Inheritance diagram for Bio::EnsEMBL::RNAProduct:

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 ()

Detailed Description

Description

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.

Synopsis

my $rnaproduct = Bio::EnsEMBL::RNAProduct->new(
  -SEQ_START => 36,
  -SEQ_END   => 58
);
 
# Stable-ID setter
$rnaproduct->stable_id('ENSS00090210');
 
# Get start and end position in the precursor transcript
my $start = $rnaproduct->start();
my $end = $rnaproduct->end();

Definition at line 33 of file RNAProduct.pm.

Member Function Documentation

◆ add_Attributes()

public void Bio::EnsEMBL::RNAProduct::add_Attributes ( )

  Arg [1..N] : Bio::EnsEMBL::Attribute $attribute
               Attributes to add.
  Example    :

$rnaproduct->add_Attributes($selenocysteine_attribute);

  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

Code:

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◆ add_DBEntry()

public void Bio::EnsEMBL::RNAProduct::add_DBEntry ( )

  Arg [1]    : Bio::EnsEMBL::DBEntry $dbe
               The dbEntry to be added
  Example    :

$rnaproduct->add_DBEntry($xref);

  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

Code:

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◆ cdna_end()

public Int Bio::EnsEMBL::RNAProduct::cdna_end ( )

    Example     :

$rnaproduct_cdna_end = $rnaproduct->cdna_end();

    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

Code:

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◆ cdna_start()

public Int Bio::EnsEMBL::RNAProduct::cdna_start ( )

    Example     :

$rnaproduct_cdna_start = $rnaproduct->cdna_start();

    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

Code:

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◆ created_date()

public String Bio::EnsEMBL::RNAProduct::created_date ( )

  Arg [1]    : (optional) string $created_date - created date to set
  Example    :

$rnaproduct->created_date('2007-01-10 20:52:00');

  Description: Getter/setter for attribute created_date
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ display_id()

public String Bio::EnsEMBL::RNAProduct::display_id ( )

  Example    :

print $rnaproduct->display_id();

  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

Code:

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◆ end()

public Int Bio::EnsEMBL::RNAProduct::end ( )

  Arg [1]    : (optional) int $end - end position to set
  Example    :

$rnaproduct->end(39);

  Description: Getter/setter for the value of end, which is a position within
               the precursor Transcript.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ end_Exon()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::RNAProduct::end_Exon ( )

  Arg [1]    : (optional) Bio::EnsEMBL::Exon || undef - start exon to assign
  Example    :

$rnaproduct->end_Exon($exon1);

  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

Code:

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◆ genomic_end()

public Int Bio::EnsEMBL::RNAProduct::genomic_end ( )

    Args        : None
    Example     :

$rnaproduct_genomic_end = $rnaproduct->genomic_end();

    Description : Returns the end position of the RNAProduct in genomic
                  coordinates on the forward strand.
    Return type : Integer
    Exceptions  : None
    Caller      : General
    Status      : Stable

Code:

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◆ genomic_start()

public Int Bio::EnsEMBL::RNAProduct::genomic_start ( )

    Args        : None
    Example     :

$rnaproduct_genomic_start = $rnaproduct->genomic_start();

    Description : Returns the start position of the RNAProduct in
                  genomic coordinates on the forward strand.
    Return type : Integer
    Exceptions  : None
    Caller      : General
    Status      : Stable

Code:

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◆ get_all_Attributes()

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    :

($n_attr) = @{$tl->get_all_Attributes('note')};

@rp_attributes = @{$rnaproduct->get_all_Attributes()};

  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

Code:

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◆ get_all_DBEntries()

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    :

my @dbentries = @{ $rnaproduct->get_all_DBEntries() };
              @dbentries = @{ $rnaproduct->get_all_DBEntries('Uniprot%') };
              @dbentries = @{ $rnaproduct->get_all_DBEntries('%', 'ENSEMBL') };

  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

Code:

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◆ get_all_DBLinks()

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    :

my @dblinks = @{ $rnaproduct->get_all_DBLinks() };
               @dblinks = @{ $rnaproduct->get_all_DBLinks('mirbase%') };
               @dblinks = @{ $rnaproduct->get_all_DBLinks('%', 'ENSEMBL') };

  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

Code:

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◆ get_all_object_xrefs()

public Listref Bio::EnsEMBL::RNAProduct::get_all_object_xrefs ( )

  Arg [1]    : (optional) String, external database name

  Arg [2]    : (optional) String, external_db type

  Example    :

@oxrefs = @{ $rnaproduct->get_all_object_xrefs() };

  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

Code:

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◆ get_all_xrefs()

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    :

@xrefs = @{ $rnaproduct->get_all_xrefs() };

@xrefs = @{ $rnaproduct->get_all_xrefs('mirbase%') };

  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

Code:

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◆ length()

public Int Bio::EnsEMBL::RNAProduct::length ( )

  Example    :

print "RNA length =", $rnaproduct->length();

  Description: Retrieves the length of the nucleotide sequence represented
               by this RNAProduct object.
  Returntype : int
  Exceptions : none
  Caller     : webcode (protview etc.)
  Status     : Stable

Code:

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◆ load()

public void Bio::EnsEMBL::RNAProduct::load ( )

  Arg [1]       : Boolean $load_xrefs
                  Load (or don't load) xrefs.  Default is to load xrefs.
  Example       :

$rnaproduct->load();

  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

Code:

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◆ modified_date()

public String Bio::EnsEMBL::RNAProduct::modified_date ( )

  Arg [1]    : (optional) string $modified_date - modification date to set
  Example    :

$rnaproduct->modified_date('2007-01-10 20:52:00');

  Description: Getter/setter for attribute modified_date
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ new()

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    :

my $rp = Bio::EnsEMBL::RNAProduct->new(
                -SEQ_START => 36,
                -SEQ_END   => 58
              );

  Description: Constructor.  Creates a new RNAProduct object
  Returntype : Bio::EnsEMBL::RNAProduct
  Exceptions : none
  Caller     : general
  Status     : In Development

Code:

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◆ seq()

public String Bio::EnsEMBL::RNAProduct::seq ( )

  Example    :

print $rnaproduct->seq();

  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

Code:

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◆ stable_id()

public String Bio::EnsEMBL::RNAProduct::stable_id ( )

  Arg [1]    : (optional) string $stable_id - stable ID to set
  Example    :

$rnaproduct->stable_id('ENSS00090210');

  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

Code:

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◆ stable_id_version()

public String Bio::EnsEMBL::RNAProduct::stable_id_version ( )

  Arg [1]    : (optional) String - the stable ID with version to set
  Example    :

$rnaproduct->stable_id("ENSS0059890.3");

  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

Code:

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◆ start()

public Int Bio::EnsEMBL::RNAProduct::start ( )

  Arg [1]    : (optional) int $start - start position to set
  Example    :

$rnaproduct->start(17);

  Description: Getter/setter for the value of start, which is a position within
               the precursor Transcript.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ start_Exon()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::RNAProduct::start_Exon ( )

  Arg [1]    : (optional) Bio::EnsEMBL::Exon || undef - start exon to assign
  Example    :

$rnaproduct->start_Exon($exon1);

  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

Code:

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◆ summary_as_hash()

public Hashref Bio::EnsEMBL::RNAProduct::summary_as_hash ( )

  Example       :

$rnaproduct_summary = $rnaproduct->summary_as_hash();

  Description   : Retrieves a textual summary of this RNAProduct.
                  Not inherited from Feature.
  Returns       : hashref of arrays of descriptive strings
  Status        : Intended for internal use

Code:

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◆ synchronise_attributes()

public void Bio::EnsEMBL::RNAProduct::synchronise_attributes ( )

  Example       :

$rnaproduct->synchronise_attributes();

  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:
if no corresponding attribute exists, create one;
if there is one, update its value.
                  Class-specific maps of attributes to synchronise are
                  provided by
                  RNAProductTypeMapper::class_attribute_cache_map() .
  Returntype    : none
  Exceptions    : throws if the object contains multiple attributes with the
                  given code and the choice which one to update is
                  ambiguous.
  Caller        : RNAProductAdaptor
  Status        : At Risk (In Development)

Code:

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◆ transcript()

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

Code:

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◆ type_code()

public String Bio::EnsEMBL::RNAProduct::type_code ( )

  Example    :

my $rp_type_code = $rnaproduct->type_code();

  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

Code:

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◆ version()

public String Bio::EnsEMBL::RNAProduct::version ( )

  Arg [1]    : (optional) string $version - version to set
  Example    :

$rnaproduct->version(2);

  Description: Getter/setter for attribute version
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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

ensembl/modules/Bio/EnsEMBL/RNAProduct.pm

Public Member Functions

Detailed Description

Description

Synopsis

Member Function Documentation

◆ add_Attributes()

◆ add_DBEntry()

◆ cdna_end()

◆ cdna_start()

◆ created_date()

◆ display_id()

◆ end()

◆ end_Exon()

◆ genomic_end()

◆ genomic_start()

◆ get_all_Attributes()

◆ get_all_DBEntries()

◆ get_all_DBLinks()

◆ get_all_object_xrefs()

◆ get_all_xrefs()

◆ length()

◆ load()

◆ modified_date()

◆ new()

◆ seq()

◆ stable_id()

◆ stable_id_version()

◆ start()

◆ start_Exon()

◆ summary_as_hash()

◆ synchronise_attributes()

◆ transcript()

◆ type_code()

◆ version()