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Man Pages


Manual Reference Pages  -  BIO::NEXUS::TREESBLOCK (3)

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NAME

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

CONTENTS

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 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



    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



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perl v5.20.3 BIO::NEXUS::TREESBLOCK (3) 2007-09-24

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