ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::DnaDnaAlignFeature | new () |
protected Int | _hit_unit () |
protected Int | _query_unit () |
public Bio::EnsEMBL::DnaDnaAlignFeature | restrict_between_positions () |
public Array | alignment_strings () |
protected Array | _ensembl_alignment_strings () |
public A | get_SimpleAlign () |
protected A | _ensembl_SimpleAlign () |
public Listref | get_all_Attributes () |
public void | add_Attributes () |
public Bio::EnsEMBL::DnaDnaAlignFeature | transfer () |
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 () |
protected Array Bio::EnsEMBL::DnaDnaAlignFeature::_ensembl_alignment_strings | ( | ) |
Arg [1] : list of string $flags Description: Allows to rebuild the alignment string of both the seq and hseq sequence using the cigar_string information for ensembl cigar strings Returntype : array reference containing 2 strings the first corresponds to seq the second corresponds to hseq Exceptions : Caller : Status : Stable
protected A Bio::EnsEMBL::DnaDnaAlignFeature::_ensembl_SimpleAlign | ( | ) |
Arg [1] : list of string $flags Description: Internal method to build alignment string for ensembl type cigar strings using the cigar_string information and the slice and hslice objects Returntype : a Bio::SimpleAlign object Exceptions : Caller : Status : Stable
protected Int Bio::EnsEMBL::DnaDnaAlignFeature::_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::DnaDnaAlignFeature::_query_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
public void Bio::EnsEMBL::DnaDnaAlignFeature::add_Attributes | ( | ) |
Arg [1-N] : list of Bio::EnsEMBL::Attribute's @attribs Attribute(s) to add Example :
Description: Adds an Attribute to the feature. Returntype : none Exceptions : throw on incorrect arguments Caller : general Status : Stable
public Array Bio::EnsEMBL::DnaDnaAlignFeature::alignment_strings | ( | ) |
Arg [1] : list of string $flags FIX_SEQ = does not introduce gaps (dashes) in seq aligned sequence and delete the corresponding insertions in hseq aligned sequence FIX_HSEQ = does not introduce gaps (dashes) in hseq aligned sequence and delete the corresponding insertions in seq aligned sequence NO_SEQ = return the seq aligned sequence as an empty string NO_HSEQ = return the hseq aligned sequence as an empty string This 2 last flags would save a bit of time as doing so no querying to the core database in done to get the sequence. Example :
Description: Allows to rebuild the alignment string of both the seq and hseq sequence using the cigar_string information and the slice and hslice objects Returntype : array reference containing 2 strings the first corresponds to seq the second corresponds to hseq Exceptions : Caller : Status : Stable
public Listref Bio::EnsEMBL::DnaDnaAlignFeature::get_all_Attributes | ( | ) |
Arg [1] : (optional) String $attrib_code The code of the attribute type to retrieve values for Example :
Description: Gets a list of Attributes of this gene. Optionally just get Attributes for given code. Returntype : Listref of Bio::EnsEMBL::Attribute Exceptions : Caller : general Status : Stable
public A Bio::EnsEMBL::DnaDnaAlignFeature::get_SimpleAlign | ( | ) |
Arg [1] : list of string $flags translated = by default, the sequence alignment will be on nucleotide. With translated flag the aligned sequences are translated. uc = by default aligned sequences are given in lower cases. With uc flag, the aligned sequences are given in upper cases. Example :
Description: Allows to rebuild the alignment string of both the seq and hseq sequence using the cigar_string information and the slice and hslice objects Returntype : a Bio::SimpleAlign object Exceptions : Caller : Status : Stable
public Bio::EnsEMBL::DnaDnaAlignFeature Bio::EnsEMBL::DnaDnaAlignFeature::new | ( | ) |
Arg [..] : List of named arguments. defined in this constructor, others defined in BaseFeaturePair and SeqFeature superclasses. Example :
Description: Creates a new DnaDnaAlignFeature using either a cigarstring or a list of ungapped features. Returntype : Bio::EnsEMBL::DnaDnaAlignFeature Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::DnaDnaAlignFeature Bio::EnsEMBL::DnaDnaAlignFeature::restrict_between_positions | ( | ) |
Arg [1] : int $start Arg [2] : int $end Arg [3] : string $flags SEQ = $start and $end apply to the seq sequence i.e. start and end methods HSEQ = $start and $end apply to the hseq sequence i.e. hstart and hend methods Example :
Description: Build a new DnaDnaAlignFeature object that fits within the new specified coordinates and sequence reference, cutting any pieces hanging upstream and downstream. Returntype : Bio::EnsEMBL::DnaDnaAlignFeature object Exceptions : Caller : Status : Stable
public Bio::EnsEMBL::DnaDnaAlignFeature Bio::EnsEMBL::DnaDnaAlignFeature::transfer | ( | ) |
Arg [1] : Bio::EnsEMBL::Slice $destination_slice Example :
Description: Moves this feature to given target slice coordinates. Returns a new feature. Returntype : Bio::EnsEMBL::DnaDnaAlignFeature Exceptions : none Caller : general Status : Stable