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Bio-EnsEMBL-113_51
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LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
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Questions may also be sent to the Ensembl help desk at
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NAME

Bio::EnsEMBL::DnaDnaAlignFeature - Ensembl specific dna-dna pairwise alignment feature

SYNOPSIS

See BaseAlignFeature

new

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     : Stable

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    : $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     : Stable

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    : $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     : Stable

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    : $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     : Stable

get_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     : Stable

add_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     : Stable

transfer

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