| Bio::Tools::Run::Phylo::PhyloBase(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Phylo::PhyloBase(3pm) |
Bio::Tools::Run::Phylo::PhyloBase- base module for phylo wrappers
use base qw(Bio::Tools::Run::Phylo::PhyloBase);
For use by Bio::Tools::Run::Phylo modules as a base in place of Bio::Tools::Run::WrapperBase.
This is based on WrapperBase but provides additional phylo-related private helper subs.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : _alignment
Usage : $aln = $obj->_alignment()
Function: Get/set an alignment object, generating one from a file if desired.
Returns : Bio::Align::AlignI (probably a Bio::SimpleAlign)
Args : none to get
OR filename & input format of the alignment file (latter defaults to
guess) to set from file
OR Bio::Align::AlignI to set
Title : _write_alignment
Usage : $obj->_write_alignment()
Function: Writes the alignment object returned by _alignment() out in the
desired format to a temp file.
Returns : filename
Args : string to describe format (default 'fasta'), any other options to pass
to AlignIO
Title : _tree
Usage : $tree = $obj->_tree()
Function: Get/set a tree object, generating one from a file/database if desired
Returns : Bio::Tree::TreeI
Args : none to get, OR to set:
OR filename & input format of the tree file (latter defaults to
guess) to set from file
OR Bio::Tree::TreeI
OR Bio::DB::Taxonomy when _alignment() has been set and where
sequences in the alignment have ids matching species in the taxonomy
database
Title : _write_tree
Usage : $obj->_write_tree()
Function: Writes the tree object returned by _tree() out in the desired format
to a temp file.
Returns : filename
Args : string to describe format (default 'newick')
Title : _get_seq_names
Usage : @names = $obj->_get_seq_names()
Function: Get all the sequence names (from id()) of the sequenes in the
alignment. _alignment() must be set prior to calling this.
Returns : list of strings (seq ids)
Args : none
Title : _get_node_names
Usage : @names = $obj->_get_node_names()
Function: Get all the node names (from id()) of the nodes in the tree.
_tree must be set prior to calling this.
Returns : list of strings (node ids)
Args : none
Title : _check_names
Usage : if ($obj->_check_names) { ... }
Function: Determine if all sequences in the alignment file have a corresponding
node in the tree file. _alignment() and _tree() must be set
prior to calling this.
Returns : boolean (will also warn about the specific problems when returning
false)
Args : none
| 2020-10-28 | perl v5.30.3 |