/ 
Bio-NEXUS-0.76
River stage one • 1 direct dependent • 1 total dependent
/ Bio::NEXUS::SetsBlock

NAME

Bio::NEXUS::SetsBlock - Represents SETS block of a NEXUS file

SYNOPSIS

$block_object = new Bio::NEXUS::SetsBlock($block_type, $block, $verbose);

DESCRIPTION

Parses Sets block of NEXUS file and stores Sets data.

FEEDBACK

All feedback (bugs, feature enhancements, etc.) are greatly appreciated.

AUTHORS

Thomas Hladish (tjhladish at yahoo)

VERSION

$Revision: 1.32 $

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 OTU's
Returns : OTU's
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
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

add_otu_clone

Title   : add_otu_clone
Usage   : ...
Function: ...
Returns : ...
Args    : ...

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