ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::DensityFeature | new () |
public Int | strand () |
public Float | density_value () |
public Bio::EnsEMBL::Analysis | analysis () |
public Bio::EnsEMBL::DensityType | density_type () |
public Scalar | scaledvalue () |
public String | url () |
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 () |
A density feature represents a count, density, or percentage coverage, etc. for a given region. This module is part of the Ensembl project http://www.ensembl.org
Definition at line 29 of file DensityFeature.pm.
public Bio::EnsEMBL::Analysis Bio::EnsEMBL::DensityFeature::analysis | ( | ) |
Arg [1] : (optional) Bio::EnsEMBL::Analysis $analysis New value for the analysis of the attached DensityType Example :
Description: Overridden superclass analysis method, to chain to analysis method on attached DensityType. Returntype : Bio::EnsEMBL::Analysis Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::DensityType Bio::EnsEMBL::DensityFeature::density_type | ( | ) |
Arg [1] : string $newval (optional) The new value to set the density_value_type attribute to Example :
Description: Getter/Setter for the density_value_type attribute Returntype : Bio::EnsEMBL::DensityType Exceptions : if object passed is not of type DensityType Caller : general Status : Stable
public Float Bio::EnsEMBL::DensityFeature::density_value | ( | ) |
Arg [1] : (optional) float $density_value Example :
Description: Getter/Setter for the density value of this DensityFeature. The density value may be a count, a percentage, or a coverage of a feature type in the area defined by this feature. Returntype : float Exceptions : throw if a negative density value is provided Caller : general Status : Stable
public Bio::EnsEMBL::DensityFeature Bio::EnsEMBL::DensityFeature::new | ( | ) |
Arg [SEQ_REGION] : the sequence over which the density was calculated.
Arg [START] : start point on the seq at which density was calulated.
Arg [END] : end point on the seq at which density was calulated.
Arg [DENSITY_TYPE] : the type of density calculated.
Arg [DENSITY_VALUE] : the density.
Arg [...] : Named arguments passed to superclass Example :
Description: Creates a new density feature. Returntype : Bio::EnsEMBL::DensityFeature Exceptions : throw if invalid density value type is provided Caller : general Status : Stable
public Scalar Bio::EnsEMBL::DensityFeature::scaledvalue | ( | ) |
Title : scaledvalue Usage : $obj->scaledvalue($newval) Function: Returns : scalar - object's scaled value Args : newvalue (optional) Status : Stable
public Int Bio::EnsEMBL::DensityFeature::strand | ( | ) |
Arg [1] : none Example :
Description: Getter fot the strand attribute. Density features always have strand 0 and this attribute is not settable. Returntype : int (always 0) Exceptions : warning if an attempt is made to set the strand Caller : general Status : Stable
public String Bio::EnsEMBL::DensityFeature::url | ( | ) |
Title : url Usage : $obj->url($newval) Function: Returns : String containing this object's url Args : newvalue (optional) Status : Stable