Bio::Phylo::Util::CONSTANT - This package defines global constants and utility functions that operate on them.
This package defines globals used in the Bio::Phylo libraries. The constants are called internally by the other packages. There is no direct usage.
Type : CIPRES constant Title : INT_SCORE_TYPE Usage : my $scoretype = INT_SCORE_TYPE; Function: A constant subroutine to indicate tree score is an integer value. Returns : INT Args : NONE
Type : CIPRES constant Title : DOUBLE_SCORE_TYPE Usage : my $scoretype = DOUBLE_SCORE_TYPE; Function: A constant subroutine to indicate tree score is a double value. Returns : INT Args : NONE
Type : CIPRES constant Title : NO_SCORE_TYPE Usage : my $scoretype = NO_SCORE_TYPE; Function: A constant subroutine to indicate tree has no score. Returns : INT Args : NONE
Type : constant Title : IUPAC Usage : no direct usage Function: no direct usage Returns : INT Args : NONE
Type : Type checker Title : symbol_ok Usage : if ( symbol_ok( -type => $type, -char => $sym ) ) { # do something } Function: Checks whether $sym is a valid symbol for $type data Returns : BOOLEAN Args : -type => one of [DNA|RNA|STANDARD|PROTEIN|NUCLEOTIDE|CONTINUOUS] -char => a symbol, e.g. 'ACGT', '0.242 0.4353 0.324', etc.
Type : Type checker Title : type_ok Usage : if ( type_ok( $type ) ) { # do something } Function: Checks whether $type is a recognized data type Returns : BOOLEAN Args : one of [DNA|RNA|STANDARD|PROTEIN|NUCLEOTIDE|CONTINUOUS]
Type : Type checker Title : infer_type Usage : my $type = infer_type( $chars ); Function: Attempts to identify what type $chars holds. Returns : one of DNA|STANDARD|PROTEIN|CONTINUOUS, or error if not found Args : A string of characters.
Type : Type convertor Title : cipres_type Usage : my $cipres_type = cipres_type($type) Function: Returns the cipres constant for $type Returns : CONSTANT Args : one of [DNA|RNA|STANDARD|PROTEIN|NUCLEOTIDE|CONTINUOUS]
Type : Type convertor Title : sym2ambig Usage : my @ambig = @{ sym2ambig( -type => 'DNA', -char => 'N' ) }; Function: Returns the set of symbols defined by the ambiguity symbol Returns : ARRAY Args : -type => one of [DNA|RNA|PROTEIN|NUCLEOTIDE] -char => an IUPAC ambiguity symbol
Type : Type convertor Title : ambig2sym Usage : my $sym = ambig2sym( -type => 'DNA', -char => [ 'A', 'C' ] ); Function: Returns the iupac ambiguity symbol for a set of symbols Returns : SCALAR Args : -type => one of [DNA|RNA|PROTEIN|NUCLEOTIDE] -char => an array of symbols
Type : Constant Title : nuc_symbols Usage : my @symbols = @{ nuc_symbols }; Function: Returns the iupac ambiguity symbols for nucleotide data Returns : ARRAY Args : NONE
Type : Constant Title : prot_symbols Usage : my @symbols = @{ prot_symbols }; Function: Returns the iupac ambiguity symbols for protein data Returns : ARRAY Args : NONE
Type : Constant Title : looks_like_number Usage : do 'something' if looks_like_number $var; Function: Tests whether $var looks like a number. Returns : TRUE or undef Args : $var = a variable to test
Also see the manual: Bio::Phylo::Manual.
CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo
Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:
bug-bio-phylo@rt.cpan.org
$Id: CONSTANT.pm 2189 2006-09-07 08:06:13Z rvosa $
Rutger A. Vos,
rvosa@sfu.ca
The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.
Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.