Bio::NEXUS::TreesBlock - Represents TREES block of a NEXUS file
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.
All feedback (bugs, feature enhancements, etc.) are all greatly appreciated.
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)
$Revision: 1.63 $
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)
Title : treetype Usage : $block->treetype('Bio::NEXUS::Tree'); Function: sets a tree type class to instantiate on parse Returns : none Args : a tree class
Title : nodetype Usage : $block->nodetype('Bio::NEXUS::Node'); Function: sets a node type class to instantiate on parse Returns : none Args : a node class
Title : clone Usage : my $newblock = $block->clone(); Function: clone a block object (shallow) Returns : Block object Args : none
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
Title : add_tree Usage : $block->add_tree($tree); Function: Add trees (Bio::NEXUS::Tree object) Returns : none Args : a Bio::NEXUS::Tree object
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)
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
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
Title : set_translate Usage : $block->set_translate($translate); Function: Sets the hash of translates for nodes names Returns : none Args : hash of translates
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.
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
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
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
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
Title : add_otu_clone Usage : ... Function: ... Returns : ... Args : ...
Name : select_tree Usage : $nexus->select_tree($treename); Function: select a tree Returns : a new nexus object Args : a tree name
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
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
Name : equals Usage : $nexus->equals($another); Function: compare if two NEXUS objects are equal Returns : boolean Args : a NEXUS object
To install Bio::NEXUS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::NEXUS
CPAN shell
perl -MCPAN -e shell install Bio::NEXUS
For more information on module installation, please visit the detailed CPAN module installation guide.