Arlin Stoltzfus > Bio-NEXUS > Bio::NEXUS::TreesBlock

Download:
Bio-NEXUS-0.78.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  1
Open  2
View/Report Bugs
Source  

NAME ^

Bio::NEXUS::TreesBlock - Represents TREES block of a NEXUS file

SYNOPSIS ^

 if ( $type =~ /trees/i ) {
     $block_object = new Bio::NEXUS::TreesBlock( $block_type, $block, $verbose );
 }

DESCRIPTION ^

If a NEXUS block is a Trees Block, this module parses the block and stores the tree data.

FEEDBACK ^

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

AUTHORS ^

 Chengzhi Liang (liangc@umbi.umd.edu)
 Eugene Melamud (melamud@carb.nist.gov)
 Weigang Qiu (weigang@genectr.hunter.cuny.edu)
 Peter Yang (pyang@rice.edu)
 Thomas Hladish (tjhladish at yahoo)

VERSION ^

$Revision: 1.63 $

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)

treetype

 Title   : treetype
 Usage   : $block->treetype('Bio::NEXUS::Tree');
 Function: sets a tree type class to instantiate on parse
 Returns : none
 Args    : a tree class

nodetype

 Title   : nodetype
 Usage   : $block->nodetype('Bio::NEXUS::Node');
 Function: sets a node type class to instantiate on parse
 Returns : none
 Args    : a node class

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 number's translated name.
           If it can't 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

add_otu_clone

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

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
syntax highlighting: