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

List of all members.


Class Summary

Description

Currently the GeneTreeMember objects are used to represent the leaves of
the gene trees (whether they contain proteins or non-coding RNas).
Each GeneTreeMember object is simultaneously a tree node (inherits from
GeneTreeNode) and an aligned member (inherits from AlignedMember).
 

Definition at line 13 of file GeneTreeMember.pm.

Available Methods

protected _add_neighbor_link_to_hash ()
protected _add_nodeI_to_node ()
protected _compose_sequence_exon_bounded ()
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 _parent_id ()
protected _recursive_get_all_leaves ()
protected Listref _recursive_get_all_sorted_leaves ()
protected _root_id ()
protected _set_parent_link ()
protected _unlink_node_in_hash ()
protected _walk_graph_until ()
public Subclass adaptor ()
public adaptor ()
public Undef add_child ()
public Boolean add_tag ()
public String alignment_string ()
public String alignment_string_bounded ()
public all_links_in_graph ()
public all_nodes_in_graph ()
public alloc ()
public void AUTOLOAD ()
public Bio::Seq bioseq ()
public build_leftright_indexing ()
public cascade_unlink ()
public String cdna_alignment_string ()
public Array children ()
public chr_end ()
public chr_name ()
public chr_start ()
public Boolean chr_strand ()
public Int cigar_end ()
public String cigar_line ()
public Int cigar_start ()
public consensus_cigar_line ()
public
Bio::EnsEMBL::Compara::GeneTreeMember 
copy ()
public copy_graph ()
public copy_shallow_links ()
public create_directed_link_to_node ()
public Compara::Graph::Link create_link_to_node ()
public dbID ()
public dealloc ()
public delete_lineage ()
public delete_tag ()
public String description ()
public DESTROY ()
public Undef disavow_parent ()
public display_label ()
public Float distance_to_ancestor ()
public Float distance_to_node ()
public Int distance_to_parent ()
public distance_to_root ()
public each_child ()
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 gene ()
public
Bio::EnsEMBL::Compara::Member 
gene_member ()
public Int gene_member_id ()
public genome_db ()
public genome_db_id ()
public Listref get_all_adjacent_subtrees ()
public Listref get_all_ancestors ()
public Reference get_all_leaves ()
public get_all_leaves_indexed ()
public Listref get_all_nodes ()
public Listref get_all_nodes_by_tag_value ()
public Array get_all_peptide_Members ()
public Listref get_all_sorted_leaves ()
public Listref get_all_subnodes ()
public Array get_all_tags ()
public ArrayRef get_all_values_for_tag ()
public
Bio::EnsEMBL::Compara::Member 
get_canonical_peptide_Member ()
public
Bio::EnsEMBL::Compara::Member 
get_canonical_transcript_Member ()
public get_child_count ()
public get_exon_bounded_sequence ()
public Bio::EnsEMBL::Gene get_Gene ()
public get_leaf_by_Member ()
public get_SimpleAlign ()
public Scalar get_tagvalue ()
public Hashref get_tagvalue_hash ()
public Bio::EnsEMBL::Transcript get_Transcript ()
public Bio::EnsEMBL::Gene get_Translation ()
public get_TreeI ()
public Scalar get_value_for_tag ()
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
Bio::EnsEMBL::Compara::GeneTreeNode 
keep_nodes_by_taxon_ids ()
public left_index ()
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 member_id ()
public merge_children ()
public merge_node_via_shared_ancestor ()
public Int method_link_species_set_id ()
public minimize_node ()
public
Bio::EnsEMBL::Compara::NestedSet 
minimize_tree ()
public String name ()
public neighbors ()
public new ()
public
Bio::EnsEMBL::Compara::Member 
new ()
public new_fast ()
public
Bio::Ensembl::Compara::Member 
new_from_gene ()
public new_from_newick ()
public
Bio::Ensembl::Compara::Member 
new_from_transcript ()
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 Int perc_cov ()
public Int perc_id ()
public Int perc_pos ()
public print_links ()
public void print_member ()
public void print_node ()
public Undef print_tree ()
public Undef re_root ()
public refcount ()
public release ()
public release_children ()
public Undef release_tree ()
public
Bio::EnsEMBL::Compara::NestedSet 
remove_nodes ()
public
Bio::EnsEMBL::Compara::GeneTreeNode 
remove_nodes_by_taxon_ids ()
public retain ()
public right_index ()
public root ()
public scale ()
public scale_max_to ()
public Int seq_length ()
public String sequence ()
public sequence_cds ()
public sequence_exon_bounded ()
public String sequence_exon_cased ()
public Int sequence_id ()
public Array sorted_children ()
public source_name ()
public stable_id ()
public store ()
public store_tag ()
public string_node ()
public string_tree ()
public subroot ()
public taxon ()
public taxon_id ()
public transcript ()
public translation ()
public tree ()
public unlink_all ()
public Undef unlink_neighbor ()
public version ()

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::Member::_compose_sequence_exon_bounded ( ) [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 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 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 Bio::EnsEMBL::Compara::Member::adaptor ( ) [inherited]
  Arg [1]    : string $adaptor (optional)
               corresponding to a perl module
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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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::AlignedMember::alignment_string ( ) [inherited]
  Arg [1]     : (optional) bool $exon_cased
  Example     : my $alignment_string = $object->alignment_string();
  Example     : my $alignment_string = $object->alignment_string(1);
  Description : Returns the aligned sequence for this object. For sequences
                split in exons, the $exon_cased flag permits to request
                that each exon is represented in alternative upper and lower
                case.
                For local alignments, when the alignment does not cover the
                whole protein, only the part of the sequence in the alignemnt
                is returned. Currently only global alignments are provided.
                Therefore the alignment_string always returns the whole aligned
                sequence.
  Returntype  : string
  Exceptions  : throws if the cigar_line is not defined for this object.
  Caller      : general
  Status      : Stable
 
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public String Bio::EnsEMBL::Compara::AlignedMember::alignment_string_bounded ( ) [inherited]
  Arg [1]     : none
  Example     : my $alignment_string_bounded = $object->alignment_string_bounded();
  Description : Returns the aligned sequence for this object with padding characters
                representing the introns.
  Returntype  : string
  Exceptions  : throws if the cigar_line is not defined for this object or if the
                cigar_start or cigar_end are defined.
  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 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::Seq Bio::EnsEMBL::Compara::Member::bioseq ( ) [inherited]
  Args       : none
  Example    : my $primaryseq = $member->primaryseq;
  Description: returns sequence this member as a Bio::Seq object
  Returntype : Bio::Seq object
  Exceptions : none
  Caller     : general
 
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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 String Bio::EnsEMBL::Compara::AlignedMember::cdna_alignment_string ( ) [inherited]
  Arg [1]    : none
  Example    : my $cdna_alignment = $aligned_member->cdna_alignment_string();
  Description: Converts the peptide alignment string to a cdna alignment
               string.  This only works for EnsEMBL peptides whose cdna can
               be retrieved from the attached core databse.
               If the cdna cannot be retrieved undef is returned and a
               warning is thrown.
  Returntype : string
  Exceptions : none
  Caller     : general
 
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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::Member::chr_end ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::Member::chr_name ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::Member::chr_start ( ) [inherited]
 
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public Boolean Bio::EnsEMBL::Compara::Member::chr_strand ( ) [inherited]
  Arg [1]    : integer
  Description: Returns the strand of the member.  Defined strands are 1 or -1.
               0 is undefined strand.
  Returntype : 1,0,-1
  Exceptions : none
  Caller     : general
 
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public Int Bio::EnsEMBL::Compara::AlignedMember::cigar_end ( ) [inherited]
  Arg [1]     : (optional) $cigar_end
  Example     : $object->cigar_end($cigar_end);
  Example     : $cigar_end = $object->cigar_end();
  Description : Getter/setter for the cigar_end attribute. For non-global
                alignments, this represent the ending point of the local
                alignment.
                Currently the data provided as AlignedMembers (leaves of the
                GeneTree) are obtained using global alignments and the
                cigar_end is always undefined.
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public String Bio::EnsEMBL::Compara::AlignedMember::cigar_line ( ) [inherited]
  Arg [1]     : (optional) $cigar_line
  Example     : $object->cigar_line($cigar_line);
  Example     : $cigar_line = $object->cigar_line();
  Description : Getter/setter for the cigar_line attribute. The cigar line
                represents the modifications that are required to go from
                the original sequence to the aligned sequence. In particular,
                it shows the location of the gaps in the sequence. The cigar
                line is built with a series of numbers and characters where
                the number represents the number of positions in the mode
                defined by the next charcater. When the number is 1, it can be
                omitted. For example, the cigar line '23MD4M' means that there
                are 23 matches or mismatches, then 1 deletion (gap) and then
                another 4 matches or mismatches. The aligned sequence is
                obtained by inserting 1 gap at the right location.
  Returntype  : string
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Int Bio::EnsEMBL::Compara::AlignedMember::cigar_start ( ) [inherited]
  Arg [1]     : (optional) $cigar_start
  Example     : $object->cigar_start($cigar_start);
  Example     : $cigar_start = $object->cigar_start();
  Description : Getter/setter for the cigar_start attribute. For non-global
                alignments, this represent the starting point of the local
                alignment.
                Currently the data provided as AlignedMembers (leaves of the
                GeneTree) are obtained using global alignments and the
                cigar_start is always undefined.
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Bio::EnsEMBL::Compara::GeneTreeNode::consensus_cigar_line ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::GeneTreeMember Bio::EnsEMBL::Compara::GeneTreeMember::copy ( )
  Arg [1]     : none
  Example     : $copy = $gene_tree_member->copy();
  Description : Creates a new GeneTreeMember object from an existing one
  Returntype  : Bio::EnsEMBL::Compara::GeneTreeMember
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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Reimplemented from Bio::EnsEMBL::Compara::AlignedMember.

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::Member::dbID ( ) [inherited]
  Arg [1]    : int $dbID (optional)
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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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 String Bio::EnsEMBL::Compara::Member::description ( ) [inherited]
  Arg [1]    : string $description (optional)
  Example    :
  Description:
  Returntype : string
  Exceptions :
  Caller     :
 
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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 Bio::EnsEMBL::Compara::Member::display_label ( ) [inherited]
  Arg [1]    : string $display_label (optional)
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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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 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

Code:
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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 Bio::EnsEMBL::Compara::Member::gene ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::Member::gene_member ( ) [inherited]
  Arg[1]     : Bio::EnsEMBL::Compara::Member $geneMember (optional)
  Example    : my $gene_member = $member->gene_member;
  Description: returns gene member object for this protein member
  Returntype : Bio::EnsEMBL::Compara::Member object
  Exceptions : if arg[0] is not a Bio::EnsEMBL::Compara::Member object
  Caller     : MemberAdaptor(set), general
 
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public Int Bio::EnsEMBL::Compara::Member::gene_member_id ( ) [inherited]
  Arg [1]    : int $gene_member_id
  Example    : my $gene_member_id = $member->gene_member_id;
  Description: Gene_member_id of this protein member
  Returntype : int
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member::genome_db ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::Member::genome_db_id ( ) [inherited]
 
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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 Reference Bio::EnsEMBL::Compara::NestedSet::get_all_leaves ( ) [inherited]
 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
 Example :
 Returns : reference to list of NestedSet objects (all leaves)
 Args    : none
 
Code:
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Reimplemented in Bio::EnsEMBL::Compara::GenomicAlignTree.

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 Array Bio::EnsEMBL::Compara::Member::get_all_peptide_Members ( ) [inherited]
  Args       : none
  Example    : $pepMembers = $gene_member->get_all_peptide_Members
  Description: return listref of all peptide members of this gene_member
  Returntype : array ref of Bio::EnsEMBL::Compara::Member 
  Exceptions : throw if not an ENSEMBLGENE
  Caller     : general
 
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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::Member Bio::EnsEMBL::Compara::Member::get_canonical_peptide_Member ( ) [inherited]
  Args       : none
  Example    : $canonicalPepMember = $member->get_canonical_peptide_Member
  Description: if member is an "ENSEMBLGENE" it will return the canonical peptide member
               if member is an 'ENSEMBLPEP' it will get its gene member and have it
               return the canonical peptide (which could be the same as the starting member)
  Returntype : Bio::EnsEMBL::Compara::Member or undef
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::Member::get_canonical_transcript_Member ( ) [inherited]
  Args       : none
  Example    : $canonical_trans_member = $member->get_canonical_transcript_Member
  Description: if member is an "ENSEMBLGENE" it will return the canonical transcript member
               if member is an 'ENSEMBLTRANS' it will get its gene member and have it
               return the canonical transcript (which could be the same as the starting member).
               Note: This method is intended for ncRNA genes only. To access the canonical
               transcript for a protein-coding gene, please refer to the
               get_canonical_peptide_Member method
  Returntype : Bio::EnsEMBL::Compara::Member or undef
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::NestedSet::get_child_count ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Member::get_exon_bounded_sequence ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Gene Bio::EnsEMBL::Compara::Member::get_Gene ( ) [inherited]
  Args       : none
  Example    : $gene = $member->get_Gene
  Description: if member is an 'ENSEMBLGENE' returns Bio::EnsEMBL::Gene object
               by connecting to ensembl genome core database
               REQUIRES properly setup Registry conf file or
               manually setting genome_db->db_adaptor for each genome.
  Returntype : Bio::EnsEMBL::Gene or undef
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::GeneTreeNode::get_leaf_by_Member ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::GeneTreeNode::get_SimpleAlign ( ) [inherited]

Undocumented method

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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::Transcript Bio::EnsEMBL::Compara::Member::get_Transcript ( ) [inherited]
  Args       : none
  Example    : $transcript = $member->get_Transcript
  Description: if member is an 'ENSEMBLPEP' returns Bio::EnsEMBL::Transcript object
               by connecting to ensembl genome core database
               REQUIRES properly setup Registry conf file or
               manually setting genome_db->db_adaptor for each genome.
  Returntype : Bio::EnsEMBL::Transcript or undef
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Gene Bio::EnsEMBL::Compara::Member::get_Translation ( ) [inherited]
  Args       : none
  Example    : $translation = $member->get_Translation
  Description: if member is an 'ENSEMBLPEP' returns Bio::EnsEMBL::Translation object
               by connecting to ensembl genome core database
               REQUIRES properly setup Registry conf file or
               manually setting genome_db->db_adaptor for each genome.
  Returntype : Bio::EnsEMBL::Gene or undef
  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 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::GeneTreeNode Bio::EnsEMBL::Compara::GeneTreeNode::keep_nodes_by_taxon_ids ( ) [inherited]
  Arg [1]     : arrayref of taxon_ids
  Example     : my $ret_tree = $tree->keep_nodes_by_taxon_ids($taxon_ids);
  Description : Returns the tree with kept nodes in taxon_id list.
  Returntype  : Bio::EnsEMBL::Compara::GeneTreeNode object
  Exceptions  :
  Caller      : general
  Status      : At risk (behaviour on exceptions could change)
 
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public Bio::EnsEMBL::Compara::NestedSet::left_index ( ) [inherited]

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::Member::member_id ( ) [inherited]
  Arg [1]    : int $member_id (optional)
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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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 Int Bio::EnsEMBL::Compara::AlignedMember::method_link_species_set_id ( ) [inherited]
  Arg [1]     : (optional) $method_link_species_set_id
  Example     : $object->method_link_species_set_id($method_link_species_set_id);
  Example     : $method_link_species_set_id = $object->method_link_species_set_id();
  Description : Getter/setter for the method_link_species_set_id attribute. Please,
                refer to the Bio::EnsEMBL::Compara::MethodLinkSpeciesSet module
                for more information on the method_link_species_set_id.
  Returntype  : int
  Exceptions  : Returns 0 if the method_link_species_set_id is not defined.
  Caller      : general
  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 String Bio::EnsEMBL::Compara::GeneTreeMember::name ( )
  Arg [1]     : none
  Example     : $aligned_member->name();
  Description : Returns the stable_id of the object (from the Bio::EnsEMBL::Compara::Member object).
  Returntype  : string
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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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::Member Bio::EnsEMBL::Compara::Member::new ( ) [inherited]
    Arg [-DBID] : (opt) 
        : int $dbID (the database internal ID for this object)
    Arg [-ADAPTOR] 
        : Bio::EnsEMBL::Compara::DBSQL::Member $adaptor
                (the adaptor for connecting to the database)
    Arg [-DESCRIPTION] (opt) 
         : string $description
    Arg [-SOURCE_NAME] (opt) 
         : string $source_name 
         (e.g., "ENSEMBLGENE", "ENSEMBLPEP", "Uniprot/SWISSPROT", "Uniprot/SPTREMBL")
    Arg [-TAXON_ID] (opt)
         : int $taxon_id
         (NCBI taxonomy id for the member)
    Arg [-GENOME_DB_ID] (opt)
        : int $genome_db_id
        (the $genome_db->dbID for a species in the database)
    Arg [-SEQUENCE_ID] (opt)
        : int $sequence_id
        (the $sequence_id for the sequence table in the database)
    Example :
	my $member = new Bio::EnsEMBL::Compara::Member;
       Description: Creates a new Member object
       Returntype : Bio::EnsEMBL::Compara::Member
       Exceptions : none
       Caller     : general
       Status     : Stable
 
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public Bio::EnsEMBL::Compara::Member::new_fast ( ) [inherited]
  Arg [1]    : hash reference $hashref
  Example    : none
  Description: This is an ultra fast constructor which requires knowledge of
               the objects internals to be used.
  Returntype :
  Exceptions : none
  Caller     :
 
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public Bio::Ensembl::Compara::Member Bio::EnsEMBL::Compara::Member::new_from_gene ( ) [inherited]
  Args       : Requires both an Bio::Ensembl:Gene object and a
             : Bio::Ensembl:Compara:GenomeDB object
  Example    : $member = Bio::EnsEMBL::Compara::Member->new_from_gene(
                -gene   => $gene,
                -genome_db => $genome_db);
  Description: contructor method which takes an Ensembl::Gene object
               and Compara:GenomeDB object and creates a new Member object
               translating from the Gene object
  Returntype : Bio::Ensembl::Compara::Member
  Exceptions :
  Caller     :
 
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public Bio::EnsEMBL::Compara::NestedSet::new_from_newick ( ) [inherited]

Undocumented method

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public Bio::Ensembl::Compara::Member Bio::EnsEMBL::Compara::Member::new_from_transcript ( ) [inherited]
  Arg[1]     : Bio::Ensembl:Transcript object
  Arg[2]     : Bio::Ensembl:Compara:GenomeDB object
  Arg[3]     : string where value='translate' causes transcript object to translate
               to a peptide
  Example    : $member = Bio::EnsEMBL::Compara::Member->new_from_transcript(
                  $transcript, $genome_db,
                -translate);
  Description: contructor method which takes an Ensembl::Gene object
               and Compara:GenomeDB object and creates a new Member object
               translating from the Gene object
  Returntype : Bio::Ensembl::Compara::Member
  Exceptions :
  Caller     :
 
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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 Int Bio::EnsEMBL::Compara::AlignedMember::perc_cov ( ) [inherited]
  Arg [1]     : (optional) $perc_cov
  Example     : $object->perc_cov($perc_cov);
  Example     : $perc_cov = $object->perc_cov();
  Description : Getter/setter for the perc_cov attribute. For non-global
                alignments, this represent the coverage of the alignment in
                percentage of the total length of the sequence.
                Currently the data provided as AlignedMembers (leaves of the
                GeneTree) are obtained using global alignments (the whole
                sequence is always included) and the perc_cov is always undefined.
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Int Bio::EnsEMBL::Compara::AlignedMember::perc_id ( ) [inherited]
  Arg [1]     : (optional) $perc_id
  Example     : $object->perc_id($perc_id);
  Example     : $perc_id = $object->perc_id();
  Description : Getter/setter for the perc_id attribute. This is generally
                used for pairwise relationships. The percentage identity
                reprensents the number of positions that are identical in
                the alignment in both sequences.
                Currently the data provided as AlignedMembers (leaves of the
                GeneTree) are obtained using multiple alignments and the
                perc_id is always undefined.
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
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public Int Bio::EnsEMBL::Compara::AlignedMember::perc_pos ( ) [inherited]
  Arg [1]     : (optional) $perc_pos
  Example     : $object->perc_pos($perc_pos);
  Example     : $perc_pos = $object->perc_pos();
  Description : Getter/setter for the perc_pos attribute. This is generally
                used for pairwise relationships. The percentage positivity
                reprensents the number of positions that are positive in
                the alignment in both sequences. Currently, this is calculated
                for protein sequences using the BLOSUM62 scoring matrix.
                Currently the data provided as AlignedMembers (leaves of the
                GeneTree) are obtained using multiple alignments and the
                perc_cov is always undefined.
  Returntype  : integer
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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public Bio::EnsEMBL::Compara::Graph::Node::print_links ( ) [inherited]

Undocumented method

public void Bio::EnsEMBL::Compara::Member::print_member ( ) [inherited]
  Arg[1]     : string $postfix
  Example    : $member->print_member("BRH");
  Description: used for debugging, prints out key descriptive elements
               of member
  Returntype : none
  Exceptions : none
  Caller     : general
 
Code:
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public void Bio::EnsEMBL::Compara::GeneTreeMember::print_node ( )
  Arg [1]     : none
  Example     : $aligned_member->print_node();
  Description : Outputs the info for this GeneTreeMember. First, the node_id, the
                left and right indexes are printed, then the species name. If the
                gene member can be determined, the methods prints the stable_id,
                the display label and location of the gene member, otherwise the
                member_id and stable_id of the object are printed.
  Returntype  : none
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Compara::NestedSet.

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)
 
Code:
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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::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::GeneTreeNode::release_tree ( ) [inherited]
  Overview   : Removes the to/from GeneTree reference to
               allow freeing memory 
  Example    : $self->release_tree;
  Returntype : undef
  Exceptions : none
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::Compara::NestedSet.

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::GeneTreeNode Bio::EnsEMBL::Compara::GeneTreeNode::remove_nodes_by_taxon_ids ( ) [inherited]
  Arg [1]     : arrayref of taxon_ids
  Example     : my $ret_tree = $tree->remove_nodes_by_taxon_ids($taxon_ids);
  Description : Returns the tree with removed nodes in taxon_id list.
  Returntype  : Bio::EnsEMBL::Compara::GeneTreeNode object
  Exceptions  :
  Caller      : general
  Status      : At risk (behaviour on exceptions could change)
 
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public Bio::EnsEMBL::Compara::Graph::CGObject::retain ( ) [inherited]

Undocumented method

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

Undocumented method

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public Bio::EnsEMBL::Compara::GeneTreeNode::root ( ) [inherited]

Undocumented method

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Reimplemented from Bio::EnsEMBL::Compara::NestedSet.

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

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public Int Bio::EnsEMBL::Compara::Member::seq_length ( ) [inherited]
  Example    : my $seq_length = $member->seq_length;
  Description: get the sequence length of this member
  Returntype : int
  Exceptions : none
  Caller     : general
 
Code:
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public String Bio::EnsEMBL::Compara::Member::sequence ( ) [inherited]
  Arg [1]    : string $sequence
  Example    : my $seq = $member->sequence;
  Description: Get/set the sequence string of this member
               Will lazy load by sequence_id if needed and able
  Returntype : string
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::Member::sequence_cds ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Member::sequence_exon_bounded ( ) [inherited]

Undocumented method

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public String Bio::EnsEMBL::Compara::Member::sequence_exon_cased ( ) [inherited]
  Args       : none
  Example    : my $sequence_exon_cased = $member->sequence_exon_cased;
  Description: Get/set the sequence string of this peptide member with
               alternating upper and lower case corresponding to the translateable exons.
  Returntype : string
  Exceptions : none
  Caller     : general
 
Code:
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public Int Bio::EnsEMBL::Compara::Member::sequence_id ( ) [inherited]
  Arg [1]    : int $sequence_id
  Example    : my $sequence_id = $member->sequence_id;
  Description: Extracts the sequence_id of this member
  Returntype : int
  Exceptions : none
  Caller     : general
 
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
 
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public Bio::EnsEMBL::Compara::Member::source_name ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::Member::stable_id ( ) [inherited]
  Arg [1]    : string $stable_id (optional)
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
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public Bio::EnsEMBL::Compara::Graph::CGObject::store ( ) [inherited]

Undocumented method

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

Undocumented method

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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::Member::taxon ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::Member::taxon_id ( ) [inherited]
 
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public Bio::EnsEMBL::Compara::Member::transcript ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Member::translation ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::GeneTreeNode::tree ( ) [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
 
public Bio::EnsEMBL::Compara::Member::version ( ) [inherited]
  Arg [1]    :
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
Code:
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The documentation for this class was generated from the following file: