ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::AltAlleleGroup | new () |
public | add_member () |
public | get_all_members_with_type () |
public HashRef | attribs () |
public | set_attribs () |
public | remove_attribs () |
public | remove_member () |
public Boolean | contains_member () |
public | remove_all_members () |
public Int | rep_Gene_id () |
public | unset_rep_Gene_id () |
public ArrayRef | get_all_Gene_ids () |
public Bio::EnsEMBL::Gene | get_representative_Gene () |
public ArrayRef | get_all_Genes () |
public ArrayRef | get_all_Genes_types () |
public Int | size () |
public ArrayRef | get_all_members () |
Public Member Functions inherited from Bio::EnsEMBL::Storable | |
public Bio::EnsEMBL::Storable | new () |
public Instance | new_fast () |
public Int | dbID () |
public Bio::EnsEMBL::DBSQL::BaseAdaptor | adaptor () |
public Boolean | is_stored () |
public | get_all_DAS_Features () |
Alt allele groups keep track of which alleles are tied to a particular Gene They allow related genes to be located. This class allows fetching of both IDs and fully fledged Gene objects. AltAlleleGroup members are assigned types to differentiate them by their origin. These types are set as flags, allowing you to select the union of types as well as by individual ones. No flags set denotes a situation of no information. Valid flags are as follows: 'IS_REPRESENTATIVE', 'IS_MOST_COMMON_ALLELE', 'IN_CORRECTED_ASSEMBLY', 'HAS_CODING_POTENTIAL', 'IN_ARTIFICIALLY_DUPLICATED_ASSEMBLY', 'IN_SYNTENIC_REGION', 'HAS_SAME_UNDERLYING_DNA_SEQUENCE', 'IN_BROKEN_ASSEMBLY_REGION', 'IS_VALID_ALTERNATE', 'SAME_AS_REPRESENTATIVE', 'SAME_AS_ANOTHER_ALLELE', 'MANUALLY_ASSIGNED', 'AUTOMATICALLY_ASSIGNED'
Definition at line 67 of file AltAlleleGroup.pm.
public Bio::EnsEMBL::AltAlleleGroup::add_member | ( | ) |
Arg [1] : Gene dbID Arg [2] : Type List, used for assigning type flags of this member, see Description above Description : Adds a record of one new member to the AltAlleleGroup. Once a change is made, this must be persisted to the database with AltAlleleGroupAdaptor->store or ->update Example :
public HashRef Bio::EnsEMBL::AltAlleleGroup::attribs | ( | ) |
Arg [1] : Int gene id to record attributes against Description : Returns all known attributes of the given gene id. Attributes are returned as a HashRef but is a copy of the interally held attribute list Returntype : HashRef copy of all the given id's attributes Example :
public Boolean Bio::EnsEMBL::AltAlleleGroup::contains_member | ( | ) |
Arg [1] : Int gene id to retrieve attributes against Description : Searches through the members list looking for the specified gene id. Returns true if it was found or false if not. Returntype : Boolean indicating if the given gene id is held in this group Example :
public ArrayRef Bio::EnsEMBL::AltAlleleGroup::get_all_Gene_ids | ( | ) |
Arg[1] : Boolean - Do not include representative gene in list of ids. Arg[2] : ArrayRef - Can contain dbIDs or Gene objects to exclude from the returned list Description : fetches all the Gene dbIDs within the allele group. It can also be used to list those ids that are not the representative Gene. Returntype : ArrayRef of gene dbIDs
public ArrayRef Bio::EnsEMBL::AltAlleleGroup::get_all_Genes | ( | ) |
Arg[1] : Boolean - Do not include representative gene in list of ids. Arg[2] : ArrayRef - Can contain dbIDs or Gene objects to exclude from the returned list Description : Fetches all the Gene objects within the allele group. It can also be used to list those Genes that are not the representative Gene. Returntype : ArrayRef of Bio::EnsEMBL::Gene objects
public ArrayRef Bio::EnsEMBL::AltAlleleGroup::get_all_Genes_types | ( | ) |
Arg[1] : Boolean - Do not include representative gene in list of ids. Arg[2] : ArrayRef - Can contain dbIDs or Gene objects to exclude from the returned list Description : Fetches all the Gene objects within the allele group and their associcated attributes. It can also be used to list those Genes that are not the representative Gene. Returntype : ArrayRef. 2 dimensional holding [Bio::EnsEMBL::Gene, {attribute_hash}]
public ArrayRef Bio::EnsEMBL::AltAlleleGroup::get_all_members | ( | ) |
Description : Retrieves all of the information about all members. Be aware that this emits the interal data structure so direct modification should be done with caution. Returntype : ArrayRef of id and type list: [gene_id,type] Caller : AltAlleleGroupAdaptor->store
public Bio::EnsEMBL::AltAlleleGroup::get_all_members_with_type | ( | ) |
Arg [1] : String The type to search members by Description : Loops through the internal members array returning all attributes of the same type as what has been specified Example :
public Bio::EnsEMBL::Gene Bio::EnsEMBL::AltAlleleGroup::get_representative_Gene | ( | ) |
Description : Used to fetch a Gene object which has been marked as the representative Gene for this alt allele group. Returntype : Bio::EnsEMBL::Gene object which is the representative gene
public Bio::EnsEMBL::AltAlleleGroup Bio::EnsEMBL::AltAlleleGroup::new | ( | ) |
Arg [-MEMBERS]: A list reference of [gene_id,type_flags] : gene_id is a dbID for Gene (consistent only within one release) : type_flags is a hash ref of attributes for this member Example :
Description: Creates a new alt-allele group object Returntype : Bio::EnsEMBL::AltAlleleGroup Exceptions : none Caller : general
public Bio::EnsEMBL::AltAlleleGroup::remove_all_members | ( | ) |
Description : Remove members from this object, but NOT the database. See AltAlleleGroupAdaptor->remove() to remove the group from the database
public Bio::EnsEMBL::AltAlleleGroup::remove_attribs | ( | ) |
Arg [1] : Int gene id to retrieve attributes against Arg [2] : ArrayRef/HashRef/Scalar The attribute you wish to remove Description : Removes the given type from this group against the specified gene identifier Example :
public Bio::EnsEMBL::AltAlleleGroup::remove_member | ( | ) |
Arg [1] : Int gene id to retrieve attributes against Arg [2] : ArrayRef/HashRef/Scalar The attribute you wish to remove Description : Removes the given member from this group. Any changes must be persisted back to the database via update() or store() methods in Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor. Example :
public Int Bio::EnsEMBL::AltAlleleGroup::rep_Gene_id | ( | ) |
Arg[1] : Optional - set a new representative Gene id for the group Description : Reports or sets the representative Gene for this AltAlleleGroup If you wish to remove the representative status of all genes without setting a new one, see unset_rep_Gene_id Returntype : Integer or undef if none set
public Bio::EnsEMBL::AltAlleleGroup::set_attribs | ( | ) |
Arg [1] : Int gene id to set attributes against Arg [2] : ArrayRef/HashRef/Scalar The attribute you wish to record Description : Adds the given type to the specified gene id in this group. You can specify the type using an ArrayRef, HashRef or a single scalar Example :
public Int Bio::EnsEMBL::AltAlleleGroup::size | ( | ) |
Description : Returns the current size of this group in members Returntype : Int the size of the current alt allele group
public Bio::EnsEMBL::AltAlleleGroup::unset_rep_Gene_id | ( | ) |
Description : Removes the representative Gene flag from this AltAlleleGroup. This action is not possible through rep_Gene_id due to validation of inputs.