NAME

Bio::Phylo::Util::CONSTANT - This package defines global constants and utility functions that operate on them.

DESCRIPTION

This package defines globals used in the Bio::Phylo libraries. The constants are called internally by the other packages. There is no direct usage.

PUBLIC CONSTANTS

AA_DATATYPE()

Type    : Constant
Title   : AA_DATATYPE
Usage   : my $datatype = AA_DATATYPE;
Function: A constant subroutine to indicate matrix datatype is amino acid.
Returns : INT
Args    : NONE

CATEGORICAL_DATATYPE()

Type    : Constant
Title   : CATEGORICAL_DATATYPE
Usage   : my $datatype = CATEGORICAL_DATATYPE;
Function: A constant subroutine to indicate matrix datatype is 'standard'.
Returns : INT
Args    : NONE

CONTINUOUS_DATATYPE()

Type    : Constant
Title   : CONTINUOUS_DATATYPE
Usage   : my $datatype = CONTINUOUS_DATATYPE;
Function: A constant subroutine to indicate matrix datatype is 'continuous'.
Returns : INT
Args    : NONE

DNA_DATATYPE()

Type    : Constant
Title   : DNA_DATATYPE
Usage   : my $datatype = DNA_DATATYPE;
Function: A constant subroutine to indicate matrix datatype is dna/nucleotides.
Returns : INT
Args    : NONE

RNA_DATATYPE()

Type    : Constant
Title   : RNA_DATATYPE
Usage   : my $datatype = RNA_DATATYPE;
Function: A constant subroutine to indicate matrix datatype is rna.
Returns : INT
Args    : NONE

CUSTOM_DATATYPE()

Type    : Constant
Title   : CUSTOM_DATATYPE
Usage   : my $datatype = CUSTOM_DATATYPE;
Function: A constant subroutine to indicate matrix datatype is defined by
          a custom ambiguity lookup table, e.g. for "mixed" molecular
          and standard categorical data.
Returns : INT
Args    : NONE

INT_SCORE_TYPE()

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

DOUBLE_SCORE_TYPE()

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

NO_SCORE_TYPE()

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

IUPAC ()

Type    : constant
Title   : IUPAC
Usage   : no direct usage
Function: no direct usage
Returns : INT
Args    : NONE

AMBIG ()

Type    : constant
Title   : IUPAC
Usage   : no direct usage
Function: no direct usage
Returns : INT
Args    : NONE

SUBROUTINES

symbol_ok()

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_ok()

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]

infer_type()

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.

cipres_type()

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]

sym2ambig()

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

ambig2sym()

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

nuc_symbols()

Type    : Constant
Title   : nuc_symbols
Usage   : my @symbols = @{ nuc_symbols };
Function: Returns the iupac ambiguity symbols for nucleotide data
Returns : ARRAY
Args    : NONE

prot_symbols()

Type    : Constant
Title   : prot_symbols
Usage   : my @symbols = @{ prot_symbols };
Function: Returns the iupac ambiguity symbols for protein data
Returns : ARRAY
Args    : NONE

looks_like_number()

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

SEE ALSO

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual.

FORUM

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

BUGS

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:

$Id: CONSTANT.pm 4169 2007-07-11 01:36:59Z rvosa $

AUTHOR

Rutger A. Vos,

email: rvosa@sfu.ca

web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

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 & LICENSE

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.