/ 
Bio-NEXUS-0.75
River stage one • 1 direct dependent • 1 total dependent
/ Bio::NEXUS::SpanBlock

NAME

Bio::NEXUS::SpanBlock - Represent SPAN block in a NEXUS file (contains meta data).

SYNOPSIS

if ( $type =~ /spanblock/i ) {
    $block_object = new Bio::NEXUS::SpanBlock($type, $block, $verbose);
}

DESCRIPTION

This module representing a SPAN block in a NEXUS file for meta data.

FEEDBACK

All feedback (bugs, feature enhancements, etc.) are greatly appreciated.

AUTHORS

Chengzhi Liang (liangc@umbi.umd.edu)
Thomas Hladish (tjhladish at yahoo)

CONTRIBUTORS

METHODS

new

Title   : new
Usage   : block_object = new Bio::NEXUS::SpanBlock($block_type, $commands, $verbose);
Function: Creates a new Bio::NEXUS::SpanBlock object 
Returns : Bio::NEXUS::SpanBlock object
Args    : type (string), the commands/comments to parse (array ref), and a verbose flag (0 or 1; optional)

get_spandex

Title   : get_spandex
Usage   : $hash_ref = $span_block->get_spandex(;
Function: Gets the SPANDEX command contents as hash_reference
Returns : hash reference of the SPANDEX command contents
Args    : none

add_spandex

Title   : add_spandex
Usage   : $span_block->add_spandex(;
Function: Adds the SPANDEX command contents as hash_reference
Returns : none 
Args    : hash reference of the SPANDEX command contents

get_add

Title   : get_add
Usage   : $hash_ref = $span_block->get_add();
Function: gets ADD command content to the span block
Returns : hash reference of ADD command's attributes and values 
Args    : none

add_add

Title   : add_add
Usage   : $span_block->add_add($hash_ref);
Function: Adds ADD command contents to the span block
Returns : none
Args    : hash reference of ADD command's attributes and values

get_method

Title   : get_method
Usage   : $hash_ref = $span_block->get_method();
Function: gets METHOD command content to the span block
Returns : hash reference of METHOD command's attributes and values 
Args    : none

add_method

Title   : add_method
Usage   : $span_block->add_method($string);
Function: Adds METHOD command content to the span block
Returns : none
Args    : hash reference of METHOD command's attributes and values

get_attributes

Title   : get_attributes
Usage   : $attr_array_ref = $span_block->get_attributes($name);
Function: get the attributes of a particular identifier name
Returns : array reference of attributes.
Args    : identifier name

get_data

Title   : get_data
Usage   : $data_array_ref = $span_block->get_data($name);
Function: get the data of a particular identifier 
Returns : array reference of data
Args    : identifier name

rename_otus

Title   : rename_otus
Usage   : $block->rename_otus($names);
Function: rename all OTUs
Returns : none
Args    : hash of OTU names

add_otu_clone

Title   : add_otu_clone
Usage   : ...
Function: ...
Returns : ...
Args    : ...

equals

Name    : equals
Usage   : $span->equals($another);
Function: compare if two Bio::NEXUS::SpanBlock objects are equal
Returns : boolean 
Args    : a Bio::NEXUS::SpanBlock object