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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
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<http://www.ensembl.org/Help/Contact>.NAME
Bio::EnsEMBL::DnaDnaAlignFeature - Ensembl specific dna-dna pairwise alignment feature
SYNOPSIS
See BaseAlignFeaturenew
Arg [..] : List of named arguments. defined
in this constructor, others defined in BaseFeaturePair and
SeqFeature superclasses.
Example : $daf = new DnaDnaAlignFeature(-cigar_string => '3M3I12M');
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_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_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 : Stablerestrict_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 : $daf->restrict_between_positions(150,543,"SEQ")
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 : Stablealignment_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 : $daf->alignment_strings or
$daf->alignment_strings("FIX_HSEQ") or
$daf->alignment_strings("NO_SEQ","FIX_SEQ")
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_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 : Stableget_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 : $daf->get_SimpleAlign or
$daf->get_SimpleAlign("translated") or
$daf->get_SimpleAlign("translated","uc")
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_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 : Stableget_all_Attributes
Arg [1] : (optional) String $attrib_code
The code of the attribute type to retrieve values for
Example : my ($description) = @{ $feature->get_all_Attributes('description') };
my @attributes = @{ $feature->get_all_Attributes };
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 : Stableadd_Attributes
Arg [1-N] : list of Bio::EnsEMBL::Attribute's @attribs
Attribute(s) to add
Example : my $attrib = Bio::EnsEMBL::Attribute->new(...);
$gene->add_Attributes($attrib);
Description: Adds an Attribute to the feature.
Returntype : none
Exceptions : throw on incorrect arguments
Caller : general
Status : Stabletransfer
Arg [1] : Bio::EnsEMBL::Slice $destination_slice
Example : my $new_feature = $feature->transfer($slice);
Description: Moves this feature to given target slice coordinates.
Returns a new feature.
Returntype : Bio::EnsEMBL::DnaDnaAlignFeature
Exceptions : none
Caller : general
Status : Stable