ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::FeaturePair | new () |
public Int | strand () |
public String | idesc () |
public String | ilabel () |
public String | interpro_ac () |
public String | translation_id () |
public | external_data () |
public Hashref | summary_as_hash () |
public Array | alignment_strings () |
public | transform () |
protected Int | _hit_unit () |
protected Int | _query_unit () |
Public Member Functions inherited from Bio::EnsEMBL::BaseAlignFeature | |
public Bio::EnsEMBL::BaseAlignFeature | new () |
public String | cigar_string () |
public String | align_type () |
public Int | alignment_length () |
protected Int | _ensembl_cigar_alignment_length () |
public List | ungapped_features () |
public Int | strands_reversed () |
public void | reverse_complement () |
protected void | _ensembl_reverse_complement () |
public Bio::EnsEMBL::BaseAlignFeature | transform () |
protected List | _parse_ensembl_cigar () |
protected | _parse_cigar () |
protected void | _parse_features () |
protected | _parse_ensembl_features () |
protected Int | _hit_unit () |
protected Int | _query_unit () |
protected Int | _mdtag_alignment_length () |
protected Array | _get_mdz_chunks () |
protected Array | _get_mdz_alignment_length () |
protected String | _get_mdz_chunk_type () |
protected Array | _mdz_alignment_string () |
Public Member Functions inherited from Bio::EnsEMBL::FeaturePair | |
public Bio::EnsEMBL::FeaturePair | new () |
public String | hseqname () |
public Int | hstart () |
public Int | hend () |
public | hstrand () |
public Bio::EnsEMBL::Slice | hslice () |
public String | hseq_region_name () |
public Boolean | hseq_region_strand () |
public Int | hseq_region_start () |
public Int | hseq_region_end () |
public Float | score () |
public Float | percent_id () |
public String | species () |
public String | hspecies () |
public String | coverage () |
public String | hcoverage () |
public String | external_db_id () |
public String | db_name () |
public String | db_display_name () |
public Float | p_value () |
public String | hdescription () |
public String | display_id () |
public Int | identical_matches () |
public Int | positive_matches () |
public Int | group_id () |
public Int | level_id () |
public void | invert () |
public | extra_data () |
public | type () |
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 () |
ProteinFeature objects represent domains or other features of interest on a peptide sequence.
Definition at line 24 of file ProteinFeature.pm.
protected Int Bio::EnsEMBL::ProteinFeature::_hit_unit | ( | ) |
Arg [1] : none Description: PRIVATE implementation of abstract superclass method. Returns 1 as the 'unit' used for the hit sequence. Returntype : int Exceptions : none Caller : Bio::EnsEMBL::BaseAlignFeature Status : Stable
protected Int Bio::EnsEMBL::ProteinFeature::_query_unit | ( | ) |
Arg [1] : none Description: PRIVATE implementation of abstract superclass method. Returns 3 as the 'unit' used for the query sequence. Returntype : int Exceptions : none Caller : Bio::EnsEMBL::BaseAlignFeature Status : Stable
public Array Bio::EnsEMBL::ProteinFeature::alignment_strings | ( | ) |
Arg [1] : list of string $flags Example :
Description: Allows to rebuild the alignment string of both the query and target sequence using the sequence from translation object and MD Z String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)* (Refer: SAM/BAM specification) eg: MD:Z:96^RHKTDSFVGLMGKRALNS0V14 Returntype : array reference containing 2 strings the first corresponds to seq the second corresponds to hseq Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::ProteinFeature::external_data | ( | ) |
Undocumented method
public String Bio::EnsEMBL::ProteinFeature::idesc | ( | ) |
Arg [1] : (optional) string The interpro description Example :
Description: Getter/Setter for the interpro description of this protein feature. Returntype : string Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::ProteinFeature::ilabel | ( | ) |
Arg [1] : (optional) string The interpro label Example :
Description: Getter/Setter for the interpro label of this protein feature. Returntype : string Exceptions : none Caller : general Status : Stable
public String Bio::EnsEMBL::ProteinFeature::interpro_ac | ( | ) |
Arg [1] : (optional) string The interpro accession Example :
Description: Getter/Setter for the interpro accession of this protein feature. Returntype : string Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::FeaturePair Bio::EnsEMBL::ProteinFeature::new | ( | ) |
Arg [IDESC] : (optional) string An interpro description Arg [INTERPRO_AC] : (optional) string An interpro accession Arg [TRANSLATION_ID] : (optional) integer A translation dbID Arg [...] : named arguments to FeaturePair superclass Example :
Description: Instantiates a Bio::EnsEMBL::ProteinFeature Returntype : Bio::EnsEMBL::FeaturePair Exceptions : none Caller : general Status : Stable
public Int Bio::EnsEMBL::ProteinFeature::strand | ( | ) |
Arg [1] : Ignored Description: Overwrites Bio::EnsEMBL::Feature->strand to not allow : the strand to be set. Returntype : int Status : Stable
public Hashref Bio::EnsEMBL::ProteinFeature::summary_as_hash | ( | ) |
Example :
Description : Retrieves a textual summary of this Protein feature. Not inherited from Feature. Returns : hashref of arrays of descriptive strings Status : Intended for internal use
public Bio::EnsEMBL::ProteinFeature::transform | ( | ) |
Undocumented method
public String Bio::EnsEMBL::ProteinFeature::translation_id | ( | ) |
Arg [1] : (optional) integer The dbID of the translation Example :
Description: Getter/Setter for the translation dbID of this protein feature. Returntype : string Exceptions : none Caller : general Status : Stable