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()

Constant for amino acid data type.

 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()

Constant for categorical data type.

 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()

Constant for continuous data type.

 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()

Constant for dna data type.

 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()

Constant for rna data type.

 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()

Constant for custom data type.

 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()

Constant for integer tree score.

 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()

Constant for double tree score.

 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()

Constant for no tree score.

 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 ()

IUPAC constants.

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

AMBIG ()

IUPAC ambiguity codes.

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

SUBROUTINES

symbol_ok()

Checks symbol (deprecated).

 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()

Checks data type (deprecated)

 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()

Infers data type (deprecated)

 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()

Converts to CIPRES data type constant.

 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()

Returns the set of symbols defined by the ambiguity symbol (deprecated)

 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()

Returns the iupac ambiguity symbol for a set of symbols (deprecated)

 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()

Returns the iupac ambiguity symbols for nucleotide data (deprecated)

 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()

Returns the iupac ambiguity symbols for protein data (deprecated)

 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()

Tests if argument looks like a 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.

REVISION

 $Id: CONSTANT.pm 4213 2007-07-15 03:11:27Z rvosa $