Bio::NEXUS::AssumptionsBlock - Represents ASSUMPTIONS block of a NEXUS file
if ( $type =~ /assumptions/i ) { $block_object = new Bio::NEXUS::AssumptionsBlock($block_type, $block, $verbose); }
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.
All feedback (bugs, feature enhancements, etc.) are greatly appreciated.
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)
$Revision: 1.36 $
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)
Title : add_weightset Usage : $block->add_weightset(weightset); Function: add a weightset to this assumption block Returns : none Args : WeightSet object
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
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
Name : equals Usage : $assump->equals($another); Function: compare if two Bio::NEXUS::AssumptionsBlock objects are equal Returns : boolean Args : a Bio::NEXUS::AssumptionsBlock object
To install Bio::NEXUS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::NEXUS
CPAN shell
perl -MCPAN -e shell install Bio::NEXUS
For more information on module installation, please visit the detailed CPAN module installation guide.