Bio::LiveSeq Mutation
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::LiveSeq::Mutation - Mutation event descriptor class
Package variables
No package variables defined.
Inherit
Bio::Root::Root
Synopsis
  # 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 );
Description
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. Bio::LiveSeq::Mutator) might check for its
validity.
Methods
new
No description
Code
seqDescriptionCode
seqoriDescriptionCode
posDescriptionCode
lenDescriptionCode
labelDescriptionCode
transposDescriptionCode
issueDescriptionCode
prelabelDescriptionCode
postlabelDescriptionCode
lastlabelDescriptionCode
Methods description
seqcode    nextTop
 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
seqoricodeprevnextTop
 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
poscodeprevnextTop
 Title   : pos
Usage : $obj->pos();
Function:
Sets and returns the position of the first element in the sequence. Example : Returns : string Args : integer
lencodeprevnextTop
 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 length of the mutated sequence (seq). Example : Returns : string Args : string
labelcodeprevnextTop
 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. Example : Returns : string Args : string
transposcodeprevnextTop
 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
issuecodeprevnextTop
 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
prelabelcodeprevnextTop
 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. Example : Returns : string Args : string
postlabelcodeprevnextTop
 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. Example : Returns : string Args : string
lastlabelcodeprevnextTop
 Title   : lastlabel
Usage : $obj->lastlabel();
Function:
Sets and returns the lastlabel of the affected original allele location. Lastlabel is a stable identifier whereas location can be changed by mutations. Lastlabel comes from l. Example : Returns : string Args : string
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    my $self;
    $self = {};
    bless $self, $class;

    my ($seq, $seqori, $pos, $len, $label) =
	    $self->_rearrange([qw(SEQ
				  SEQORI
				  POS
				  LEN
				  )],
			      @args);

    $seq && $self->seq($seq);
    $seqori && $self->seqori($seqori);
    $pos && $self->pos($pos);
    defined($len) && $self->len($len); # defined() added otherwise won't work for len==0
return $self; # success - we hope!
}
seqdescriptionprevnextTop
sub seq {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'seq'} = $value;
    }
    return $self->{'seq'} || '';
}
seqoridescriptionprevnextTop
sub seqori {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'seqori'} = $value;
    }
    return $self->{'seqori'} || '';
}
posdescriptionprevnextTop
sub pos {
    my ($self,$value) = @_;
    if( defined $value) {
	if ( $value !~ /^([+-])?\d+$/ ) {
	    $self->throw("[$value] for pos has to be an integer\n");
	} else {
	    $self->{'pos'} = $value;
	}
    }
    return $self->{'pos'};
}
lendescriptionprevnextTop
sub len {
   my ($self,$value) = @_;
   if ( defined $value) {
       $self->{'len'} = $value;
  }
   if ( ! exists $self->{'len'} ) {
       return length $self->{'seq'};
   }
   return $self->{'len'};
}
labeldescriptionprevnextTop
sub label {
   my ($self,$value) = @_;
   if ( defined $value) {
       $self->{'label'} = $value;
   }
   if ( ! exists $self->{'label'} ) {
       return;
   } 
   return $self->{'label'};
}
transposdescriptionprevnextTop
sub transpos {
    my ($self,$value) = @_;
    if( defined $value) {
	if ( $value !~ /^([+-])?\d+$/ ) {
	    $self->throw("[$value] for transpos has to be an integer\n");
	} else {
	    $self->{'transpos'} = $value;
	}
    }
    return $self->{'transpos'};
}
issuedescriptionprevnextTop
sub issue {
    my ($self,$value) = @_;
    if( defined $value) {
	if ( $value !~ /^([+-])?\d+$/ ) {
	    $self->throw("[$value] for issue has to be an integer\n");
	} else {
	    $self->{'issue'} = $value;
	}
    }
    return $self->{'issue'};
}
prelabeldescriptionprevnextTop
sub prelabel {
   my ($self,$value) = @_;
   if ( defined $value) {
       $self->{'prelabel'} = $value;
   }
   if ( ! exists $self->{'prelabel'} ) {
       return;
   } 
   return $self->{'prelabel'};
}
postlabeldescriptionprevnextTop
sub postlabel {
   my ($self,$value) = @_;
   if ( defined $value) {
       $self->{'postlabel'} = $value;
   }
   if ( ! exists $self->{'postlabel'} ) {
       return;
   } 
   return $self->{'postlabel'};
}
lastlabeldescriptionprevnextTop
sub lastlabel {
   my ($self,$value) = @_;
   if ( defined $value) {
       $self->{'lastlabel'} = $value;
   }
   if ( ! exists $self->{'lastlabel'} ) {
       return;
   } 
   return $self->{'lastlabel'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _