/ 
Bio-NEXUS-0.72
River stage one • 1 direct dependent • 1 total dependent
/ Bio::NEXUS::AssumptionsBlock

NAME

Bio::NEXUS::AssumptionsBlock - Represents ASSUMPTIONS block of a NEXUS file

SYNOPSIS

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

DESCRIPTION

If a NEXUS block is an assumptions block, this module parses the block and stores the assumptions data. Currently this only works with SOAP weight data, but we hope to extend its functionality.

FEEDBACK

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

AUTHORS

Chengzhi Liang (liangc@umbi.umd.edu)
Weigang Qiu (weigang@genectr.hunter.cuny.edu)
Eugene Melamud (melamud@carb.nist.gov)
Peter Yang (pyang@rice.edu)
Thomas Hladish (tjhladish at yahoo)

VERSION

$Revision: 1.50 $

METHODS

new

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

get_option

Title   : get_option
Usage   : $val = $assump_block->get_option($option_type);
Function: Returns the value of the specified option
Returns : $value (string)
Args    : $option_type (string); nexus standard permits: deftype, polytcount, gapmode

set_option

Title   : set_option
Usage   : $assumption_block->set_option($option, $value)
Function: Updates/sets a particular option (DefType, PolyTCount, GapMode, etc.)
Returns : n/a
Args    : $option (string) , $value (string)

get_all_options

Title   : get_all_options
Usage   : $hash_ref = $assumption_block->get_all_options();
Function: Retrieve all the options stored in the block
Returns : a hash reference (key-value pair), where each 'key' is an option (subcommand) and the 'value' is the corresponding value
Args    : none

set_all_options

Title   : set_all_options
Usage   : $assumption_block->set_all_options($options);
Function: Updates/sets options (of this assumptions block) and their values
Returns : n/a
Args    : $options (hashref) {'option' => 'value', ... }

add_weightset

Title   : add_weightset
Usage   : $block->add_weightset(weightset);
Function: add a weightset to this assumption block
Returns : none
Args    : WeightSet object

get_assumptions

Title   : get_assumptions
Usage   : $block->get_assumptions();
Function: Gets the list of assumptions (Bio::NEXUS::WeightSet objects) and returns it
Returns : ref to array of Bio::NEXUS::WeightSet objects
Args    : none

select_assumptions

Title   : select_assumptions
Usage   : $block->select_assumptions($columns);
Function: select assumptions (Bio::NEXUS::WeightSet objects) for a set of characters (columns)
Returns : none
Args    : column numbers for the set of characters to be selected

add_otu_clone

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

equals

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