ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::RNAProduct | new () |
public void | add_Attributes () |
public void | add_DBEntry () |
public Int | cdna_end () |
public Int | cdna_start () |
public String | created_date () |
public String | display_id () |
public Int | end () |
public Bio::EnsEMBL::Exon | end_Exon () |
public Int | genomic_end () |
public Int | genomic_start () |
public Listref | get_all_Attributes () |
public Listref | get_all_DBEntries () |
public Listref | get_all_DBLinks () |
public Listref | get_all_object_xrefs () |
public Listref | get_all_xrefs () |
public String | modified_date () |
public Int | length () |
public void | load () |
public String | seq () |
public String | stable_id () |
public String | stable_id_version () |
public Int | start () |
public Bio::EnsEMBL::Exon | start_Exon () |
public Hashref | summary_as_hash () |
public void | synchronise_attributes () |
public Bio::EnsEMBL::Transcript | transcript () |
public String | type_code () |
public String | version () |
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 () |
Objects of this class represent mature RNA products of transcripts. Examples of such products include MicroRNA (miRNA), circular RNA (circRNA) or piwi-interacting RNA (piRNA), and they commonly play a role in gene expression.
Definition at line 33 of file RNAProduct.pm.
public void Bio::EnsEMBL::RNAProduct::add_Attributes | ( | ) |
Arg [1..N] : Bio::EnsEMBL::Attribute $attribute Attributes to add. Example :
Description: Adds an Attribute to the RNAProduct. If you add an attribute before you retrieve any from database, lazy load will be disabled. Returntype : none Exceptions : throw on incorrect arguments Caller : general Status : Stable
public void Bio::EnsEMBL::RNAProduct::add_DBEntry | ( | ) |
Arg [1] : Bio::EnsEMBL::DBEntry $dbe The dbEntry to be added Example :
Description: Associates a DBEntry with this RNAProduct. Note that adding DBEntries will prevent future lazy-loading of DBEntries for this RNAProduct (see get_all_DBEntries). Returntype : none Exceptions : thrown on incorrect argument type Caller : general Status : Stable
public Int Bio::EnsEMBL::RNAProduct::cdna_end | ( | ) |
Example :
Description : Returns the end position of the RNAProduct in cDNA coordinates. Since RNAProducts do not span multiple exons, this is simply an alias for end(). Return type : Integer Caller : General Status : Stable
public Int Bio::EnsEMBL::RNAProduct::cdna_start | ( | ) |
Example :
Description : Returns the start position of the RNAProduct in cDNA coordinates. Since RNAProducts do not span multiple exons, this is simply an alias for start(). Return type : Integer Caller : General Status : Stable
public String Bio::EnsEMBL::RNAProduct::created_date | ( | ) |
Arg [1] : (optional) string $created_date - created date to set Example :
Description: Getter/setter for attribute created_date Returntype : string Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::RNAProduct::display_id | ( | ) |
Example :
Description: This method returns a string that is considered to be the 'display' identifier. For RNAProducts this is (depending on availability and in this order) the stable ID, the dbID or an empty string. Returntype : string Exceptions : none Caller : web drawing code Status : Stable
public Int Bio::EnsEMBL::RNAProduct::end | ( | ) |
Arg [1] : (optional) int $end - end position to set Example :
Description: Getter/setter for the value of end, which is a position within the precursor Transcript. Returntype : int Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::Exon Bio::EnsEMBL::RNAProduct::end_Exon | ( | ) |
Arg [1] : (optional) Bio::EnsEMBL::Exon || undef - start exon to assign Example :
Description: Getter/setter for the value of end_Exon, which denotes the exon at which RNAProduct ends. Returntype : Bio::EnsEMBL::Exon Exceptions : thrown on wrong argument type Caller : general Status : Stable
public Int Bio::EnsEMBL::RNAProduct::genomic_end | ( | ) |
Args : None Example :
Description : Returns the end position of the RNAProduct in genomic coordinates on the forward strand. Return type : Integer Exceptions : None Caller : General Status : Stable
public Int Bio::EnsEMBL::RNAProduct::genomic_start | ( | ) |
Args : None Example :
Description : Returns the start position of the RNAProduct in genomic coordinates on the forward strand. Return type : Integer Exceptions : None Caller : General Status : Stable
public Listref Bio::EnsEMBL::RNAProduct::get_all_Attributes | ( | ) |
Arg [1] : optional string $attrib_code The code of the attribute type to retrieve values for. Example :
Description: Gets a list of Attributes of this RNAProduct. Optionally just get Attributes for given code. Returntype : listref Bio::EnsEMBL::Attribute Exceptions : none Caller : general Status : Stable
public Listref Bio::EnsEMBL::RNAProduct::get_all_DBEntries | ( | ) |
Arg [1] : (optional) String, external database name, SQL wildcard characters (_ and %) can be used to specify patterns.
Arg [2] : (optional) String, external_db type, ('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'), SQL wildcard characters (_ and %) can be used to specify patterns.
Example :
Description: Retrieves DBEntries (xrefs) for this RNAProduct.
This method will attempt to lazy-load DBEntries from a database if an adaptor is available and no DBEntries are present on the RNAProduct (i.e. they have not already been added or loaded).
Returntype : Listref to Bio::EnsEMBL::DBEntry objects Exceptions : none Caller : ? Status : Stable
public Listref Bio::EnsEMBL::RNAProduct::get_all_DBLinks | ( | ) |
Arg [1] : (optional) String, database name SQL wildcard characters (_ and %) can be used to specify patterns.
Arg [2] : (optional) String, external database type, can be one of ('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'), SQL wildcard characters (_ and %) can be used to specify patterns.
Example :
Description: This is here for consistancy with the Transcript and Gene classes. It is a synonym for the get_all_DBEntries() method.
Return type: Listref to Bio::EnsEMBL::DBEntry objects Exceptions : none Caller : general Status : Stable
public Listref Bio::EnsEMBL::RNAProduct::get_all_object_xrefs | ( | ) |
Arg [1] : (optional) String, external database name
Arg [2] : (optional) String, external_db type
Example :
Description: Retrieves xrefs for this RNAProduct.
This method will attempt to lazy-load xrefs from a database if an adaptor is available and no xrefs are present on the RNAProduct (i.e. they have not already been added or loaded).
NB: This method is an alias for the get_all_DBentries() method.
Return type: Listref of Bio::EnsEMBL::DBEntry objects
Status : Stable
public Listref Bio::EnsEMBL::RNAProduct::get_all_xrefs | ( | ) |
Arg [1] : String database name (optional) SQL wildcard characters (_ and %) can be used to specify patterns.
Example :
Description: This method is here for consistancy with the Gene and Transcript classes. It is an alias for the get_all_DBLinks() method, which in turn directly calls get_all_DBEntries().
Return type: Listref of Bio::EnsEMBL::DBEntry objects
Status : Stable
public Int Bio::EnsEMBL::RNAProduct::length | ( | ) |
Example :
Description: Retrieves the length of the nucleotide sequence represented by this RNAProduct object. Returntype : int Exceptions : none Caller : webcode (protview etc.) Status : Stable
public void Bio::EnsEMBL::RNAProduct::load | ( | ) |
Arg [1] : Boolean $load_xrefs Load (or don't load) xrefs. Default is to load xrefs. Example :
Description : The Ensembl API makes extensive use of lazy-loading. Under some circumstances (e.g., when copying genes between databases), all data of an object needs to be fully loaded. This method loads the parts of the object that are usually lazy-loaded. Returns : none
public String Bio::EnsEMBL::RNAProduct::modified_date | ( | ) |
Arg [1] : (optional) string $modified_date - modification date to set Example :
Description: Getter/setter for attribute modified_date Returntype : string Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::RNAProduct Bio::EnsEMBL::RNAProduct::new | ( | ) |
Arg [-SEQ_START] : The offset in the Transcript indicating the start position of the product sequence. Arg [-SEQ_END] : The offset in the Transcript indicating the end position of the product sequence. Arg [-START_EXON] : The Exon object in which the RNAProduct starts Arg [-END_EXON] : The Exon object in which the RNAProduct ends Arg [-STABLE_ID] : The stable identifier for this RNAPRoduct Arg [-VERSION] : The version of the stable identifier Arg [-DBID] : The internal identifier of this RNAProduct Arg [-ADAPTOR] : The RNAProductAdaptor for this RNAProduct Arg [-SEQ] : Manually sets the nucleotide sequence of this RNAProduct. May be useful if this RNAProduct is not stored in a database. Arg [-CREATED_DATE] : the date the RNAProduct was created Arg [-MODIFIED_DATE]: the date the RNAProduct was modified Example :
Description: Constructor. Creates a new RNAProduct object Returntype : Bio::EnsEMBL::RNAProduct Exceptions : none Caller : general Status : In Development
public String Bio::EnsEMBL::RNAProduct::seq | ( | ) |
Example :
Description: Retrieves a string representation of the nucleotide sequence of this RNAProduct. This retrieves the transcript from the database and gets its sequence, or retrieves the sequence which was set via the constructor/setter. Returntype : string Exceptions : warning if the sequence is not set and cannot be retrieved from the database. Caller : webcode (protview etc.) Status : Stable
public String Bio::EnsEMBL::RNAProduct::stable_id | ( | ) |
Arg [1] : (optional) string $stable_id - stable ID to set Example :
Description: Getter/setter for attribute stable_id. Unlike stable_id_version(), setting a new stable ID does NOT reset the version number. Returntype : string Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::RNAProduct::stable_id_version | ( | ) |
Arg [1] : (optional) String - the stable ID with version to set Example :
Description: Getter/setter for stable id with version for this RNAProduct. If the input string omits the version part, the version gets reset to undef; use stable_id() if you want to avoid this. Returntype : String Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::RNAProduct::start | ( | ) |
Arg [1] : (optional) int $start - start position to set Example :
Description: Getter/setter for the value of start, which is a position within the precursor Transcript. Returntype : int Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::Exon Bio::EnsEMBL::RNAProduct::start_Exon | ( | ) |
Arg [1] : (optional) Bio::EnsEMBL::Exon || undef - start exon to assign Example :
Description: Getter/setter for the value of start_Exon, which denotes the exon at which RNAProduct starts. Returntype : Bio::EnsEMBL::Exon Exceptions : thrown on wrong argument type Caller : general Status : Stable
public Hashref Bio::EnsEMBL::RNAProduct::summary_as_hash | ( | ) |
Example :
Description : Retrieves a textual summary of this RNAProduct. Not inherited from Feature. Returns : hashref of arrays of descriptive strings Status : Intended for internal use
public void Bio::EnsEMBL::RNAProduct::synchronise_attributes | ( | ) |
Example :
Description : Some RNAProduct attributes, e.g. stem-loop arm in case of MicroRNA, use a local cache of their value for convenience. Unless the corresponding setters update both the cache value and the attribute (which would defeat the convenience thing), we have to make sure the former get propagated to the latter before storing the object in the database:
public Bio::EnsEMBL::Transcript Bio::EnsEMBL::RNAProduct::transcript | ( | ) |
Arg [1] : Transcript object (optional) Description : Sets or retrieves the transcript object associated with this RNAProduct object. Exceptions : Throws if there is no adaptor or no dbID defined for the RNAProduct object. Returntype : Bio::EnsEMBL::Transcript
public String Bio::EnsEMBL::RNAProduct::type_code | ( | ) |
Example :
Description: Getter for the RNAProduct type (e.g. miRNA, circRNA, ...). The type is expressed as human-readable code. This is somewhat redundant because similar information can be obtained simply by looking at the class of the object, indeed type_code is not meant to be modified independently of the class. However, there are certain use cases when the latter are more convenient than the former. Returntype : string Exceptions : none Caller : ? Status : In Development
public String Bio::EnsEMBL::RNAProduct::version | ( | ) |
Arg [1] : (optional) string $version - version to set Example :
Description: Getter/setter for attribute version Returntype : string Exceptions : none Caller : general Status : Stable