/ 
FAST-1.06
River stage zero No dependents
/ FAST::Bio::Tree::TreeFunctionsI

NAME

FAST::Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods

SYNOPSIS

use FAST::Bio::TreeIO;
my $in = FAST::Bio::TreeIO->new(-format => 'newick', -file => 'tree.tre');

my $tree = $in->next_tree;

my @nodes = $tree->find_node('id1');

if( $tree->is_monophyletic(-nodes => \@nodes, -outgroup => $outnode) ){
 #...
}

DESCRIPTION

This interface provides a set of implementated Tree functions which only use the defined methods in the TreeI or NodeI interface.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is 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.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich, Aaron Mackey, Justin Reese

Email jason-at-bioperl-dot-org Email amackey-at-virginia.edu Email jtr4v-at-virginia.edu

CONTRIBUTORS

Sendu Bala, bix@sendu.me.uk

Rerooting code was worked on by

Daniel Barker d.barker-at-reading.ac.uk
Ramiro Barrantes Ramiro.Barrantes-at-uvm.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

find_node

Title   : find_node
Usage   : my @nodes = $self->find_node(-id => 'node1');
Function: returns all nodes that match a specific field, by default this
          is id, but different branch_length, 
Returns : List of nodes which matched search
Args    : text string to search for
          OR
          -fieldname => $textstring

remove_Node

Title   : remove_Node
Usage   : $tree->remove_Node($node)
Function: Removes a node from the tree
Returns : boolean represent status of success
Args    : either FAST::Bio::Tree::NodeI or string of the node id

get_lineage_nodes

Title   : get_lineage_nodes
Usage   : my @nodes = $tree->get_lineage_nodes($node);
Function: Get the full lineage of a node (all its ancestors, in the order
          root->most recent ancestor)
Returns : list of nodes
Args    : either FAST::Bio::Tree::NodeI or string of the node id

splice

Title   : splice
Usage   : $tree->splice(-remove_id => \@ids);
Function: Remove all the nodes from a tree that correspond to the supplied
          args, making all the descendents of a removed node the descendents
          of the removed node's ancestor.
          You can ask to explicitly remove certain nodes by using -remove_*,
          remove them conditionally by using -remove_* in combination with
          -keep_*, or remove everything except certain nodes by using only
          -keep_*.
Returns : n/a
Args    : just a list of FAST::Bio::Tree::NodeI objects to remove, OR
          -key => value pairs, where -key has the prefix 'remove' or 'keep',
          followed by an underscore, followed by a fieldname (like for the
          method find_node). Value should be a scalar or an array ref of
          scalars (again, like you might supply to find_node).

          So (-remove_id => [1, 2]) will remove all nodes from the tree that
          have an id() of '1' or '2', while
          (-remove_id => [1, 2], -keep_id => [2]) will remove all nodes with
          an id() of '1'.
          (-keep_id => [2]) will remove all nodes unless they have an id() of
          '2' (note, no -remove_*).

          -preserve_lengths => 1 : setting this argument will splice out
          intermediate nodes, preserving the original total length between
          the ancestor and the descendants of the spliced node. Undef 
          by default.

get_lca

Title   : get_lca
Usage   : get_lca(-nodes => \@nodes ); OR
          get_lca(@nodes);
Function: given two or more nodes, returns the lowest common ancestor (aka most
          recent common ancestor)
Returns : node object or undef if there is no common ancestor
Args    : -nodes => arrayref of nodes to test, OR
          just a list of nodes

merge_lineage

Title   : merge_lineage
Usage   : merge_lineage($node)
Function: Merge a lineage of nodes with this tree.
Returns : n/a
Args    : FAST::Bio::Tree::TreeI with only one leaf, OR
          FAST::Bio::Tree::NodeI which has an ancestor

For example, if we are the tree $tree:

+---B
|
A
|
+---C

and we want to merge the lineage $other_tree:

A---C---D

After calling $tree->merge_lineage($other_tree), $tree looks like:

+---B
|
A
|
+---C---D

contract_linear_paths

Title   : contract_linear_paths
Usage   : contract_linear_paths()
Function: Splices out all nodes in the tree that have an ancestor and only one
          descendent.
Returns : n/a
Args    : none for normal behaviour, true to dis-regard the ancestor requirment
          and re-root the tree as necessary

For example, if we are the tree $tree:

            +---E
            |
A---B---C---D
            |
            +---F

After calling $tree->contract_linear_paths(), $tree looks like:

    +---E
    |
A---D
    |
    +---F

Instead, $tree->contract_linear_paths(1) would have given:

+---E
|
D
|
+---F

is_binary

Example    : is_binary(); is_binary($node);
Description: Finds if the tree or subtree defined by
             the internal node is a true binary tree
             without polytomies
Returns    : boolean
Exceptions : 
Args       : Internal node FAST::Bio::Tree::NodeI, optional

force_binary

Title   : force_binary
Usage   : force_binary()
Function: Forces the tree into a binary tree, splitting branches arbitrarily
          and creating extra nodes as necessary, such that all nodes have
          exactly two or zero descendants.
Returns : n/a
Args    : none

For example, if we are the tree $tree:

+---G
|
+---F
|
+---E
|
A
|
+---D
|
+---C
|
+---B

(A has 6 descendants B-G)

After calling $tree->force_binary(), $tree looks like:

        +---X
        |
    +---X
    |   |
    |   +---X
    |
+---X
|   |
|   |   +---G
|   |   |
|   +---X
|       |
|       +---F
A
|       +---E
|       |
|   +---X
|   |   |
|   |   +---D
|   |
+---X
    |
    |   +---C
    |   |
    +---X
        |
        +---B

(Where X are artificially created nodes with ids 'artificial_n', where n is
an integer making the id unique within the tree)

simplify_to_leaves_string

Title   : simplify_to_leaves_string
Usage   : my $leaves_string = $tree->simplify_to_leaves_string()
Function: Creates a simple textual representation of the relationship between
          leaves in self. It forces the tree to be binary, so the result may
          not strictly correspond to the tree (if the tree wasn't binary), but
          will be as close as possible. The tree object is not altered. Only
          leaf node ids are output, in a newick-like format.
Returns : string
Args    : none

distance

Title   : distance
Usage   : distance(-nodes => \@nodes )
Function: returns the distance between two given nodes
Returns : numerical distance
Args    : -nodes => arrayref of nodes to test
          or ($node1, $node2)

is_monophyletic

 Title   : is_monophyletic
 Usage   : if( $tree->is_monophyletic(-nodes => \@nodes, 
				      -outgroup => $outgroup)
 Function: Will do a test of monophyly for the nodes specified
           in comparison to a chosen outgroup
 Returns : boolean
 Args    : -nodes    => arrayref of nodes to test
           -outgroup => outgroup to serve as a reference

is_paraphyletic

 Title   : is_paraphyletic
 Usage   : if( $tree->is_paraphyletic(-nodes =>\@nodes,
				      -outgroup => $node) ){ }
 Function: Tests whether or not a given set of nodes are paraphyletic
           (representing the full clade) given an outgroup
 Returns : [-1,0,1] , -1 if the group is not monophyletic
                       0 if the group is not paraphyletic
                       1 if the group is paraphyletic
 Args    : -nodes => Array of FAST::Bio::Tree::NodeI objects which are in the tree
           -outgroup => a FAST::Bio::Tree::NodeI to compare the nodes to

reroot

Title   : reroot
Usage   : $tree->reroot($node);
Function: Reroots a tree making a new node the root
Returns : 1 on success, 0 on failure
Args    : FAST::Bio::Tree::NodeI that is in the tree, but is not the current root

reroot_at_midpoint

Title   : reroot_at_midpoint
Usage   : $tree->reroot_at_midpoint($node, $new_root_id);
Function: Reroots a tree on a new node created halfway between the 
          argument and its ancestor
Returns : the new midpoint FAST::Bio::Tree::NodeIon success, 0 on failure
Args    : non-root FAST::Bio::Tree::NodeI currently in $tree
          scalar string, id for new node (optional)

findnode_by_id

Title   : findnode_by_id
Usage   : my $node = $tree->findnode_by_id($id);
Function: Get a node by its id (which should be 
          unique for the tree)
Returns : L<FAST::Bio::Tree::NodeI>
Args    : node id

move_id_to_bootstrap

Title   : move_id_to_bootstrap
Usage   : $tree->move_id_to_bootstrap
Function: Move internal IDs to bootstrap slot
Returns : undef
Args    : undef

add_trait

Example    : $key = $tree->add_trait($trait_file, 3);
Description: Add traits to a FAST::Bio::Tree:Tree nodes
             of a tree from a file.
Returns    : trait name
Exceptions : log an error if a node has no value in the file
Args       : name of trait file (scalar string), 
             index of trait file column (scalar int)
Caller     : main()

The trait file is a tab-delimited text file and needs to have a header line giving names to traits. The first column contains the leaf node ids. Subsequent columns contain different trait value sets. Columns numbering starts from 0. The default trait column is the second (1). The returned hashref has one special key, my_trait_name, that holds the trait name. Single or double quotes are removed.