class Bio::LiveSeq::Mutation {
#in good time we will finally have a Root
#use base qw(Bio::Root::Root);

method new(*%args) {
    #if len of zero given, we ignore it
    if (%args.exists('len') && %args{'len'} == 0 ) {
        %args.delete('len');
    }
    return self.bless(*,|%args);
}

# 

head


#  Title   : seq
#  Usage   : $obj.seq();
#  Function: 

#             Sets and returns the mutated sequence. No checking is done
#             to validate the symbols.

#  Example : 
#  Returns : string
#  Args    : integer

# =cut

has $!seq is rw;
method seq($value?) {
     if ( defined $value) {
 	$!seq = $value;
     }
     return $!seq || '';
}


# 


#  Title   : seqori
#  Usage   : $obj.seqori();
#  Function: 

#             Sets and returns the original subsequence in the reference
#             sequence. No checking is done to validate the symbols.
#             Optional value.

#  Example : 
#  Returns : string
#  Args    : string

# =cut

has $!seqori is rw;
method seqori($value?) {
    if ( defined $value) {
 	$!seqori = $value;
    }
    return $!seqori || '';
}


# 


#  Title   : pos
#  Usage   : $obj.pos();
#  Function: 

#             Sets and returns the position of the first element in the
#             sequence.

#  Example : 
#  Returns : string
#  Args    : integer

# =cut

has $!pos is rw;
method pos($value?) {
    if ( defined $value) {
	if ( $value !~~ /^(<[\+\-]>)? \d+ $/ ) {
            die "'$value' for pos has to be an integer";
	    self.throw("[$value] for pos has to be an integer\n");
	} else {
	    $!pos = $value;
	}
    }
    return $!pos;
}

# 


#  Title   : len
#  Usage   : $obj.len();
#  Function: 

#             Sets and returns the len of the affected original allele
#             sequence.  If value is not set, defaults to the lenght of
#             the mutated sequence (seq).

#  Example : 
#  Returns : string
#  Args    : string

# =cut
has $!len is rw;

method len($value?) {
    if ( defined $value) {
        $!len = $value;
    }
    if ( ! (defined $!len ) ) {
        return $!seq.chars;
    }
    return $!len;
}

# 


#  Title   : label
#  Usage   : $obj.label();
#  Function: 

#             Sets and returns the label of the affected original allele
#             location. Label is a stable identifier whereas location
#             can be changed by mutations. Label comes from
#             l<Bio::LiveSeq::Gene>.

#  Example : 
#  Returns : string
#  Args    : string

# =cut

has $!label is rw;
method label($value?) {
   if ( defined $value) {
       $!label = $value;
   }
   if ( ! defined $!label ) {
       return;
   } 
   return $!label;
}


# 


#  Title   : transpos
#  Usage   : $obj.transpos();
#  Function: 

#             Sets and returns the transcript position of the mutation.
#             Set when associated with a reference sequence. Value
#             depends on reference molecule and the co-ordinate system
#             used.

#  Example : 
#  Returns : string
#  Args    : integer

# =cut

has $!transpos is rw;

method transpos($value?) {
    if ( defined $value) {
 	if ( $value !~~ /^ (<[\+\-]>)? \d+ $/ ) {
            die "'$value' for transpos has to be an integer";
# 	    self.throw("[$value] for transpos has to be an integer\n");
 	} else {
 	    $!transpos = $value;
 	}
    }
    return $!transpos;
}


# 


#  Title   : issue
#  Usage   : $obj.issue();
#  Function: 

#             Sets and returns the position of the mutation in an array
#             of mutations to be issued. Set after the validity of the
#             mutation has been confirmed.

#  Example : 
#  Returns : string
#  Args    : integer

# =cut

has $!issue is rw;
method issue($value?) {
     if ( defined $value) {
 	if ( $value !~~ /^(<[\+\-]>)? \d+ $/ ) {
            die "'$value' for issue has to be an integer";
# 	    self.throw("[$value] for issue has to be an integer\n");
 	} else {
 	    $!issue = $value;
 	}
     }
     return $!issue;
}


# 


#  Title   : prelabel
#  Usage   : $obj.prelabel();
#  Function: 

#             Sets and returns the prelabel of the affected original allele
#             location. Prelabel is a stable identifier whereas location
#             can be changed by mutations. Prelabel comes from
#             l<Bio::LiveSeq::Gene>.

#  Example : 
#  Returns : string
#  Args    : string

# =cut

has $!prelabel is rw;
method prelabel($value?) {
    if ( defined $value) {
        $!prelabel = $value;
    }
    if ( ! defined $!prelabel ) {
        return;
    } 
    return $!prelabel;
}


# 


#  Title   : postlabel
#  Usage   : $obj.postlabel();
#  Function: 

#             Sets and returns the postlabel of the affected original allele
#             location. Postlabel is a stable identifier whereas location
#             can be changed by mutations. Postlabel comes from
#             l<Bio::LiveSeq::Gene>.

#  Example : 
#  Returns : string
#  Args    : string

# =cut

has $!postlabel is rw;
method postlabel($value?) {
    if ( defined $value) {
        $!postlabel = $value;
    }
    if ( ! defined $!postlabel ) {
        return;
    } 
    return $!postlabel;
}


# 


#  Title   : lastlabel
#  Usage   : $obj.lastlabel();
#  Function: 

#             Sets and returns the lastlabel of the affected original allele
#             location. Lastlabel is a stable identifier whereas location
#             can be changed by mutations. Lastlabel comes from
#             l<Bio::LiveSeq::Gene>.

#  Example : 
#  Returns : string
#  Args    : string

# =cut

has $!lastlabel is rw;
method lastlabel($value?) {
    if ( defined $value) {
        $!lastlabel = $value;
    }
    if ( ! defined $!lastlabel ) {
        return;
    } 
    return $!lastlabel;
}

}

# # $Id: Mutation.pm 16123 2009-09-17 12:57:27Z cjfields $
# #
# # BioPerl module for Bio::LiveSeq::Mutation
# #
# # Please direct questions and support issues to <bioperl-l@bioperl.org> 
# #
# # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
# #
# # Copyright Heikki Lehvaslaiho
# #
# # You may distribute this module under the same terms as perl itself

# # POD documentation - main docs before the code

# 


# Bio::LiveSeq::Mutation - Mutation event descriptor class

# 


#   # full descrition of a point mutation
#   $mutation1a = Bio::LiveSeq::Mutation.new ( -seq => 'A',
# 					      -seqori => 'T',
# 					      -pos  => 100,
# 					      -len => 1 # optional, defaults to length(seq)
# 					     );

#   # minimal information for a point mutation
#   $mutation1b = Bio::LiveSeq::Mutation.new ( -seq => 'A',
# 					      -pos  => 100
# 					      );
#   # insertion
#   $mutation2 = Bio::LiveSeq::Mutation.new ( -seq => 'ATT',
# 					     -pos  => 100,
# 					     -len => 0
# 					     );
#   # deletion
#   $mutation3 = Bio::LiveSeq::Mutation.new ( -seq => '',  # optional
# 					     -seqori => 'TTG',  # optional
# 					     -pos  => 100
# 					     -len => 3
# 					     );
#   # complex
#   $mutation4 = Bio::LiveSeq::Mutation.new ( -seq => 'CC', 
# 					     -seqori => 'TTG',  # optional
# 					     -pos  => 100
# 					     -len => 3
# 					     );


# 


# This class describes a local mutation event using minimalistic
# description.  It is not necessary to know anything about the original
# sequence. You need to give the changed sequence, the position of the
# mutation in the (unidentified) reference sequence, and the length of
# the affected subsequence in the reference sequence. If the original
# allele sequence is given, the objects applying the mutation into the
# reference sequence (e.g. L<Bio::LiveSeq::Mutator>) might check for its
# validity.

# 


# User feedback is an integral part of the evolution of this and other
# Bioperl modules. Send your comments and suggestions preferably to 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:

# I<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


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Mutation

seq

seqori

pos

len

label

transpos

issue

prelabel

postlabel

lastlabel

NAME

SYNOPSIS

DESCRIPTION

FEEDBACK

Mailing Lists

Support

Reporting Bugs

AUTHOR - Heikki Lehvaslaiho

APPENDIX