bio::tree::nodenhx(3pm) [debian man page]
Bio::Tree::NodeNHX(3pm) User Contributed Perl Documentation Bio::Tree::NodeNHX(3pm) NAME
Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags SYNOPSIS
use Bio::Tree::NodeNHX; my $nodeA = Bio::Tree::NodeNHX->new(); my $nodeL = Bio::Tree::NodeNHX->new(); my $nodeR = Bio::Tree::NodeNHX->new(); my $node = Bio::Tree::NodeNHX->new(); $node->add_Descendents($nodeL); $node->add_Descendents($nodeR); print "node is not a leaf " if( $node->is_leaf); DESCRIPTION
Makes a Tree Node with NHX tags, 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://redmine.open-bio.org/projects/bioperl/ AUTHOR - Aaron Mackey Email amackey@virginia.edu CONTRIBUTORS
The NHX (New Hampshire eXtended) format was created by Chris Zmasek, and is described at: http://sourceforge.net/projects/forester-atv/ 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::NodeNHX->new(); Function: Builds a new Bio::Tree::NodeNHX object Returns : Bio::Tree::NodeNHX Args : -left => pointer to Left descendent (optional) -right => pointer to Right descenent (optional) -branch_length => branch length [integer] (optional) -bootstrap => bootstrap value (string) -description => description of node -id => unique id for node -nhx => hashref of NHX tags and values nhx_tag Title : nhx_tag Usage : my $tag = $nodenhx->nhx_tag(%tags); Function: Set tag-value pairs for NHX nodes Returns : none Args : hashref to update the tags/value pairs OR with a scalar value update the bootstrap value by default perl v5.14.2 2012-03-02 Bio::Tree::NodeNHX(3pm)
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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 " 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://redmine.open-bio.org/projects/bioperl/ 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 perl v5.14.2 2012-03-02 Bio::Tree::AnnotatableNode(3pm)