Arlin Stoltzfus > Bio-NEXUS > Bio::NEXUS::SpanBlock

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Bio-NEXUS-0.78.tar.gz

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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
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