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Bio::EnsEMBL::Compara::GenomicAlignTree Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::GenomicAlignTree:

List of all members.


Class Summary

Synopsis

Description

Specific subclass of NestedSet to add functionality when the nodes of this tree
are GenomicAlign objects and the tree is a representation of a Protein derived
Phylogenetic tree
 

Definition at line 22 of file GenomicAlignTree.pm.

Available Methods

protected _add_neighbor_link_to_hash ()
protected _add_nodeI_to_node ()
protected _distance ()
protected _internal_newick_format ()
protected _internal_newick_format_ryo ()
protected _internal_nhx_format ()
protected _internal_print_tree ()
protected _internal_string_tree ()
protected _invert_tree_above ()
protected void _load_tags ()
protected String _name_for_sorting ()
protected _parent_id ()
protected _recursive_get_all_leaves ()
protected Listref _recursive_get_all_sorted_leaves ()
protected _root_id ()
protected _set_parent_link ()
protected Int _sort_children ()
protected _unlink_node_in_hash ()
protected _walk_graph_until ()
public Subclass adaptor ()
public Undef add_child ()
public Boolean add_tag ()
public String aligned_sequence ()
public Array alignment_strings ()
public all_links_in_graph ()
public all_nodes_in_graph ()
public alloc ()
public Int ancestral_genomic_align_block_id ()
public void AUTOLOAD ()
public build_leftright_indexing ()
public cascade_unlink ()
public Array children ()
public
Bio::EnsEMBL::Compara::GenomicAlignTree 
copy ()
public copy_graph ()
public copy_shallow_links ()
public create_directed_link_to_node ()
public Compara::Graph::Link create_link_to_node ()
public dealloc ()
public delete_lineage ()
public delete_tag ()
public DESTROY ()
public Undef disavow_parent ()
public Float distance_to_ancestor ()
public Float distance_to_node ()
public Int distance_to_parent ()
public distance_to_root ()
public each_child ()
public Int end ()
public equals ()
public extract_subtree_from_leaves ()
public
Bio::EnsEMBL::Compara::NestedSet 
find_first_shared_ancestor ()
public find_first_shared_ancestor_from_leaves ()
public find_leaf_by_name ()
public find_leaf_by_node_id ()
public find_node_by_name ()
public find_node_by_node_id ()
public Undef flatten_tree ()
public Listref genomic_align_array ()
public
Bio::EnsEMBL::Compara::GenomicAlignGroup 
genomic_align_group ()
public Listref get_all_adjacent_subtrees ()
public Listref get_all_ancestors ()
public Listref get_all_genomic_aligns_for_node ()
public Listref get_all_GenomicAligns ()
public Reference get_all_leaves ()
public get_all_leaves_indexed ()
public Listref get_all_nodes ()
public Listref get_all_nodes_by_tag_value ()
public
Bio::EnsEMBL::Compara::GenomicAlignTree 
get_all_nodes_from_leaves_to_this ()
public
Bio::EnsEMBL::Compara::GenomicAlignTree 
get_all_sorted_genomic_align_nodes ()
public Listref get_all_sorted_leaves ()
public Listref get_all_subnodes ()
public Array get_all_tags ()
public ArrayRef get_all_values_for_tag ()
public get_child_count ()
public void get_original_strand ()
public Scalar get_tagvalue ()
public Hashref get_tagvalue_hash ()
public get_TreeI ()
public Scalar get_value_for_tag ()
public Int group_id ()
public has_ancestor ()
public has_child ()
public has_neighbor ()
public has_parent ()
public Boolean has_tag ()
public init ()
public is_leaf ()
public is_member_of ()
public is_subset_of ()
public left_index ()
public
Bio::EnsEMBL::Compara::GenomicAlignTree 
left_node ()
public Int left_node_id ()
public length ()
public like ()
public link_count ()
public link_for_neighbor ()
public Array links ()
public load_children_if_needed ()
public Int max_depth ()
public Int max_distance ()
public merge_children ()
public merge_node_via_shared_ancestor ()
public
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet 
method_link_species_set ()
public Int method_link_species_set_id ()
public minimize_node ()
public
Bio::EnsEMBL::Compara::NestedSet 
minimize_tree ()
public modern_genomic_align_block_id ()
public String name ()
public neighbors ()
public new ()
public new_from_newick ()
public new_from_TreeI ()
public String newick_format ()
public Undef newick_simple_format ()
public nhx_format ()
public no_autoload_children ()
public Int node_id ()
public Int num_leaves ()
public obj_id ()
public Undef parent ()
public parent_link ()
public void print ()
public print_links ()
public print_node ()
public Undef print_tree ()
public Undef re_root ()
public refcount ()
public
Bio::EnsEMBL::Compara::GenomicAlign 
reference_genomic_align ()
public Int reference_genomic_align_id ()
public
Bio::EnsEMBL::Compara::GenomicAlignTree 
reference_genomic_align_node ()
public Bio::EnsEMBL::Slice reference_slice ()
public Int reference_slice_end ()
public Int reference_slice_start ()
public Int reference_slice_strand ()
public release ()
public release_children ()
public Undef release_tree ()
public
Bio::EnsEMBL::Compara::NestedSet 
remove_nodes ()
public
Bio::EnsEMBL::Compara::GenomicAlignBlock 
restrict_between_alignment_positions ()
public
Bio::EnsEMBL::Compara::GenomicAlignBlock 
restrict_between_reference_positions ()
public retain ()
public void reverse_complement ()
public right_index ()
public
Bio::EnsEMBL::Compara::GenomicAlignTree 
right_node ()
public Int right_node_id ()
public Undef root ()
public scale ()
public scale_max_to ()
public Bio::EnsEMBL::Slice slice ()
public Array sorted_children ()
public Int start ()
public store ()
public store_tag ()
public Int strand ()
public string_node ()
public string_tree ()
public subroot ()
public unlink_all ()
public Undef unlink_neighbor ()

Method Documentation

protected Bio::EnsEMBL::Compara::Graph::Node::_add_neighbor_link_to_hash ( ) [inherited]

Undocumented method

protected Bio::EnsEMBL::Compara::NestedSet::_add_nodeI_to_node ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::NestedSet::_distance ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::NestedSet::_internal_newick_format ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::NestedSet::_internal_newick_format_ryo ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::NestedSet::_internal_nhx_format ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::NestedSet::_internal_print_tree ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::NestedSet::_internal_string_tree ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::NestedSet::_invert_tree_above ( ) [inherited]

Undocumented method

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protected void Bio::EnsEMBL::Compara::Taggable::_load_tags ( ) [inherited]
  Description: loads all the tags (from the database) if possible.
               Otherwise, an empty hash is created
  Example    : $ns_node->_load_tags();
  Returntype : none
  Exceptions : none
  Caller     : internal
 
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protected String Bio::EnsEMBL::Compara::GenomicAlignTree::_name_for_sorting ( )
  Arg         : none
  Example     : my $species_a = $a->_name_for_sorting;
  Description : if the node is a leaf, create a name based on the species
                name, dnafrag name, group_id and the start position. If the 
                node is an internal node, create a name based on the species 
                name, dnafrag name and the start position
  Returntype  : string 
  Exceptions  : none
  Caller      : _sort_children
  Status      : At risk
 
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protected Bio::EnsEMBL::Compara::NestedSet::_parent_id ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::NestedSet::_recursive_get_all_leaves ( ) [inherited]

Undocumented method

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protected Listref Bio::EnsEMBL::Compara::NestedSet::_recursive_get_all_sorted_leaves ( ) [inherited]
  Arg [1]     : hashref $score_by_node
  Example     : my $sorted_leaves = $object->_recursive_get_all_sorted_leaves($score_by_node);
  Description : Recursive code for the get_all_sorted_leaves() method
  Returntype  : listref of Bio::EnsEMBL::Compara::NestedSet (sorted leaves)
  Exceptions  : none
  Caller      : private
  Status      : Stable
 
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protected Bio::EnsEMBL::Compara::NestedSet::_root_id ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::Compara::NestedSet::_set_parent_link ( ) [inherited]

Undocumented method

protected Int Bio::EnsEMBL::Compara::GenomicAlignTree::_sort_children ( )
  Arg         : none
  Example     : sort _sort_children @$children
  Description : sort function for sorting the nodes of a Bio::EnsEMBL::Compara::GenomicAlignTree object
  Returntype  : int (-1,0,1)
  Exceptions  : none
  Caller      : general
  Status      : At risk
 
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protected Bio::EnsEMBL::Compara::Graph::Node::_unlink_node_in_hash ( ) [inherited]

Undocumented method

protected Bio::EnsEMBL::Compara::Graph::Node::_walk_graph_until ( ) [inherited]

Undocumented method

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public Subclass Bio::EnsEMBL::Compara::Graph::CGObject::adaptor ( ) [inherited]
  Arg [1]    : (opt.) subcalss of Bio::EnsEMBL::DBSQL::BaseAdaptor
  Example    : my $object_adaptor = $object->adaptor();
  Example    : $object->adaptor($object_adaptor);
  Description: Getter/Setter for the adaptor this object uses for database
               interaction.
  Returntype : subclass of Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general
 
Code:
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Reimplemented in Bio::EnsEMBL::Compara::SpeciesSet.

public Undef Bio::EnsEMBL::Compara::NestedSet::add_child ( ) [inherited]
  Overview   : attaches child nestedset node to this nested set
  Arg [1]    : Bio::EnsEMBL::Compara::NestedSet $child
  Arg [2]    : (opt.) distance between this node and child
  Example    : $self->add_child($child);
  Returntype : undef
  Exceptions : if child is undef or not a NestedSet subclass
  Caller     : general
 
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public Boolean Bio::EnsEMBL::Compara::Taggable::add_tag ( ) [inherited]
  Description: adds metadata tags to a node.  Both tag and value are added
               as metdata with the added ability to retreive the value given
               the tag (like a perl hash). In case of one to many relation i.e.
               one tag and different values associated with it, the values are
               returned in a array reference.
  Arg [1]    : <string> tag
  Arg [2]    : <string> value
  Arg [3]    : (optional) <int> allows overloading the tag with different values
               default is 0 (no overloading allowed, one tag points to one value)
  Example    : $ns_node->add_tag('scientific name', 'Mammalia');
               $ns_node->add_tag('lost_taxon_id', 9593, 1);
  Returntype : Boolean indicating if the tag could be added
  Exceptions : none
  Caller     : general
 
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public String Bio::EnsEMBL::Compara::GenomicAlignTree::aligned_sequence ( )
  Arg [1]     : -none-
  Example     : $aligned_sequence = $object->aligned_sequence();
  Description : Get the aligned sequence for this node. When the node
                contains one single sequence, it returns its aligned sequence.
                For composite segments, it returns the combined aligned seq.
  Returntype  : string
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Array Bio::EnsEMBL::Compara::GenomicAlignTree::alignment_strings ( )
  Arg [1]    : none
  Example    : $genomic_align_tree->alignment_strings
  Description: Returns the alignment string of all the sequences in the
               alignment
  Returntype : array reference containing several strings
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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public Bio::EnsEMBL::Compara::Graph::Node::all_links_in_graph ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::Compara::Graph::Node::all_nodes_in_graph ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Graph::CGObject::alloc ( ) [inherited]

Undocumented method

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public Int Bio::EnsEMBL::Compara::GenomicAlignTree::ancestral_genomic_align_block_id ( )
  Arg [1]     : (optional) $ancestral_genomic_align_block_id
  Example     : $object->ancestral_genomic_align_block_id($ancestral_genomic_align_block_id);
  Example     : $ancestral_genomic_align_block_id = $object->ancestral_genomic_align_block_id();
  Description : Getter/setter for the ancestral_genomic_align_block_id attribute
                This attribute is intended for the root of the tree only!
  Returntype  : int
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public void Bio::EnsEMBL::Compara::Taggable::AUTOLOAD ( ) [inherited]
  Description: matches the get_value_for_XXX calls to get_value_for_tag('XXX') and other calls
  Returntype : none
  Exceptions : none
  Caller     : system
 
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public Bio::EnsEMBL::Compara::NestedSet::build_leftright_indexing ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Graph::Node::cascade_unlink ( ) [inherited]
  Overview   : release all neighbors and clear arrays and hashes
               will cause potential deletion of neighbors if refcount reaches Zero.
  Example    : $self->cascade_unlink
  Returntype : $self
  Exceptions : none
  Caller     : general
 
public Array Bio::EnsEMBL::Compara::NestedSet::children ( ) [inherited]
  Overview   : returns a list of NestedSet nodes directly under this parent node
  Example    : my @children = @{$object->children()};
  Returntype : array reference of Bio::EnsEMBL::Compara::NestedSet objects (could be empty)
  Exceptions : none
  Caller     : general
  Algorithm  : new algorithm for fetching children:
                for each link connected to this NestedsSet node, a child is defined if
                  old: the link is not my parent_link
                  new: the link's neighbors' parent_link is the link
               This allows one (with a carefully coded algorithm) to overlay a tree on top
               of a fully connected graph and use the parent/children methods of NestedSet
               to walk the 'tree' substructure of the graph.  
               Trees that are really just trees are still trees.
 
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public Bio::EnsEMBL::Compara::GenomicAlignTree Bio::EnsEMBL::Compara::GenomicAlignTree::copy ( )
  Arg         : none
  Example     : my $new_tree = $this_tree->copy()
  Description : Create a copy of this Bio::EnsEMBL::Compara::GenomicAlignTree
                object
  Returntype  : Bio::EnsEMBL::Compara::GenomicAlignTree
  Exceptions  : none
  Caller      : general
  Status      : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::NestedSet.

public Bio::EnsEMBL::Compara::Graph::Node::copy_graph ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Graph::Node::copy_shallow_links ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::Compara::Graph::Node::create_directed_link_to_node ( ) [inherited]

Undocumented method

public Compara::Graph::Link Bio::EnsEMBL::Compara::Graph::Node::create_link_to_node ( ) [inherited]
  Overview   : attaches neighbor Graph::Node to this nested set
  Arg [1]    : Bio::EnsEMBL::Compara::Graph::Node $node
  Arg [2]    : (opt.) <float> distance to node
  Example    : $self->add_child($node);
  Returntype : Compara::Graph::Link object
  Exceptions : if neighbor is undef or not a NestedSet subclass
  Caller     : general
 
public Bio::EnsEMBL::Compara::NestedSet::dealloc ( ) [inherited]

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

public Bio::EnsEMBL::Compara::NestedSet::delete_lineage ( ) [inherited]
  Arg [1]     : Bio::EnsEMBL::Compara::NestedSet $node
  Example     : $tree->delete_lineage($node);
  Description : Removes $node from tree. Nodes should be in the tree.
  Returntype  : 
  Exceptions  :
  Caller      : general
  Status      : At risk (behaviour on exceptions could change)
 
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public Bio::EnsEMBL::Compara::Taggable::delete_tag ( ) [inherited]
  Description: removes a tag from the metadata. If the value is provided, it tries
               to delete only it (if present). Otherwise, it just clears the tag,
               whatever value it was containing
  Arg [1]    : <string> tag
  Arg [2]    : (optional) <string> value
  Example    : $ns_node->remove_tag('scientific name', 'Mammalia');
               $ns_node->remove_tag('lost_taxon_id', 9593);
  Returntype : 0 if the tag couldn't be removed,
               1 if it is only in the PERL object,
               2 if it is also stored in the database
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Graph::CGObject::DESTROY ( ) [inherited]

Undocumented method

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public Undef Bio::EnsEMBL::Compara::NestedSet::disavow_parent ( ) [inherited]
  Overview   : unlink and release self from its parent
               might cause self to delete if refcount reaches Zero.
  Example    : $self->disavow_parent
  Returntype : undef
  Caller     : general
 
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public Float Bio::EnsEMBL::Compara::NestedSet::distance_to_ancestor ( ) [inherited]
  Arg [1]     : Bio::EnsEMBL::Compara::NestedSet $ancestor
  Example     : my $distance = $this_node->distance_to_ancestor($ancestor);
  Description : Calculates the distance in the tree between this node and
                its ancestor $ancestor
  Returntype  : float
  Exceptions  : throws if $ancestor is not an ancestor of this node.
  Caller      : general
  Status      : Stable
 
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public Float Bio::EnsEMBL::Compara::NestedSet::distance_to_node ( ) [inherited]
  Arg [1]     : Bio::EnsEMBL::Compara::NestedSet $node
  Example     : my $distance = $this_node->distance_to_node($other_node);
  Description : Calculates the distance in the tree between these
                two nodes.
  Returntype  : float
  Exceptions  : returns undef if no ancestor can be found, no distances are
                defined in the tree, etc.
  Caller      : general
  Status      : Stable
 
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public Int Bio::EnsEMBL::Compara::NestedSet::distance_to_parent ( ) [inherited]
  Arg [1]    : (opt.) <int or double> distance
  Example    : my $dist = $object->distance_to_parent();
  Example    : $object->distance_to_parent(1.618);
  Description: Getter/Setter for the distance between this child and its parent
  Returntype : integer node_id
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::NestedSet::distance_to_root ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::each_child ( ) [inherited]

Undocumented method

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public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::end ( ) [inherited]
  Arg [1]    : (optional) integer $end
  Example    : my $end = $genomic_align_block->end;
  Example    : $genomic_align_block->end(1283);
  Description: get/set for attribute reference_slice_end. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Graph::Node::equals ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::extract_subtree_from_leaves ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::NestedSet::find_first_shared_ancestor ( ) [inherited]
  Arg [1]     : Bio::EnsEMBL::Compara::NestedSet $node
  Example     : my $ancestor = $this_node->find_first_shared_ancestor($other_node);
  Description : Gets the first common ancestor between this node and the other one.
  Returntype  : Bio::EnsEMBL::Compara::NestedSet object
  Exceptions  :
  Caller      : general
  Status      : Stable
 
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public Bio::EnsEMBL::Compara::NestedSet::find_first_shared_ancestor_from_leaves ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::find_leaf_by_name ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::find_leaf_by_node_id ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::find_node_by_name ( ) [inherited]

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

public Bio::EnsEMBL::Compara::NestedSet::find_node_by_node_id ( ) [inherited]

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

public Undef Bio::EnsEMBL::Compara::NestedSet::flatten_tree ( ) [inherited]
  Overview   : Removes all internal nodes and attaches leaves to the tree root, creating
               a "flattened" star tree structure.
  Example    : $node->flatten_tree();
  Returntype : undef or Bio::EnsEMBL::Compara::NestedSet
  Exceptions : none
  Caller     : general
 
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public Listref Bio::EnsEMBL::Compara::GenomicAlignTree::genomic_align_array ( )
  Arg [1]     : -none-
  Example     : $genomic_aligns = $object->genomic_align_array
  Description : Alias for get_all_genomic_aligns_for_node. TO BE

Deprecated:
Returntype : listref of Bio::EnsEMBL::Compara::GenomicAlign objects Exceptions : none Caller : general Status : Stable
 
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public Bio::EnsEMBL::Compara::GenomicAlignGroup Bio::EnsEMBL::Compara::GenomicAlignTree::genomic_align_group ( )
  Arg [1]     : (optional) $genomic_align_group
  Example     : $object->genomic_align_group($genomic_align_group);
  Example     : $genomic_align_group = $object->genomic_align_group();
  Description : Getter/setter for the genomic_align_group attribute
  Returntype  : Bio::EnsEMBL::Compara::GenomicAlignGroup object
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Listref Bio::EnsEMBL::Compara::NestedSet::get_all_adjacent_subtrees ( ) [inherited]
  Arg 1       : 
  Example     : my @subtrees = @{$node->get_all_adjacent_subtrees};
  Description : Returns subtree 'root' nodes where the subtree is adjacent
                to this node. Used e.g. by the web code for the 'collapse 
                other nodes' action 
  ReturnType  : listref of Bio::EnsEMBL::Compara::NestedSet objects
  Exceptions  : none
  Caller      : EnsEMBL::Web::Component::Gene::ComparaTree
  Status      :
 
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public Listref Bio::EnsEMBL::Compara::NestedSet::get_all_ancestors ( ) [inherited]
  Arg 1       : 
  Example     : my @ancestors = @{$node->get_all_ancestors};
  Description : Returns all ancestor nodes for a given node
  ReturnType  : listref of Bio::EnsEMBL::Compara::NestedSet objects
  Exceptions  : none
  Caller      : general
  Status      :
 
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public Listref Bio::EnsEMBL::Compara::GenomicAlignTree::get_all_genomic_aligns_for_node ( )
  Arg [1]     : -none-
  Example     : $genomic_aligns = $object->get_all_genomic_aligns_for_node
  Description : Getter for all the GenomicAligns contained in the
                genomic_align_group object on a node. This method is a short
                cut for $object->genomic_align_group->get_all_GenomicAligns()
  Returntype  : listref of Bio::EnsEMBL::Compara::GenomicAlign objects
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Listref Bio::EnsEMBL::Compara::GenomicAlignTree::get_all_GenomicAligns ( )
  Arg [1]     : -none-
  Example     : $genomic_aligns = $object->get_all_GenomicAligns
  Description : Alias for get_all_genomic_aligns_for_node. TO BE

Deprecated:
Returntype : listref of Bio::EnsEMBL::Compara::GenomicAlign objects Exceptions : none Caller : general Status : Stable
 
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public Reference Bio::EnsEMBL::Compara::GenomicAlignTree::get_all_leaves ( )
 Title   : get_all_leaves
 Usage   : my @leaves = @{$tree->get_all_leaves};
 Function: searching from the given starting node, searches and creates list
           of all leaves in this subtree and returns by reference.
           This method overwrites the parent method because it sorts
           the leaves according to their node_id. Here, we use this method
           to get all leaves in another sorting function. Not only it doesn't
           make much sense to sort something that will be sorted again, but
           it can also produce some Perl errors as sort methods uses $a and
           $b which are package global variables.
 Example :
 Returns : reference to list of NestedSet objects (all leaves)
 Args    : none
 Status  : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::NestedSet.

public Bio::EnsEMBL::Compara::NestedSet::get_all_leaves_indexed ( ) [inherited]

Undocumented method

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public Listref Bio::EnsEMBL::Compara::NestedSet::get_all_nodes ( ) [inherited]
  Arg 1       : hashref $node_hash [used for recursivity, do not use it!]
  Example     : my $all_nodes = $root->get_all_nodes();
  Description : Returns this and all underlying sub nodes
  ReturnType  : listref of Bio::EnsEMBL::Compara::NestedSet objects
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Listref Bio::EnsEMBL::Compara::NestedSet::get_all_nodes_by_tag_value ( ) [inherited]
  Arg 1       : tag_name
  Arg 2       : tag_value (optional)
  Example     : my $all_nodes = $root->get_all_nodes_by_tagvalue('taxon_name'=>'Mamalia');
  Description : Returns all underlying nodes that have a tag of the given name, and optionally a value of the given value.
  ReturnType  : listref of Bio::EnsEMBL::Compara::NestedSet objects
  Exceptions  : none
  Caller      : general
  Status      :
 
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public Bio::EnsEMBL::Compara::GenomicAlignTree Bio::EnsEMBL::Compara::GenomicAlignTree::get_all_nodes_from_leaves_to_this ( )
  Arg[1]      : Bio::EnsEMBL::Compara::GenomicAlignTree $all_nodes
  Example     : my $all_nodes = get_all_nodes_from_leaves_to_this()
  Description : 
  Returntype  : Bio::EnsEMBL::Compara::GenomicAlignTree object
  Exceptions  : none
  Caller      : general
  Status      : At risk
 
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public Bio::EnsEMBL::Compara::GenomicAlignTree Bio::EnsEMBL::Compara::GenomicAlignTree::get_all_sorted_genomic_align_nodes ( )
  Arg [1]     : (optional) Bio::EnsEMBL::Compara::GenomicAlignTree $reference_genomic_align_node
  Example     : $object->get_all_sorted_genomic_align_nodes($ref_genomic_align_node);
  Example     : $nodes = $object->get_all_sorted_genomic_align_nodes();
  Description : If ref_genomic_align_node is set, sorts the tree based on the
                reference_genomic_align_node
                If ref_genomic_align_node is not set, sorts the tree based on
                the species name
  Returntype  : Bio::EnsEMBL::Compara::GenomicAlignTree
  Exceptions  : none
  Caller      : general
  Status      : At risk
 
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public Listref Bio::EnsEMBL::Compara::NestedSet::get_all_sorted_leaves ( ) [inherited]
  Arg [1]     : Bio::EnsEMBL::Compara::NestedSet $top_leaf
  Arg [...]   : (optional) Bio::EnsEMBL::Compara::NestedSet $secondary_priority_leaf
  Example     : my $sorted_leaves = $object->get_all_sorted_leaves($human_leaf);
  Example     : my $sorted_leaves = $object->get_all_sorted_leaves($human_leaf, $mouse_leaf);
  Description : Sorts the tree such as $top_leaf is the first leave and returns
                all the other leaves in the order defined by the tree.
                It is possible to define as many secondary top leaves as you require
                to sort other branches of the tree. The priority to sort the trees
                is defined by the order in which you specify the leaves.
  Returntype  : listref of Bio::EnsEMBL::Compara::NestedSet (all sorted leaves)
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Listref Bio::EnsEMBL::Compara::NestedSet::get_all_subnodes ( ) [inherited]
  Arg 1       : hashref $node_hash [used for recursivity, do not use it!]
  Example     : my $all_nodes = $root->get_all_nodes();
  Description : Returns all underlying sub nodes
  ReturnType  : listref of Bio::EnsEMBL::Compara::NestedSet objects
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Array Bio::EnsEMBL::Compara::Taggable::get_all_tags ( ) [inherited]
  Description: returns an array of all the available tags
  Example    : $ns_node->get_all_tags();
  Returntype : Array
  Exceptions : none
  Caller     : general
 
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public ArrayRef Bio::EnsEMBL::Compara::Taggable::get_all_values_for_tag ( ) [inherited]
  Description: returns all the values of the tag, or $default (undef
               if not provided) if the tag doesn't exist. In case of
               a single value, it is wrapped with an array
  Arg [1]    : <string> tag
  Arg [2]    : (optional) <scalar> default
  Example    : $ns_node->get_tagvalue('scientific name');
  Returntype : ArrayRef
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::NestedSet::get_child_count ( ) [inherited]

Undocumented method

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public void Bio::EnsEMBL::Compara::BaseGenomicAlignSet::get_original_strand ( ) [inherited]
  Args       : none
  Example    : if (!$genomic_align_block->get_original_strand()) {
                 # original GenomicAlignBlock has been reverse-complemented
               }
  Description: getter for the _orignal_strand attribute
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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public Scalar Bio::EnsEMBL::Compara::Taggable::get_tagvalue ( ) [inherited]
  Description: returns the value(s) of the tag, or $default (undef
               if not provided) if the tag doesn't exist.
  Arg [1]    : <string> tag
  Arg [2]    : (optional) <scalar> default
  Example    : $ns_node->get_tagvalue('scientific name');
  Returntype : Scalar or ArrayRef
  Exceptions : none
  Caller     : general
 
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public Hashref Bio::EnsEMBL::Compara::Taggable::get_tagvalue_hash ( ) [inherited]
  Description: returns the underlying hash that contains all
               the tags
  Example    : $ns_node->get_tagvalue_hash();
  Returntype : Hashref
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::NestedSet::get_TreeI ( ) [inherited]

Undocumented method

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public Scalar Bio::EnsEMBL::Compara::Taggable::get_value_for_tag ( ) [inherited]
  Description: returns the value of the tag, or $default (undef
               if not provided) if the tag doesn't exist. In case
               of multiple values, the first one is returned.
  Arg [1]    : <string> tag
  Arg [2]    : (optional) <scalar> default
  Example    : $ns_node->get_tagvalue('scientific name');
  Returntype : Scalar
  Exceptions : none
  Caller     : general
 
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public Int Bio::EnsEMBL::Compara::GenomicAlignTree::group_id ( )
  Arg [1]    : integer $group_id
  Example    : my $group_id = $genomic_align_tree->group_id;
  Example    : $genomic_align_tree->group_id(1234);
  Description: get/set for attribute group_id of the underlying
               GenomicAlignBlock objects
  Returntype : integer
  Exceptions : A GenomicAlignTree is made of two GenomicAlignBlock
               object. The method fail when gettign the value if the
               two group_ids do not match
  Caller     : general
 
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public Bio::EnsEMBL::Compara::NestedSet::has_ancestor ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::has_child ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Graph::Node::has_neighbor ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::has_parent ( ) [inherited]

Undocumented method

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public Boolean Bio::EnsEMBL::Compara::Taggable::has_tag ( ) [inherited]
  Description: indicates whether the tag exists in the metadata
  Arg [1]    : <string> tag
  Example    : $ns_node->has_tag('scientific name');
  Returntype : Boolean
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::NestedSet::init ( ) [inherited]

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

public Bio::EnsEMBL::Compara::NestedSet::is_leaf ( ) [inherited]

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

public Bio::EnsEMBL::Compara::NestedSet::is_member_of ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::is_subset_of ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::left_index ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::GenomicAlignTree Bio::EnsEMBL::Compara::GenomicAlignTree::left_node ( )
  Arg [1]     : -none-
  Example     : $left_node = $object->left_node();
  Description : Get the left_node object from the database.
  Returntype  : Bio::EnsEMBL::Compara::GenomicAlignTree object
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Int Bio::EnsEMBL::Compara::GenomicAlignTree::left_node_id ( )
  Arg [1]     : (optional) $left_node_id
  Example     : $object->left_node_id($left_node_id);
  Example     : $left_node_id = $object->left_node_id();
  Description : Getter/setter for the left_node_id attribute
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Bio::EnsEMBL::Compara::GenomicAlignTree::length ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Graph::Node::like ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Graph::Node::link_count ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::Compara::Graph::Node::link_for_neighbor ( ) [inherited]

Undocumented method

public Array Bio::EnsEMBL::Compara::Graph::Node::links ( ) [inherited]
  Overview   : returns a list of Compara::Graph::Link connected to this node
  Example    : my @links = @{self->links()};
  Returntype : array reference of Bio::EnsEMBL::Compara::Graph::Link objects (could be empty)
  Exceptions : none
  Caller     : general
 
public Bio::EnsEMBL::Compara::NestedSet::load_children_if_needed ( ) [inherited]

Undocumented method

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public Int Bio::EnsEMBL::Compara::NestedSet::max_depth ( ) [inherited]
 Title   : max_depth
 Args    : none
 Usage   : $tree_node->max_depth;
 Function: searching from the given starting node, calculates the maximum depth to a leaf
 Returns : int
 
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public Int Bio::EnsEMBL::Compara::NestedSet::max_distance ( ) [inherited]
 Title   : max_distance
 Args    : none
 Usage   : $tree_node->max_distance;
 Function: searching from the given starting node, calculates the maximum distance to a leaf
 Returns : int
 
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public Bio::EnsEMBL::Compara::NestedSet::merge_children ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::merge_node_via_shared_ancestor ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::MethodLinkSpeciesSet Bio::EnsEMBL::Compara::GenomicAlignTree::method_link_species_set ( )
  Arg [1]    : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $method_link_species_set
  Example    : $method_link_species_set = $genomic_align_tree->method_link_species_set;
  Description: Getter for attribute method_link_species_set. Takes this from the first Bio::EnsEMBL::Compara::GenomicAlign
               object
  Returntype : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Exceptions : thrown if $method_link_species_set is not a
               Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Caller     : general
  Status     : Stable
 
public Int Bio::EnsEMBL::Compara::GenomicAlignTree::method_link_species_set_id ( )
  Arg [1]    : integer $method_link_species_set_id
  Example    : $method_link_species_set_id = $genomic_align_tree->method_link_species_set_id;
  Description: Getter for the attribute method_link_species_set_id. Takes this from the first 
               Bio::EnsEMBL::Compara::GenomicAlign object
  Returntype : integer
  Caller     : object::methodname
  Status     : Stable
 
public Bio::EnsEMBL::Compara::NestedSet::minimize_node ( ) [inherited]

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

public Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::NestedSet::minimize_tree ( ) [inherited]
  Arg [1]     : -none-
  Example     : $leaf->disavow_parent();
                $tree = $tree->minimize_tree();
  Description : Returns the tree after removing internal nodes that do not
                represent an multi- or bi-furcation anymore. This is typically
                required after disavowing a node. Please ensure you use the
                object returned by the method and not the original object
                anymore!
  Returntype  : Bio::EnsEMBL::Compara::NestedSet object
  Exceptions  :
  Caller      : general
  Status      : Stable
 
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public Bio::EnsEMBL::Compara::GenomicAlignTree::modern_genomic_align_block_id ( )
  Arg [1]     : (optional) $modern_genomic_align_block_id
  Example     : $object->modern_genomic_align_block_id($modern_genomic_align_block_id);
  Example     : $modern_genomic_align_block_id = $object->modern_genomic_align_block_id();
  Description : Getter/setter for the modern_genomic_align_block_id attribute
  Returntype  : 
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public String Bio::EnsEMBL::Compara::GenomicAlignTree::name ( )
  Arg [1]     : (optional) string $name
  Example     : $object->name($name);
  Example     : $name = $object->name();
  Description : Getter/setter for the name attribute.
  Returntype  : string
  Exceptions  : none
  Caller      : general
  Status      : At risk
 
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Reimplemented from Bio::EnsEMBL::Compara::Graph::CGObject.

public Bio::EnsEMBL::Compara::Graph::Node::neighbors ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Graph::CGObject::new ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::Compara::Graph::Link, and Bio::EnsEMBL::Compara::SpeciesSet.

public Bio::EnsEMBL::Compara::NestedSet::new_from_newick ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::new_from_TreeI ( ) [inherited]

Undocumented method

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public String Bio::EnsEMBL::Compara::NestedSet::newick_format ( ) [inherited]
  Arg [1]     : string $format_mode
  Example     : $this_node->newick_format("full");
  Description : Prints this tree in Newick format. Several modes are
                available: full, display_label_composite, simple, species,
                species_short_name, ncbi_taxon, ncbi_name, njtree and phylip
  Returntype  : string
  Exceptions  :
  Caller      : general
  Status      : Stable
 
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public Undef Bio::EnsEMBL::Compara::NestedSet::newick_simple_format ( ) [inherited]
  Arg [1]     : -none-
  Example     : $this_node->newick_simple_format();
  Description : Prints this tree in simple Newick format. This is an
                alias for $this_node->newick_format("simple");
  Returntype  : undef
  Exceptions  :
  Caller      : general
  Status      : Stable
 
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public Bio::EnsEMBL::Compara::NestedSet::nhx_format ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::no_autoload_children ( ) [inherited]

Undocumented method

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public Int Bio::EnsEMBL::Compara::Graph::Node::node_id ( ) [inherited]
  Arg [1]    : (opt.) integer node_id
  Example    : my $nsetID = $object->node_id();
  Example    : $object->node_id(12);
  Description: Getter/Setter for the node_id of this object in the database
  Returntype : integer node_id
  Exceptions : none
  Caller     : general
 
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public Int Bio::EnsEMBL::Compara::NestedSet::num_leaves ( ) [inherited]
  Example     : my $num_leaves = $node->num_leaves
  Description : Returns the number of leaves underlying the node
  ReturnType  : integer
  Exceptions  : none
  Caller      : general
  Status      : At risk (relies on left and right indexes)
 
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public Bio::EnsEMBL::Compara::Graph::CGObject::obj_id ( ) [inherited]
  Example    : my $nsetID = $object->obj_id();
  Description: returns the unique identifier of this object.  
  Returntype : <string> uuid
  Exceptions : none
  Caller     : general
 
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public Undef Bio::EnsEMBL::Compara::NestedSet::parent ( ) [inherited]
  Overview   : returns the parent NestedSet object for this node
  Example    : my $my_parent = $object->parent();
  Returntype : undef or Bio::EnsEMBL::Compara::NestedSet
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::NestedSet::parent_link ( ) [inherited]

Undocumented method

public void Bio::EnsEMBL::Compara::GenomicAlignTree::print ( )
  Arg         : none
  Example     : print()
  Description : Print the fields in a Bio::EnsEMBL::Compara::GenomicAlignTree 
  Returntype  : none
  Exceptions  : none
  Caller      : general
  Status      : At risk
 
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public Bio::EnsEMBL::Compara::Graph::Node::print_links ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::print_node ( ) [inherited]

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

Reimplemented in Bio::EnsEMBL::Compara::GeneTreeMember, and Bio::EnsEMBL::Compara::NCBITaxon.

public Undef Bio::EnsEMBL::Compara::NestedSet::print_tree ( ) [inherited]
  Arg [1]     : int $scale
  Example     : $this_node->print_tree(100);
  Description : Prints this tree in ASCII format. The scale is used to define
                the width of the tree in the output
  Returntype  : undef
  Exceptions  :
  Caller      : general
  Status      : At risk (as the output might change)
 
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public Undef Bio::EnsEMBL::Compara::NestedSet::re_root ( ) [inherited]
  Overview   : rearranges the tree structure so that the root is moved to 
               beetween this node and its parent.  If the old root was more than
	       bifurcated (2 children) a new node is created where it was to hold
	       the multiple children that arises from the re-rooting.  
	       The old root is returned.
  Example    : $node->re_root();
  Returntype : undef or Bio::EnsEMBL::Compara::NestedSet
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Graph::CGObject::refcount ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::GenomicAlign Bio::EnsEMBL::Compara::GenomicAlignTree::reference_genomic_align ( )
  Arg [1]     : (optional) $reference_genomic_align
  Example     : $object->reference_genomic_align($reference_genomic_align);
  Example     : $reference_genomic_align = $object->reference_genomic_align();
  Description : Getter/setter for the reference_genomic_align attribute
  Returntype  : Bio::EnsEMBL::Compara::GenomicAlign object
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Int Bio::EnsEMBL::Compara::GenomicAlignTree::reference_genomic_align_id ( )
  Arg [1]    : integer $reference_genomic_align_id
  Example    : $genomic_align_block->reference_genomic_align_id(4321);
  Description: get/set for attribute reference_genomic_align_id. A value of 0 will set the
               reference_genomic_align_id attribute to undef. When looking for genomic
               alignments in a given slice or dnafrag, the reference_genomic_align
               corresponds to the Bio::EnsEMBL::Compara::GenomicAlign included in the
               starting slice or dnafrag. The reference_genomic_align_id is the dbID
               corresponding to the reference_genomic_align. All remaining
               Bio::EnsEMBL::Compara::GenomicAlign objects included in the
               Bio::EnsEMBL::Compara::GenomicAlignBlock are the
               non_reference_genomic_aligns.
               Synchronises reference_genomic_align and reference_genomic_align_id
               attributes.
  Returntype : integer
  Exceptions : throw if $reference_genomic_align_id id not a postive number
  Caller     : $genomic_align_block->reference_genomic_align_id(int)
  Status     : Stable
 
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public Bio::EnsEMBL::Compara::GenomicAlignTree Bio::EnsEMBL::Compara::GenomicAlignTree::reference_genomic_align_node ( )
  Arg [1]     : (optional) $reference_genomic_align_node
  Example     : $object->reference_genomic_align_node($reference_genomic_align_node);
  Example     : $reference_genomic_align_node = $object->reference_genomic_align_node();
  Description : Getter/setter for the reference_genomic_align_node attribute
  Returntype  : Bio::EnsEMBL::Compara::GenomicAlignTree object
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice ( ) [inherited]
  Arg [1]    : (optional) Bio::EnsEMBL::Slice $reference_slice
  Example    : my $reference_slice = $genomic_align_block->reference_slice;
  Example    : $genomic_align_block->reference_slice($slice);
  Description: Alias for slice method. TO BE

Deprecated:
Returntype : Bio::EnsEMBL::Slice object Exceptions : Caller : general Status : Stable
 
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public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice_end ( ) [inherited]
  Arg [1]    : integer $reference_slice_end
  Example    : my $reference_slice_end = $genomic_align_block->reference_slice_end;
  Example    : $genomic_align_block->reference_slice_end(1283);
  Description: get/set for attribute reference_slice_end. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice_start ( ) [inherited]
  Arg [1]    : integer $reference_slice_start
  Example    : my $reference_slice_start = $genomic_align_block->reference_slice_start;
  Example    : $genomic_align_block->reference_slice_start(1035);
  Description: get/set for attribute reference_slice_start. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice_strand ( ) [inherited]
  Arg [1]    : integer $reference_slice_strand
  Example    : my $reference_slice_strand = $genomic_align_block->reference_slice_strand;
  Example    : $genomic_align_block->reference_slice_strand(-1);
  Description: get/set for attribute reference_slice_strand. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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public Bio::EnsEMBL::Compara::Graph::CGObject::release ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::release_children ( ) [inherited]
  Overview   : recursive releases all children
               will cause potential deletion of children if refcount reaches Zero.
  Example    : $self->release_children
  Returntype : $self
  Exceptions : none
  Caller     : general
 
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public Undef Bio::EnsEMBL::Compara::NestedSet::release_tree ( ) [inherited]
  Overview   : deletes and frees the memory used by this tree
               and all the underlying nodes.
  Example    : $self->release_tree;
  Returntype : undef
  Exceptions : none
  Caller     : general
 
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Reimplemented in Bio::EnsEMBL::Compara::GeneTreeNode.

public Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::NestedSet::remove_nodes ( ) [inherited]
  Arg [1]     : arrayref Bio::EnsEMBL::Compara::NestedSet $nodes
  Example     : my $ret_tree = $tree->remove_nodes($nodes);
  Description : Returns the tree with removed nodes in list. Nodes should be in the tree.
  Returntype  : Bio::EnsEMBL::Compara::NestedSet object
  Exceptions  :
  Caller      : general
  Status      : At risk (behaviour on exceptions could change)
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlignBlock Bio::EnsEMBL::Compara::GenomicAlignTree::restrict_between_alignment_positions ( )
  Arg[1]     : [optional] int $start, refers to the start of the alignment
  Arg[2]     : [optional] int $end, refers to the start of the alignment
  Arg[3]     : [optional] boolean $skip_empty_GenomicAligns
  Example    : none
  Description: restrict this GenomicAlignBlock. It returns a new object unless no
               restriction is needed. In that case, it returns the original unchanged
               object.
               This method uses coordinates relative to the alignment itself.
               For instance if you have an alignment like:
                            1    1    2    2    3
                   1   5    0    5    0    5    0
                   AAC--CTTGTGGTA-CTACTT-----ACTTT
                   AACCCCTT-TGGTATCTACTTACCTAACTTT
               and you restrict it between 5 and 25, you will get back a
               object containing the following alignment:
                            1    1
                   1   5    0    5
                   CTTGTGGTA-CTACTT----
                   CTT-TGGTATCTACTTACCT
               See restrict_between_reference_positions() elsewhere in this document
               for an alternative method using absolute genomic coordinates.
               NB: This method works only for GenomicAlignBlock which have been
               fetched from the DB as it is adjusting the dnafrag coordinates
               and the cigar_line only and not the actual sequences stored in the
               object if any. If you want to restrict an object with no coordinates
               a simple substr() will do!
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignBlock object
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlignBlock Bio::EnsEMBL::Compara::GenomicAlignTree::restrict_between_reference_positions ( )
  Arg[1]     : [optional] int $start, refers to the reference_dnafrag
  Arg[2]     : [optional] int $end, refers to the reference_dnafrag
  Arg[3]     : [optional] Bio::EnsEMBL::Compara::GenomicAlign $reference_GenomicAlign
  Arg[4]     : [optional] boolean $skip_empty_GenomicAligns [ALWAYS FALSE]
  Example    : none
  Description: restrict this GenomicAlignBlock. It returns a new object unless no
               restriction is needed. In that case, it returns the original unchanged
               object
               It might be the case that the restricted region coincide with a gap
               in one or several GenomicAligns. By default these GenomicAligns are
               returned with a dnafrag_end equals to its dnafrag_start + 1. For instance,
               a GenomicAlign with dnafrag_start = 12345 and dnafrag_end = 12344
               correspond to a block which goes on this region from before 12345 to
               after 12344, ie just between 12344 and 12345. You can choose to remove
               these empty GenomicAligns by setting $skip_empty_GenomicAligns to any
               true value.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignBlock object in scalar context. In
               list context, returns the previous object and the start and end
               positions of the restriction in alignment coordinates (from 1 to
               alignment_length)
  Exceptions : return undef if reference positions lie outside of the alignment
  Caller     : general
  Status     : At risk
 
Code:
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Reimplemented from Bio::EnsEMBL::Compara::BaseGenomicAlignSet.

public Bio::EnsEMBL::Compara::Graph::CGObject::retain ( ) [inherited]

Undocumented method

Code:
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public void Bio::EnsEMBL::Compara::GenomicAlignTree::reverse_complement ( )
  Args       : none
  Example    : none
  Description: reverse complement the tree,
               modifying dnafrag_strand and cigar_line of each GenomicAlign in consequence
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Bio::EnsEMBL::Compara::NestedSet::right_index ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::GenomicAlignTree Bio::EnsEMBL::Compara::GenomicAlignTree::right_node ( )
  Arg [1]     : -none-
  Example     : $left_node = $object->right_node();
  Description : Get the right_node object from the database.
  Returntype  : Bio::EnsEMBL::Compara::GenomicAlignTree object
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::GenomicAlignTree::right_node_id ( )
  Arg [1]     : (optional) $right_node_id
  Example     : $object->right_node_id($right_node_id);
  Example     : $right_node_id = $object->right_node_id();
  Description : Getter/setter for the right_node_id attribute
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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public Undef Bio::EnsEMBL::Compara::NestedSet::root ( ) [inherited]
  Overview   : returns the root NestedSet object for this node
               returns $self if node has no parent (this is the root)
  Example    : my $root = $object->root();
  Description: Returns the root of the tree for this node
               with links to all the intermediate nodes. Sister nodes
               are not included in the result.
  Returntype : undef or Bio::EnsEMBL::Compara::NestedSet
  Exceptions : none
  Caller     : general
 
Code:
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Reimplemented in Bio::EnsEMBL::Compara::GeneTreeNode.

public Bio::EnsEMBL::Compara::NestedSet::scale ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::NestedSet::scale_max_to ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::BaseGenomicAlignSet::slice ( ) [inherited]
  Arg [1]    : (optional) Bio::EnsEMBL::Slice $reference_slice
  Example    : my $slice = $genomic_align_block->slice;
  Example    : $genomic_align_block->slice($slice);
  Description: get/set for attribute slice.
  Returntype : Bio::EnsEMBL::Slice object
  Exceptions : 
  Caller     : general
  Status     : Stable
 
Code:
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public Array Bio::EnsEMBL::Compara::NestedSet::sorted_children ( ) [inherited]
  Overview   : returns a sorted list of NestedSet nodes directly under this parent node
               sort so that internal nodes<leaves and then on distance
  Example    : my @kids = @{$object->ordered_children()};
  Returntype : array reference of Bio::EnsEMBL::Compara::NestedSet objects (could be empty)
  Exceptions : none
  Caller     : general
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::start ( ) [inherited]
  Arg [1]    : (optional) integer $start
  Example    : my $start = $genomic_align_block->start;
  Example    : $genomic_align_block->start(1035);
  Description: get/set for attribute reference_slice_start. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::Graph::CGObject::store ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Taggable::store_tag ( ) [inherited]
  Description: calls add_tag and then stores the tag in the database. Has the
               exact same arguments as add_tag
  Arg [1]    : <string> tag
  Arg [2]    : <string> value
  Arg [3]    : (optional) <int> allows overloading the tag with different values
               default is 0 (no overloading allowed, one tag points to one value)
  Example    : $ns_node->store_tag('scientific name', 'Mammalia');
               $ns_node->store_tag('lost_taxon_id', 9593, 1);
  Returntype : 0 if the tag couldn't be stored,
               1 if it is only in the PERL object,
               2 if it is also stored in the database
  Exceptions : none
  Caller     : general
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::strand ( ) [inherited]
  Arg [1]    : integer $strand
  Example    : my $strand = $genomic_align_block->strand;
  Example    : $genomic_align_block->strand(-1);
  Description: get/set for attribute strand. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::NestedSet::string_node ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::NestedSet::string_tree ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::NestedSet::subroot ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Graph::Node::unlink_all ( ) [inherited]

Undocumented method

public Undef Bio::EnsEMBL::Compara::Graph::Node::unlink_neighbor ( ) [inherited]
  Overview   : unlink and release neighbor from self if its mine
               might cause neighbor to delete if refcount reaches Zero.
  Arg [1]    : $node Bio::EnsEMBL::Compara::Graph::Node instance
  Example    : $self->unlink_neighbor($node);
  Returntype : undef
  Caller     : general
 

The documentation for this class was generated from the following file: