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Bio::NEXUS::Block 0.67

  Date Added: February 19, 2010  |  Visits: 762


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Bio::NEXUS::Block is a Perl module that provides useful functions for blocks in NEXUS file (parent class). SYNOPSIS This module is the super class of all NEXUS block classes. It is not used specifically from a program; in other words, you dont create a new Bio::NEXUS::Block object. Other modules, like AssumptionsBlock, simply inherit subroutines from this module. Provides a few useful functions for general blocks (to be used by sub-classes). METHODS clone Title : clone Usage : my $newblock = $block->clone(); Function: clone a block object (shallow) Returns : Block object Args : none get_type Title : get_type Usage : print $block->get_type(); Function: Returns a string containing the block type Returns : type (string) Args : none set_ntax Title : set_ntax Usage : print $block->set_ntax(); Function: Sets the value of Dimensions:ntax Returns : none Args : number of taxa (scalar) set_dimensions Title : set_dimensions Usage : $block->set_dimensions($dimensions); Function: set a dimensions command Returns : none Args : hash content of dimensions command get_dimensions Title : get_dimensions Usage : $block->get_dimensions($attribute); Function: get a dimensions command Returns : hash content of dimensions command, or the value for a particular attribute if specified Args : none, or a string set_command Title : set_command Usage : $block->set_command($command, $content); Function: Set a command Returns : none Args : comand name, and content (string) set_title Title : set_title Usage : $block->set_title($name); Function: Set the block name Returns : none Args : block name (string) get_title Title : get_title Usage : $block->get_title(); Function: Returns a string containing the block title Returns : name (string) Args : none set_link Title : set_link Usage : $block->set_link($link_hashref); Function: Set the block link commands Returns : none Args : block link (hash) add_link Title : add_link Usage : $block->add_link($linkname, $title); Function: add a link command Returns : none Args : $link, $title (of another block) get_link Title : get_link Usage : $block->get_link(); Function: Returns a hash containing the block links Returns : link (hash) Args : none set_taxlabels Title : set_taxlabels Usage : $block->set_taxlabels($labels); Function: Set the taxa names Returns : none Args : array of taxa names add_taxlabel Title : add_taxlabel Usage : $block->add_taxlabel($label); Function: add a taxon name Returns : none Args : a taxon name get_taxlabels Title : get_taxlabels Usage : $block->get_taxlabels(); Function: Returns an array of taxa labels Returns : taxa names Args : none set_otus Title : set_otus Usage : $block->set_otus($otus); Function: sets the list of OTUs Returns : none Args : array of OTUs get_otus Title : get_otus Usage : $block->get_otus(); Function: Returns array of otus Returns : all otus Args : none set_otuset Title : set_otuset Usage : $block->set_otuset($otuset); Function: Set the otus Returns : none Args : TaxUnitSet object get_otuset Title : get_otuset Usage : $block->get_otuset(); Function: get the OTUs Returns : TaxUnitSet object Args : none select_otus Title : select_otus Usage : $block->select_otus($names); Function: select a subset of OTUs Returns : array of OTUs Args : OTU names rename_otus Title : rename_otus Usage : $block->rename_otus($names); Function: rename all OTUs Returns : none Args : hash of OTU names set_comments Title : set_comments Usage : $block->set_comments($comments); Function: Set the block comments Returns : none Args : block comments (array of strings) get_comments Title : get_comments Usage : $block->get_comments(); Function: Returns block comments Returns : comments (array of strings) Args : none add_comment Title : add_comment Usage : $block->add_comment($comment); Function: add a comment Returns : none Args : comment (string) equals Name : equals Usage : $block->equals($another); Function: compare if two Block objects are equal Returns : boolean Args : a Block object.

Requirements: No special requirements
Platforms: Linux
Keyword: Args Bionexusblock Block Libraries Link Nexus File Otus Parent Class Perl Module Programming Returns Title Usage Useful Functions
Users rating: 0/10

License: Freeware Size: 153.6 KB
Libraries  -  Bio::NEXUS::TreesBlock 0.67
Bio::NEXUS::TreesBlock is a Perl module that represents TREES block of a NEXUS file. SYNOPSIS if ( $type =~ /trees/i ) { $block_object = new Bio::NEXUS::TreesBlock( $block_type, $block, $verbose ); } If a NEXUS block is a Trees Block, this...
153.6 KB  
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Libraries  -  Bio::NEXUS::SetsBlock 0.67
Bio::NEXUS::SetsBlock is a Perl module that represents SETS block of a NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::SetsBlock($block_type, $block, $verbose); Parses Sets block of NEXUS file and stores Sets data. METHODS new...
153.6 KB  
Libraries  -  Bio::NEXUS::TaxaBlock 0.67
Bio::NEXUS::TaxaBlock is a Perl module that represents TAXA block of a NEXUS file. SYNOPSIS if ( $type =~ /taxa/i ) { $block_object = new Bio::NEXUS::TaxaBlock($type, $block, $verbose); } If a NEXUS block is a taxa block, this module...
153.6 KB  
Libraries  -  Bio::NEXUS::UnalignedBlock 0.67
Bio::NEXUS::UnalignedBlock is a Perl module that represents an UNALIGNED block of a NEXUS file. SYNOPSIS if ( $type =~ /unaligned/i ) { $block_object = new Bio::NEXUS::UnalignedBlock($type, $block, $verbose); } This is a class representing...
153.6 KB  
Libraries  -  Bio::NEXUS::HistoryBlock 0.67
Bio::NEXUS::HistoryBlock is a Perl module that represents a HISTORY block of a NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::HistoryBlock(history, $block, $verbose); This is a class representing a history block in NEXUS file METHODS...
153.6 KB  
Libraries  -  Bio::NEXUS::NotesBlock 0.67
Bio::NEXUS::NotesBlock is a Perl module that represents a NOTES block in a NEXUS file. Placeholding module for the Notes Block class..
153.6 KB  
Libraries  -  Bio::NEXUS::MatrixBlock 0.67
Bio::NEXUS::MatrixBlock is a Perl module that provides functions for handling blocks that have matrices. SYNOPSIS This module is the super class of Characters, Unaligned, and Distances block classes, and indirectly it is a super-class of Data...
153.6 KB  
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