| Bio::Tree::AnnotatableNode(3pm) | User Contributed Perl Documentation | Bio::Tree::AnnotatableNode(3pm) |
NAME¶
Bio::Tree::AnnotatableNode - A Tree Node with support for annotation
SYNOPSIS¶
use Bio::Tree::AnnotatableNode;
my $nodeA = Bio::Tree::AnnotatableNode->new();
my $nodeL = Bio::Tree::AnnotatableNode->new();
my $nodeR = Bio::Tree::AnnotatableNode->new();
my $node = Bio::Tree::AnnotatableNode->new();
$node->add_Descendents($nodeL);
$node->add_Descendents($nodeR);
print "node is not a leaf \n" if( $node->is_leaf);
# $node is-a Bio::AnnotatableI, hence:
my $ann_coll = $node->annotation();
# $ann_coll is-a Bio::AnnotationCollectionI, hence:
my @all_anns = $ann_coll->get_Annotations();
# do something with the annotation objects
DESCRIPTION¶
Makes a Tree Node with Annotations, suitable for building a Tree. See Bio::Tree::Node for a full list of functionality.
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://github.com/bioperl/bioperl-live/issues
AUTHOR - Mira Han¶
Email mirhan@indiana.edu
APPENDIX¶
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new¶
Title : new Usage : my $obj = Bio::Tree::AnnotatableNode->new(); Function: Builds a new Bio::Tree::AnnotatableNode object Returns : Bio::Tree::AnnotatableNode Args : -tostring => code reference to the tostring callback function (optional)
Methods for implementing Bio::AnnotatableI¶
annotation¶
Title : annotation
Usage : $ann = $node->annotation or
$node->annotation($ann)
Function: Gets or sets the annotation
Returns : Bio::AnnotationCollectionI object
Args : None or Bio::AnnotationCollectionI object
See L<Bio::AnnotationCollectionI> and L<Bio::Annotation::Collection>
for more information
Methods for implementing tag access through Annotation::SimpleValue¶
add_tag_value¶
Title : add_tag_value
Usage : $node->add_tag_value($tag,$value)
Function: Adds a tag value to a node
Returns : number of values stored for this tag
Args : $tag - tag name
$value - value to store for the tag
remove_tag¶
Title : remove_tag Usage : $node->remove_tag($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
remove_all_tags¶
Title : remove_all_tags Usage : $node->remove_all_tags() Function: Removes all tags Returns : None Args : None
get_all_tags¶
Title : get_all_tags Usage : my @tags = $node->get_all_tags() Function: Gets all the tag names for this Node Returns : Array of tagnames Args : None
get_tag_values¶
Title : get_tag_values Usage : my @values = $node->get_tag_value($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
has_tag¶
Title : has_tag Usage : $node->has_tag($tag) Function: Boolean test if tag exists in the Node Returns : Boolean Args : $tag - tagname
Methods for implementing to_string¶
to_string_callback¶
Title : to_string_callback Usage : $node->to_string_callback(\&func) Function: get/set callback for to_string Returns : code reference for the to_string callback function Args : \&func - code reference to be set as the callback function
Methods for accessing Bio::Seq¶
sequence¶
Title : sequence
Usage : $ann = $node->sequence or
$node->sequence($seq)
Function: Gets or sets the sequence
Returns : array reference of Bio::SeqI objects
Args : None or Bio::SeqI object
See L<Bio::SeqI> and L<Bio::Seq>
for more information
has_sequence¶
Title : has_sequence
Usage : if( $node->has_sequence) { # do something }
Function: tells if node has sequence attached
Returns : Boolean for whether or not node has Bio::SeqI attached.
Args : None
| 2021-08-15 | perl v5.32.1 |