Bio::Tree::Tree(3pm)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 Bio::Tree::Tree 💖

okay bestie, so this page is Bio::Tree::Tree(3pm) — it's a Perl module from the Bioperl fam and it's literally the whole entire tree-holding situation. Let's get into it 🫶

✨ NAME ✨

Bio::Tree::Tree — it's an implementation of the TreeI interface. that's it, that's the name, slay 💅

🌈 SYNOPSIS 🌈

use Bio::TreeIO;

# like from a TreeIO
my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'treefile.dnd');
my $tree = $treeio->next_tree;
my @nodes = $tree->get_nodes;
my $root = $tree->get_root_node;

see how easy that was?? no cap, three lines and you're holding a whole phylogenetic tree in your hands 💖

🦋 DESCRIPTION 🦋

So basically this object holds handles to Nodes which make up a tree. that's the vibe. the tree is the container, the nodes are the girlies inside it ✨

⭐ IMPLEMENTATION NOTE ⭐

okay this part is IMPORTANT so listen up bestie 👑

This implementation of Bio::Tree::Tree contains Bio::Tree:::NodeI; mainly linked via the root node. And here's the thing — NodeI can potentially contain circular references (because nodes need to refer to both their parent AND their child nodes, it's giving very codependent 😭). So Bio::Tree::Tree will remove those circular references when the object is garbage-collected.

Which has some side effects. Primarily: one must keep the Tree in scope or have at least one reference to it if working with nodes. That's the rule, don't break it.

The fix would be to count the references to the nodes and if it's greater than expected, retain all of them — but that requires an additional prereq and thus may not be worth the effort. This only shows up in minor edge cases, though (see Bug #2869).

Example of issue:

# tree is not assigned to a variable, so passes from memory after
# root node is passed
my $root = Bio::TreeIO->new(-format => 'newick', -file => 'foo.txt')->next_tree
               ->get_root_node;

# gets nothing, as all Node links are broken when Tree is garbage-collected above
my @descendents = $root->get_all_Descendents;
💀 not the tree ghosting you mid-operation!! this is exactly why you keep a reference, bestie. hold onto your tree like it's your emotional support water bottle. 🥤

🎀 FEEDBACK 🎀

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, they want to hear from you 🫶 Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. (fr fr, they said "much appreciated")

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🆘 Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. (yes, include your code AND your data, they're not psychic, bestie ✨)

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

👑 AUTHOR - Jason Stajich 👑

Email jason@bioperl.org

💜 CONTRIBUTORS 💜

  • Aaron Mackey amackey@virginia.edu
  • Sendu Bala bix@sendu.me.uk
  • Mark A. Jensen maj@fortinbras.us

🌸 APPENDIX 🌸

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (so if you see an underscore, mind your business, it's private 💅)

🧚 new

Title   : new
Usage   : my $obj = Bio::Tree::Tree->new();
Function: Builds a new Bio::Tree::Tree object
Returns : Bio::Tree::Tree
Args    : -root     => L<Bio::Tree::NodeI> object which is the root
             OR
          -node     => L<Bio::Tree::NodeI> object from which the root will be
                       determined

          -nodelete => boolean, whether or not to try and cleanup all
                       the nodes when this this tree goes out of scope.
          -id       => optional tree ID
          -score    => optional tree score value

so you build a tree, you hand it a -root Bio::Tree::NodeI object which is the root, OR you hand it a -node Bio::Tree::NodeI object from which the root will be determined. and you can also pass -nodelete (boolean, whether or not to try and cleanup all the nodes when this tree goes out of scope), -id (optional tree ID) and -score (optional tree score value). the whole package, iconic ✨

🧚 nodelete

Title   : nodelete
Usage   : $obj->nodelete($newval)
Function: Get/Set Boolean whether or not to delete the underlying
          nodes when it goes out of scope.  By default this is false
          meaning trees are cleaned up.
Returns : boolean
Args    : on set, new boolean value

get/set boolean whether or not to delete the underlying nodes when it goes out of scope. by default this is false, meaning trees are cleaned up. so if you want your nodes to stick around after the tree dips, you set this. 🙈

🧚 get_nodes

Title   : get_nodes
Usage   : my @nodes = $tree->get_nodes()
Function: Return list of Bio::Tree::NodeI objects
Returns : array of Bio::Tree::NodeI objects
Args    : (named values) hash with one value
          order => 'b|breadth' first order or 'd|depth' first order
          sortby => [optional] "height", "creation", "alpha", "revalpha",
          or coderef to be used to sort the order of children nodes. See L<Bio::Tree::Node> for details

returns an array of Bio::Tree::NodeI objects — the whole roster 💅 args are a named-values hash with order ('b|breadth' first order or 'd|depth' first order) and sortby (optional — "height", "creation", "alpha", "revalpha", or a coderef used to sort the order of children nodes; see Bio::Tree::Node for details).

🧚 get_root_node

Title   : get_root_node
Usage   : my $node = $tree->get_root_node();
Function: Get the Top Node in the tree, in this implementation
          Trees only have one top node.
Returns : Bio::Tree::NodeI object
Args    : none

gets the Top Node in the tree. in this implementation, trees only have one top node — there's no drama, there's no co-leaders, just one main character 👑

🧚 set_root_node

Title   : set_root_node
Usage   : $tree->set_root_node($node)
Function: Set the Root Node for the Tree
Returns : Bio::Tree::NodeI
Args    : Bio::Tree::NodeI

sets the Root Node for the Tree. takes a Bio::Tree::NodeI, returns a Bio::Tree::NodeI. cute, symmetrical, love that for us 🎀

🧚 total_branch_length

Title   : total_branch_length
Usage   : my $size = $tree->total_branch_length
Function: Returns the sum of the length of all branches
Returns : real
Args    : none

returns the sum of the length of all branches. that's a real number, bestie. no args needed 🦋

🧚 subtree_length

Title   : subtree_length
Usage   : my $subtree_size = $tree->subtree_length($internal_node)
Function: Returns the sum of the length of all branches in a subtree
          under the node. Calculates the size of the whole tree
          without an argument (but only if root node is defined)
Returns : real or undef
Args    : Bio::Tree::NodeI object, defaults to the root node

returns the sum of the length of all branches in a subtree under the node. and if you call it with no argument, it calculates the size of the whole tree — but only if the root node is defined. args are a Bio::Tree::NodeI object, which defaults to the root node. returns real or undef (so handle that undef, girlie 💀)

🧚 id

Title   : id
Usage   : my $id = $tree->id();
Function: An id value for the tree
Returns : scalar
Args    : [optional] new value to set

an id value for the tree. returns a scalar, and you can optionally pass a new value to set. simple, clean, iconic ✨

🧚 score

Title   : score
Usage   : $obj->score($newval)
Function: Sets the associated score with this tree
          This is a generic slot which is probably best used
          for log likelihood or other overall tree score
Returns : value of score
Args    : newvalue (optional)

sets the associated score with this tree. it's a generic slot which is probably best used for log likelihood or other overall tree score. returns the value of score, and the arg is a newvalue (optional). a little flexible slot, a little whatever-you-need-her-to-be 💅

🧚 height

Title   : height
Usage   : my $height = $tree->height
Function: Gets the height of tree - this LOG_2($number_nodes)
          WARNING: this is only true for strict binary trees.  The TreeIO
          system is capable of building non-binary trees, for which this
          method will currently return an incorrect value!!
Returns : integer
Args    : none

gets the height of tree — this is LOG_2($number_nodes).

⚠️ WARNING bestie, listen to me: this is only true for strict binary trees. The TreeIO system is capable of building non-binary trees, for which this method will currently return an incorrect value!! do not trust her outside binary tree territory, she will lie to your face 😭

returns an integer, takes no args.

🧚 number_nodes

Title   : number_nodes
Usage   : my $size = $tree->number_nodes
Function: Returns the number of nodes in the tree
Returns : integer
Args    : none

returns the number of nodes in the tree. integer. no args. we love a low-maintenance method 🫶

🧚 as_text

Title   : as_text
Usage   : my $tree_as_string = $tree->as_text($format)
Function: Returns the tree as a string representation in the
          desired format, e.g.: 'newick', 'nhx' or 'tabtree' (the default)
Returns : scalar string
Args    : format type as specified by Bio::TreeIO
Note    : This method loads the Bio::TreeIO::$format module
          on the fly, and commandeers the _write_tree_Helper
          routine therein to create the tree string.

returns the tree as a string representation in the desired format, e.g.: 'newick', 'nhx' or 'tabtree' (that's the default btw). returns a scalar string, and the arg is a format type as specified by Bio::TreeIO.

Note: This method loads the Bio::TreeIO::$format module on the fly, and commandeers the _write_tree_Helper routine therein to create the tree string. she's resourceful like that ✨

💖 Methods for associating Tag/Values with a Tree 💖

These methods associate tag/value pairs with a Tree. tag/value pairs, bestie, it's giving labeled storage but make it tree 🌈

🧚 set_tag_value

Title   : set_tag_value
Usage   : $tree->set_tag_value($tag,$value)
          $tree->set_tag_value($tag,@values)
Function: Sets a tag value(s) to a tree. Replaces old values.
Returns : number of values stored for this tag
Args    : $tag   - tag name
          $value - value to store for the tag

sets a tag value(s) to a tree. Replaces old values — so it's a full override, not an append, don't get it twisted. returns the number of values stored for this tag. args: $tag (tag name) and $value (value to store for the tag).

🧚 add_tag_value

Title   : add_tag_value
Usage   : $tree->add_tag_value($tag,$value)
Function: Adds a tag value to a tree
Returns : number of values stored for this tag
Args    : $tag   - tag name
          $value - value to store for the tag

adds a tag value to a tree — this one adds, it doesn't replace, unlike her sister above. returns the number of values stored for this tag. args: $tag (tag name) and $value (value to store for the tag) 💜

🧚 remove_tag

Title   : remove_tag
Usage   : $tree->remove_tag($tag)
Function: Remove the tag and all values for this tag
Returns : boolean representing success (0 if tag does not exist)
Args    : $tag - tagname to remove

removes the tag and all values for this tag. returns a boolean representing success — and 0 if the tag does not exist, so a zero means "she wasn't there to begin with". arg is $tag (tagname to remove) 🍓

🧚 remove_all_tags

Title   : remove_all_tags
Usage   : $tree->remove_all_tags()
Function: Removes all tags
Returns : None
Args    : None

removes all tags. returns None, args None. it's giving scorched earth but politely 💀

🧚 get_all_tags

Title   : get_all_tags
Usage   : my @tags = $tree->get_all_tags()
Function: Gets all the tag names for this Tree
Returns : Array of tagnames
Args    : None

gets all the tag names for this Tree. returns an array of tagnames, no args. the full roster, no gatekeeping 👑

🧚 get_tag_values

Title   : get_tag_values
Usage   : my @values = $tree->get_tag_values($tag)
Function: Gets the values for given tag ($tag)
Returns : Array of values or empty list if tag does not exist
Args    : $tag - tag name

gets the values for given tag ($tag). returns an array of values, or an empty list if the tag does not exist — so check before you assume, bestie. arg is $tag (tag name) 🌸

🧚 has_tag

Title   : has_tag
Usage   : $tree->has_tag($tag)
Function: Boolean test if tag exists in the Tree
Returns : Boolean
Args    : $tag - tagname

a boolean test — does this tag exist in the Tree, yes or no? returns a Boolean. arg is $tag (tagname). it's the vibe check for your tags 💅

🧚 clone

Title   : clone
Alias   : _clone
Usage   : $tree_copy = $tree->clone();
          $subtree_copy = $tree->clone($internal_node);
Function: Safe tree clone that doesn't segfault
Returns : Bio::Tree::Tree object
Args    : [optional] $start_node, Bio::Tree::Node object

a Safe tree clone that doesn't segfault — say it with me, bestie: no segfaults, we don't do that here 🔥. Alias is _clone. returns a Bio::Tree::Tree object. args: [optional] $start_node, a Bio::Tree::Node object. so you can clone the whole thing or just clone a subtree, your call 🦋

and that's the whole page, bestie!! 💖✨🎀

this was User Contributed Perl Documentation for Bio::Tree::Tree(3pm), generated against perl v5.32.1 and dated 2021-08-15 — so if you're reading this in the future, hi, hope the trees are still treeing 🌸🫶 go keep your tree in scope, drink some water, and slay 💅

📦 where this page comes from