @!string[$i] = 0;
 next;
 }
 }
 else {
 @!string[$i]++;
 my $j = -1;
 $!seq.seq = join('', map { $j++; @!alpha[$j][$_]; } ,@!string);
 my $desc = $!seq.description();
 if ( !defined $desc ) { $desc = ""; }
 
 # no idea why this is needed. No tests are depend on it and seems to have no value to convert
 # leaving it commented for now
 # $self->{'_num'}++;
 # 1 while $self->{'_num'} =~ s/(\d)(\d\d\d)(?!\d)/$1,$2/;
 # $desc =~ s/( \[Bio::Tools::IUPAC-generated\sunique sequence # [^\]]*\])|$/ \[Bio::Tools::IUPAC-generated unique sequence # $self->{'_num'}\]/;
 # $self->{'_SeqObj'}->desc($desc);
 # $self->{'_num'} =~ s/,//g;
 return $!seq;
 }
 }
 }
 
 #begin iupac_iup
 
 # Title : iupac_iup
 # Usage : my %aasymbols = $iupac.iupac_iup
 # Function: Returns a hash of PROTEIN symbols -> symbol components
 # Returns : Hash
 # Args : none
 
 #end
 
 method iupac_iup() {
 return %IUP;
 }
 
 #begin iupac_iub
 
 # Title : iupac_iub
 # Usage : my %dnasymbols = $iupac.iupac_iub
 # Function: Returns a hash of DNA symbols -> symbol components
 # Returns : Hash
 # Args : none
 
 #end
 
 method iupac_iub() {
 return %IUB;
 }
 
 #begin iupac_rev_iub
 
 # Title : iupac_rev_iub
 # Usage : my %dnasymbols = $iupac.iupac_rev_iub
 # Function: Returns a hash of nucleotide combinations -> IUPAC code
 # (a reverse of the iupac_iub hash).
 # Returns : Hash
 # Args : none
 
 #end
 
 method iupac_rev_iub() {
 return %REV_IUB;
 }
 
 #begin count
 
 # Title : count
 # Usage : my $total = $iupac.count();
 # Function: Calculates the number of unique, unambiguous sequences that
 # this ambiguous sequence could generate
 # Return : int
 # Args : none
 
 #end
 
 method count() {
 my $count = 1;
 $count *= $_.elems for @!alpha;
 return $count;
 }



}

# # $Id: IUPAC.pm 15549 2009-02-21 00:48:48Z maj $
# #
# # BioPerl module for IUPAC
# #
# # Please direct questions and support issues to <bioperl-l@bioperl.org> 
# #
# # Cared for by Aaron Mackey <amackey@virginia.edu>
# #
# # Copyright Aaron Mackey
# #
# # You may distribute this module under the same terms as perl itself

# # POD documentation - main docs before the code

#

head


# Bio::Tools::IUPAC - Generates unique Seq objects from an ambiguous Seq object

# 


#  use Bio::Seq;
#  use Bio::Tools::IUPAC;

#  my $ambiseq = Bio::Seq->new(-seq => 'ARTCGUTGR', -alphabet => 'dna');
#  my $stream  = Bio::Tools::IUPAC->new(-seq => $ambiseq);

#  while ($uniqueseq = $stream->next_seq()) {
#      # process the unique Seq object.
#  }

# 


# IUPAC is a tool that produces a stream of unique, "strict"-satisfying Seq
# objects from an ambiquous Seq object (containing non-standard characters given
# the meaning shown below)

#         Extended DNA / RNA alphabet :
#         (includes symbols for nucleotide ambiguity)
#         ------------------------------------------
#         Symbol       Meaning      Nucleic Acid
#         ------------------------------------------
#          A            A           Adenine
#          C            C           Cytosine
#          G            G           Guanine
#          T            T           Thymine
#          U            U           Uracil
#          M          A or C
#          R          A or G
#          W          A or T
#          S          C or G
#          Y          C or T
#          K          G or T
#          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

#         IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE:
#           Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030.

# -----------------------------------

#        Amino Acid alphabet:
#         ------------------------------------------
#         Symbol           Meaning
#         ------------------------------------------
#         A        Alanine
#         B        Aspartic Acid, Asparagine
#         C        Cystine
#         D        Aspartic Acid
#         E        Glutamic Acid
#         F        Phenylalanine
#         G        Glycine
#         H        Histidine
#         I        Isoleucine
#         J        Isoleucine/Leucine
#         K        Lysine
#         L        Leucine
#         M        Methionine
#         N        Asparagine
#         O        Pyrrolysine
#         P        Proline
#         Q        Glutamine
#         R        Arginine
#         S        Serine
#         T        Threonine
#         U        Selenocysteine
#         V        Valine
#         W        Tryptophan
#         X        Unknown
#         Y        Tyrosine
#         Z        Glutamic Acid, Glutamine
#         *        Terminator


#         IUPAC-IUP AMINO ACID SYMBOLS:
#           Biochem J. 1984 Apr 15; 219(2): 345-373
#           Eur J Biochem. 1993 Apr 1; 213(1): 2

# 


# 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

# 

# Please direct usage questions or support issues to the mailing list:
 
# L<bioperl-l@bioperl.org>
 
# 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.

#


# 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/

# 


# The rest of the documentation details each of the object
# methods. Internal methods are usually preceded with a _

# =cut


# Let the code begin...


root

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IUPAC

NAME

SYNOPSIS

DESCRIPTION

FEEDBACK

Mailing Lists

Support

Reporting Bugs

AUTHOR - Aaron Mackey

APPENDIX