NAME
Bio::Phylo::Parsers::Nexus - Parser used by Bio::Phylo::IO, no serviceable parts inside
DESCRIPTION
This module parses nexus files. It is called by the Bio::Phylo::IO module, there is no direct usage. The parser can handle files and strings with multiple tree, taxon, and characters blocks whose links are defined using Mesquite's "TITLE = 'some_name'" and "LINK TAXA = 'some_name'" tokens.
The parser returns a reference to an array containing one or more taxa, trees and matrices objects. Nexus comments are stripped, private nexus blocks (and the 'assumptions' block) are skipped. It currently doesn't handle 'mixed' data.
INHERITED METHODS
Bio::Phylo::Parsers::Nexus inherits from one or more superclasses. This means that objects of class Bio::Phylo::Parsers::Nexus also "do" the methods from the superclasses in addition to the ones implemented in this class. Below is the documentation for those additional methods, organized by superclass.
SUPERCLASS Bio::Phylo::IO
Bio::Phylo::Parsers::Nexus inherits from superclass Bio::Phylo::IO. Below are the public methods (if any) from this superclass.
- parse()
-
Parses a file or string.
Type : Class method Title : parse Usage : my $obj = Bio::Phylo::IO->parse(%options); Function: Creates (file) handle, instantiates appropriate parser. Returns : A Bio::Phylo::* object Args : -file => (path), or -string => (scalar), -format => (description format), -(other) => (parser specific options) Comments: The parse method makes assumptions about the capabilities of Bio::Phylo::Parsers::* modules: i) their names match those of the -format => (blah) arguments, insofar that ucfirst(blah) . '.pm' is an existing module; ii) the modules implement a _from_handle, or a _from_string method. Exceptions are thrown if either assumption is violated. If @ARGV contains even key/value pairs such as "format newick file <filename>" (note: no dashes) these will be prepended to @_, for one-liners.
- unparse()
-
Unparses object(s) to a string.
Type : Class method Title : unparse Usage : my $string = Bio::Phylo::IO->unparse( %options ); Function: Turns Bio::Phylo object into a string according to specified format. Returns : SCALAR Args : -phylo => (Bio::Phylo object), -format => (description format), -(other) => (parser specific options)
SEE ALSO
- Bio::Phylo::IO
-
The nexus parser is called by the Bio::Phylo::IO object. Look there for examples of file parsing and manipulation.
- Bio::Phylo::Manual
-
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
REVISION
$Id: Nexus.pm 843 2009-03-04 23:50:27Z rvos $