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

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

set_taxsets

Title : set_taxsets
Usage : $block->set_taxsets($taxsets);
Function: Set the taxsets hash
Returns : none
Args : hash of set name keys and element arrays

add_taxsets

Title : add_taxsets
Usage : $block->add_taxsets($taxsets);
Function: add taxa sets
Returns : none
Args : a reference to a hash of taxa sets

get_taxsets

Title : get_taxsets
Usage : $block->get_taxsets();
Function: Returns a hash of taxa sets
Returns : taxa sets
Args : none

get_taxset

Title : get_taxset
Usage : $block->get_taxset($setname);
Function: Returns a list of OTUs
Returns : OTUs
Args : none

get_taxset_names

Title : get_taxset_names
Usage : $block->get_taxset_names()
Function: gets the names of all sets
Returns : array of names
Args : none

print_all_taxsets

Title : print_all_taxsets
Usage : $block->print_all_taxsets($outfile)
Function: prints set names and elements
Returns : none
Args : filename or filehandle

delete_taxsets

Title : delete_taxsets
Usage : $block->delete_taxsets($set1 [$set2 $set3 ...])
Function: Removes the named sets from the Sets block
Returns : none
Args : Names of sets to be deleted

exclude_otus

Title : exclude_otus
Usage : $block->exclude_otus($otu_array_ref)
Function: Finds and deletes each of the given otus from any sets they appear in
Returns : none
Args : Names of otus to be removed

select_otus

Title : select_otus
Usage : $block->select_otus($otu_array_ref)
Function: Finds the given otus and removes all others from any sets they appear in
Returns : none
Args : Names of otus to be removed

rename_otus

Title : rename_otus
Usage : $block->rename_otus($names);
Function: rename all OTUs
Returns : none
Args : hash of OTU names

rename_taxsets

Title : rename_taxsets
Usage : $block->rename_taxsets($oldsetname1, $newsetname1, ...)
Function: Renames sets
Returns : none
Args : Oldname, newname pairs

equals

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