ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::PredictionExon | new () |
public String | score () |
public String | p_value () |
public Int | end_phase () |
public Bio::EnsEMBL::Exon | transform () |
public Bio::EnsEMBL::Gene | transfer () |
public Hashref | summary_as_hash () |
public Bio::EnsEMBL::PredictionTranscript | transcript () |
public Bio::EnsEMBL::PredictionTranscript | prediction_transcript () |
public void | add_supporting_features () |
public Empty | get_all_supporting_features () |
public Empty | find_supporting_evidence () |
Public Member Functions inherited from Bio::EnsEMBL::Exon | |
public Bio::EnsEMBL::Exon | new () |
public Int | end_phase () |
public Int | phase () |
public Int | frame () |
public Int | start () |
public Int | end () |
public Int | strand () |
public Int | cdna_start () |
public Int | cdna_end () |
public Int | cdna_coding_start () |
public Int | cdna_coding_end () |
public Int | coding_region_start () |
public Int | coding_region_end () |
public Int | rank () |
public Bio::EnsEMBL::Slice | slice () |
public Boolean | equals () |
public void | move () |
public Bio::EnsEMBL::Exon | transform () |
public Bio::EnsEMBL::Exon | transfer () |
public void | add_supporting_features () |
public | flush_supporting_features () |
public Listreference | get_all_supporting_features () |
public void | find_supporting_evidence () |
public String | stable_id () |
public String | created_date () |
public String | modified_date () |
public String | version () |
public String | stable_id_version () |
public Int | is_current () |
public Int | is_constitutive () |
public Int | is_coding () |
public Bio::EnsEMBL::Exon | adjust_start_end () |
public Bio::Seq | peptide () |
protected Bio::EnsEMBL::Mapper::Coordinate | _merge_ajoining_coords () |
public Bio::Seq | seq () |
public String | hashkey () |
public String | display_id () |
public Nothing | load () |
public Hashref | 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 () |
This is a class which represents an prediction exon which is part of a predcition transcript. See Bio::EnsEMBL:PredictionTranscript
Definition at line 38 of file PredictionExon.pm.
public void Bio::EnsEMBL::PredictionExon::add_supporting_features | ( | ) |
Description: For compatibility with Bio::EnsEMBL::Exon Does nothing. Returntype : none Status : Stable
public Int Bio::EnsEMBL::PredictionExon::end_phase | ( | ) |
Arg [1] : (optional) int $end_phase Example :
Description: Gets/Sets the end phase of the exon. end_phase = number of bases from the last incomplete codon of this exon. Usually, end_phase = (phase + exon_length)%3 but end_phase could be -1 if the exon is half-coding and its 3 prime end is UTR. Returntype : int Exceptions : warning if end_phase is called without an argument and the value is not set. Caller : general Status : Stable
public Empty Bio::EnsEMBL::PredictionExon::find_supporting_evidence | ( | ) |
Description: For compatibility with Bio::EnsEMBL::Exon Does nothing. Returntype : empty list. Status : Stable
public Empty Bio::EnsEMBL::PredictionExon::get_all_supporting_features | ( | ) |
Description: For compatibility with Bio::EnsEMBL::Exon Does nothing and returns empty list Returntype : empty list. Status : Stable
public Bio::EnsEMBL::PredictionExon Bio::EnsEMBL::PredictionExon::new | ( | ) |
Args : see SUPERCLASS Bio::EnsEMBL::Exon Example :
Description: create an Exon object Returntype : Bio::EnsEMBL::PredictionExon Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::PredictionExon::p_value | ( | ) |
Arg [1] : string $newval (optional) The new value to set the p_value attribute to Example :
Description: Getter/Setter for the p_value attribute Returntype : string Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::PredictionTranscript Bio::EnsEMBL::PredictionExon::prediction_transcript | ( | ) |
Example :
Description : Locates the parent prediction transcript using an exon dbID Returns : Bio::EnsEMBL::PredictionTranscript
public String Bio::EnsEMBL::PredictionExon::score | ( | ) |
Arg [1] : string $newval (optional) The new value to set the score attribute to Example :
Description: Getter/Setter for the score attribute Returntype : string Exceptions : none Caller : general Status : Stable
public Hashref Bio::EnsEMBL::PredictionExon::summary_as_hash | ( | ) |
Example :
Description : Extends Feature::summary_as_hash Retrieves a summary of this prediction exon. Returns : hashref of descriptive strings Status : Intended for internal use
public Bio::EnsEMBL::PredictionTranscript Bio::EnsEMBL::PredictionExon::transcript | ( | ) |
Example :
Description : Locates the parent prediction transcript using an exon dbID Same as prediction_transcript, duplicated for compatibility with Exon feature Returns : Bio::EnsEMBL::PredictionTranscript
public Bio::EnsEMBL::Gene Bio::EnsEMBL::PredictionExon::transfer | ( | ) |
Arg [1] : Bio::EnsEMBL::Slice $destination_slice Example :
Description: Moves this Exon to given target slice coordinates. If Features are attached they are moved as well. Returns a new exon. Returntype : Bio::EnsEMBL::Gene Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::Exon Bio::EnsEMBL::PredictionExon::transform | ( | ) |
Arg 1 : String $coordinate_system_name Arg [2] : String $coordinate_system_version Description: moves this exon to the given coordinate system. If this exon has attached supporting evidence, they move as well. Returntype : Bio::EnsEMBL::Exon Exceptions : wrong parameters Caller : general Status : Stable