GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::PHYLO::MATRICES::DATATYPE::CONTINUOUS (3)

.ds Aq ’

NAME

Bio::Phylo::Matrices::Datatype::Continuous - Validator subclass, no serviceable parts inside

CONTENTS

DESCRIPTION

The Bio::Phylo::Matrices::Datatype::* classes are used to validated data contained by Bio::Phylo::Matrices::Matrix and Bio::Phylo::Matrices::Datum objects.

METHODS

    MUTATORS

set_lookup() Sets the lookup table (no-op for continuous data!).



 Type    : Mutator
 Title   : set_lookup
 Usage   : $obj->set_gap($hashref);
 Function: Sets the symbol for gaps
 Returns : Modified object.
 Args    : Argument must be a hash
           reference that maps allowed
           single character symbols
           (including ambiguity symbols)
           onto the equivalent set of
           non-ambiguous symbols



    ACCESSORS

get_lookup() Gets the lookup table (no-op for continuous data!).



 Type    : Accessor
 Title   : get_lookup
 Usage   : my $lookup = $obj->get_lookup;
 Function: Returns the objects lookup hash
 Returns : A hash reference
 Args    : None



    TESTS

is_valid() Validates arguments for data validity.



 Type    : Test
 Title   : is_valid
 Usage   : if ( $obj->is_valid($datum) ) {
              # do something
           }
 Function: Returns true if $datum only contains valid characters
 Returns : BOOLEAN
 Args    : A list of Bio::Phylo::Matrices::Datum object, and/or
           character array references, and/or character strings,
           and/or single characters



    UTILITY METHODS

split() Splits string of characters on whitespaces.



 Type    : Utility method
 Title   : split
 Usage   : $obj->split($string)
 Function: Splits $string into characters
 Returns : An array reference of characters
 Args    : A string



join() Joins array ref of characters to a space-separated string.



 Type    : Utility method
 Title   : join
 Usage   : $obj->join($arrayref)
 Function: Joins $arrayref into a string
 Returns : A string
 Args    : An array reference



SEE ALSO

There is a mailing list at <https://groups.google.com/forum/#!forum/bio-phylo> for any user or developer questions and discussions.
Bio::Phylo::Matrices::Datatype This object inherits from Bio::Phylo::Matrices::Datatype, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Datatype::Continuous objects.
Bio::Phylo::Manual Also see the manual: Bio::Phylo::Manual and <http://rutgervos.blogspot.com>.

CITATION

If you use Bio::Phylo in published research, please cite it:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::PHYLO::MATRICES::DATATYPE::CONTINUOUS (3) 2014-02-08

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.