Bio::Align StatisticsI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Align::StatisticsI - Calculate some statistics for an alignment
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Inherit
Bio::Root::RootI
Synopsis
Give standard usage here
Description
Describe the interface here
Methods
distanceDescriptionCode
available_distance_methodsDescriptionCode
Methods description
distancecode    nextTop
 Title   : distance
 Usage   : my $distance_mat = $stats->distance(-align  => $aln, 
		 			       -method => $method);
 Function: Calculates a distance matrix for all pairwise distances of
           sequences in an alignment.
 Returns : Array ref
 Args    : -align  => Bio::Align::AlignI object
           -method => String specifying specific distance method 
                      (implementing class may assume a default)
available_distance_methodscodeprevnextTop
 Title   : available_distance_methods
 Usage   : my @methods = $stats->available_distance_methods();
 Function: Enumerates the possible distance methods
 Returns : Array of strings
 Args    : none
Methods code
distancedescriptionprevnextTop
sub distance {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
available_distance_methodsdescriptionprevnextTop
sub available_distance_methods {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
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the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org              - General discussion
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Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _