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: 1.51 $

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