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Man Pages


Manual Reference Pages  -  BIO::NEXUS::ASSUMPTIONSBLOCK (3)

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NAME

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

CONTENTS

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



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perl v5.20.3 BIO::NEXUS::ASSUMPTIONSBLOCK (3) 2012-02-07

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