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 module parses the block and stores the tree data.

METHODS

new

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

clone

Title : clone
Usage : my $newblock = $block->clone();
Function: clone a block object (shallow)
Returns : Block object
Args : none

set_trees

Title : set_trees
Usage : $block->set_trees($trees);
Function: Sets the list of trees (Bio::NEXUS::Tree objects)
Returns : none
Args : ref to array of Bio::NEXUS::Tree objects

add_tree

Title : add_tree
Usage : $block->add_tree($tree);
Function: Add trees (Bio::NEXUS::Tree object)
Returns : none
Args : a Bio::NEXUS::Tree object

add_tree_from_newick

Title : add_tree_from_newick
Usage : $block->add_tree_from_newick($newick_tree, $tree_name);
Function: Add a tree (Bio::NEXUS::Tree object)
Returns : none
Args : a tree string in newick format and a name for the tree (scalars)

get_trees

Title : get_trees
Usage : $block->get_trees();
Function: Gets the list of trees (Bio::NEXUS::Tree objects) and returns it
Returns : ref to array of Bio::NEXUS::Tree objects
Args : none

get_tree

Title : get_tree
Usage : $block->get_tree($treename);
Function: Gets the first tree (Bio::NEXUS::Tree object) that matches the name given or the first tree if $treename is not specified. If no tree matches, returns undef.
Returns : a Bio::NEXUS::Tree object
Args : tree name or none

set_translate

Title : set_translate
Usage : $block->set_translate($translate);
Function: Sets the hash of translates for nodes names
Returns : none
Args : hash of translates

translate

Title : translate
Usage : $self->translate($num);
Function: Translates a number with its associated name.
Returns : integer or string
Args : integer
Method : Returns the name associated with that numbers translated name.
If it cant find an association, returns the number.

reroot_tree

Title : reroot_tree
Usage : $block->reroot_tree($outgroup,$root_position, $treename);
Function: Reroot a tree using an OTU as new outgroup.
Returns : none
Args : outgroup name, the distance before the root position and tree name

reroot_all_trees

Title : reroot_all_trees
Usage : $block->reroot_all_trees($outgroup, $root_position);
Function: Reroot all the trees in the treesblock tree. use an OTU as new outgroup
Returns : none
Args : outgroup name and root position

rename_otus

Title : rename_otus
Usage : $block->rename_otus(%translation);
Function: Renames nodes based on a translation hash
Returns : none
Args : hash containing translation (e.g., { old_name => new_name} )
Comments: nodes not included in translation hash are unaffected

select_otus

Name : select_otus
Usage : $nexus->select_otus(@otunames);
Function: select a subset of OTUs
Returns : a new nexus object
Args : a ref to array of OTU names

select_tree

Name : select_tree
Usage : $nexus->select_tree($treename);
Function: select a tree
Returns : a new nexus object
Args : a tree name

select_subtree

Name : select_subtree
Usage : $nexus->select_subtree($inodename);
Function: select a subtree
Returns : a new nexus object
Args : an internal node name for subtree to be selected

exclude_subtree

Name : exclude_subtree
Usage : $nexus->exclude_subtree($inodename);
Function: remove a subtree
Returns : a new nexus object
Args : an internal node for subtree to be removed

equals

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