ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::MiscFeature | new () |
public void | add_Attribute () |
public void | add_MiscSet () |
public Listref | get_all_MiscSets () |
public Listref | get_all_Attributes () |
public Listref | get_all_attribute_values () |
public Scalar | get_scalar_attribute () |
public | get_first_scalar_attribute () |
public String | display_id () |
public Hash | summary_as_hash () |
Public Member Functions inherited from Bio::EnsEMBL::Feature | |
public Bio::EnsEMBL::Feature | new () |
public Int | start () |
public Int | end () |
public Int | strand () |
public void | move () |
public Int | length () |
public Bio::EnsEMBL::Analysis | analysis () |
public Bio::EnsEMBL::Slice | slice () |
public Boolean Or Undef | equals () |
public Bio::EnsEMBL::Feature | transform () |
public Bio::EnsEMBL::Feature | transfer () |
public Listref | project_to_slice () |
public Listref | project () |
public String | seqname () |
public String | display_id () |
public String | version () |
public Bio::EnsEMBL::Slice | feature_Slice () |
public String | seq_region_name () |
public Int | seq_region_length () |
public Boolean | seq_region_strand () |
public Int | seq_region_start () |
public Int | seq_region_end () |
public String | coord_system_name () |
public String | seq () |
public Listref | get_all_alt_locations () |
public Boolean | overlaps () |
public Boolean | overlaps_local () |
public List | get_overlapping_Genes () |
public Bio::EnsEMBL::Gene | get_nearest_Gene () |
public String | feature_so_acc () |
public String | feature_so_term () |
public Hashref | summary_as_hash () |
public String | species () |
public | sub_SeqFeature () |
public | add_sub_SeqFeature () |
public | flush_sub_SeqFeature () |
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 () |
MiscFeatures are extremely general features with a location, and an arbitrary group of attributes. They are grouped with other features of the same 'type' through the use of MiscSets (see Bio::EnsEMBL::MiscSet). Attributes are attached in the fom of Bio::EnsEMBL::Attribute objects. See Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor for ways to fetch or store MiscFeatures.
Definition at line 86 of file MiscFeature.pm.
public void Bio::EnsEMBL::MiscFeature::add_Attribute | ( | ) |
Arg [1] : Bio::EnsEMBL::Attribute $attribute Example :
Description: Adds an attribute to this misc. feature Returntype : none Exceptions : throw on wrong argument type Caller : general Status : Stable
public void Bio::EnsEMBL::MiscFeature::add_MiscSet | ( | ) |
Arg [1] : Bio::EnsEMBL::MiscSet $set The set to add Example :
Description: Associates this MiscFeature with a given Set. Returntype : none Exceptions : throw if the set arg is not provided, throw if the set to be added does not have a code Caller : general Status : Stable
public String Bio::EnsEMBL::MiscFeature::display_id | ( | ) |
Arg [1] : none Example :
Description: This method returns a string that is considered to be the 'display' identifier. For misc_features this is the first name or synonym attribute or '' if neither are defined. Returntype : string Exceptions : none Caller : web drawing code Status : Stable
public Listref Bio::EnsEMBL::MiscFeature::get_all_attribute_values | ( | ) |
Arg [1] : string $code The code of the Attribute object values to retrieve Example :
Description: Retrieves a list of Attribute object values for given code or all of the associated Attributes. Returntype : listref of values Exceptions : Caller : general Status : Stable
public Listref Bio::EnsEMBL::MiscFeature::get_all_Attributes | ( | ) |
Arg [1] : optional string $code The code of the Attribute objects to retrieve Example :
Description: Retrieves a list of Attribute objects for given code or all of the associated Attributes. Returntype : listref of Bio::EnsEMBL::Attribute Exceptions : Caller : general Status : Stable
public Listref Bio::EnsEMBL::MiscFeature::get_all_MiscSets | ( | ) |
Arg [1] : optional string $code The code of the set to retrieve Example :
Description: Retrieves a set that this feature is associated with via its code. Can return empty lists. Usually returns about one elements lists. Returntype : listref of Bio::EnsEMBL::MiscSet Exceptions : throw if the code arg is not provided Caller : general Status : Stable
public Bio::EnsEMBL::MiscFeature::get_first_scalar_attribute | ( | ) |
Undocumented method
public Scalar Bio::EnsEMBL::MiscFeature::get_scalar_attribute | ( | ) |
Arg [1] : string $code The code of the Attribute object values to retrieve Example :
Description: Retrieves a value for given code or all of the associated Attributes. Returntype : scalar value Exceptions : Caller : general Status : Stable
public Bio::EnsEMBL::MiscFeature Bio::EnsEMBL::MiscFeature::new | ( | ) |
Arg [-SLICE]: Bio::EnsEMBL::SLice - Represents the sequence that this feature is on. The coordinates of the created feature are relative to the start of the slice. Arg [-START]: The start coordinate of this feature relative to the start of the slice it is sitting on. Coordinates start at 1 and are inclusive. Arg [-END] : The end coordinate of this feature relative to the start of the slice it is sitting on. Coordinates start at 1 and are inclusive. Arg [-STRAND]: The orientation of this feature. Valid values are 1,-1,0. Arg [-SEQNAME] : A seqname to be used instead of the default name of the of the slice. Useful for features that do not have an attached slice such as protein features. Arg [-dbID] : (optional) internal database id Arg [-ADAPTOR]: (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor Example :
Description: Constructs a new Bio::EnsEMBL::Feature. Generally subclasses of this method are instantiated, rather than this class itself. Returntype : Bio::EnsEMBL::MiscFeature Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND ,-ADAPTOR arguments Caller : general, subclass constructors Status : Stable
public Hash Bio::EnsEMBL::MiscFeature::summary_as_hash | ( | ) |
Example :
Description: Generates a HashRef compatible with GFFSerializer. Adds all attribute key value pairs plus MiscSet codes and names Returntype : Hash Exceptions : none Caller : general Status : Stable