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Bio::EnsEMBL::Compara::AlignSlice::Slice Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::AlignSlice::Slice:

List of all members.


Class Summary

Synopsis

SET VALUES

GET VALUES

Definition at line 20 of file Slice.pm.

Available Methods

protected _calculate_a ()
protected Listref _compile_mapped_Genes ()
protected _constrain_to_region ()
protected Bio::EnsEMBL::Gene _get_mapped_Gene ()
protected _get_StructuralVariationFeatureAdaptor ()
protected _get_VariationFeatureAdaptor ()
protected Int _map_position_using_cigar_line ()
protected void _mask_features ()
protected Lisref _merge_Exons ()
protected Listref _method_returning_simple_features ()
protected Listref _separate_in_incompatible_sets_of_Exons ()
protected _sort_Exons ()
public accession_number ()
public
Bio::EnsEMBL::DBSQL::SliceAdaptor 
adaptor ()
public add_Slice_Mapper_pair ()
public void add_synonym ()
public alphabet ()
public String assembly_exception_type ()
public assembly_type ()
public calculate_pi ()
public calculate_theta ()
public Int centrepoint ()
public Int chr_end ()
public chr_name ()
public chr_start ()
public Bio::EnsEMBL::CoordSystem coord_system ()
public String coord_system_name ()
public dbID ()
public desc ()
public display_id ()
public String display_Slice_name ()
public Int end ()
public expand ()
public
Bio::EnsEMBL::Compara::GenomeDB 
genome_db ()
public get_all_AffyFeatures ()
public Listref get_all_AssemblyExceptionFeatures ()
public Listref get_all_Attributes ()
public Reference get_all_compara_DnaAlignFeatures ()
public Arrayref get_all_compara_Syntenies ()
public Ref get_all_constrained_elements ()
public Listref get_all_CopyNumberVariantProbeFeatures ()
public get_all_CopyNumberVariantProbes ()
public Hashref get_all_DAS_Features ()
public get_all_DASFactories ()
public get_all_DASFeatures ()
public get_all_DASFeatures_dsn ()
public Listref get_all_DitagFeatures ()
public Listref get_all_DnaAlignFeatures ()
public Reference get_all_Exons ()
public Listref get_all_ExternalFeatures ()
public Listref get_all_Genes ()
public Listref get_all_Genes_by_source ()
public Listref get_all_Genes_by_type ()
public get_all_genotyped_SNPs ()
public Listref get_all_genotyped_VariationFeatures ()
public Listref get_all_Haplotypes ()
public Listref get_all_IndividualSlice ()
public Listref get_all_KaryotypeBands ()
public
Bio::EnsEMBL::Variation::LDFeatureContainer 
get_all_LD_values ()
public get_all_MapFrags ()
public Reference get_all_MarkerFeatures ()
public Listref get_all_MiscFeatures ()
public get_all_OligoFeatures ()
public get_all_OligoFeatures_by_type ()
public Listref get_all_PredictionTranscripts ()
public Listref get_all_ProteinAlignFeatures ()
public Listref get_all_QtlFeatures ()
public Listref get_all_RepeatFeatures ()
public Listref get_all_SearchFeatures ()
public Listref get_all_SimilarityFeatures ()
public Listref get_all_SimpleFeatures ()
public List get_all_Slice_Mapper_pairs ()
public get_all_SNPs ()
public get_all_SNPs_transcripts ()
public Listref get_all_somatic_VariationFeatures ()
public Listref get_all_somatic_VariationFeatures_with_annotation ()
public Listref get_all_StructuralVariationFeatures ()
public Listref get_all_StructuralVariationFeatures_by_VariationSet ()
public get_all_StructuralVariations ()
public get_all_supercontig_Slices ()
public Reference get_all_synonyms ()
public Reference get_all_Transcripts ()
public Listref get_all_underlying_Slices ()
public Listref get_all_VariationFeatures ()
public Listref get_all_VariationFeatures_by_Population ()
public Listref get_all_VariationFeatures_by_VariationSet ()
public Listref get_all_VariationFeatures_with_annotation ()
public Hashref get_base_count ()
public Bio::EnsEMB::IndividualSlice get_by_Individual ()
public Bio::EnsEMB::StrainSlice get_by_strain ()
public get_Chromosome ()
public Txt get_cigar_line ()
public Hash get_generic_features ()
public Reference get_MarkerFeatures_by_Name ()
public get_original_seq_region_position ()
public
Bio::EnsEMBL::RepeatMaskedSlice 
get_repeatmasked_seq ()
public Int get_seq_region_id ()
public get_tiling_path ()
public has_MapSet ()
public id ()
public invert ()
public Int is_circular ()
public Int is_reference ()
public Int is_toplevel ()
public Int length ()
public Listref map_original_Slice ()
public moltype ()
public String name ()
public new ()
public Bio::EnsEMBL::Slice new_fast ()
public old_get_all_DASFeatures ()
public primary_id ()
public List project ()
public List project_to_slice ()
public String seq ()
public Int seq_region_length ()
public String seq_region_name ()
public Bio::EnsEMBL::Slice seq_region_Slice ()
public Int start ()
public Int strand ()
public Bio::EnsEMBL::Slice sub_Slice ()
public Txt subseq ()
public Hashref summary_as_hash ()

Method Documentation

protected Listref Bio::EnsEMBL::Compara::AlignSlice::Slice::_compile_mapped_Genes ( )
  Arg[1]     : listref of Bio::EnsEMBL::Gene $mapped_genes
  Arg[2]     : int $max_repetition_length
  Arg[3]     : int $max_gap_length
  Arg[4]     : int $max_intron_length
  Arg[5]     : int $strict_order_of_exon_pieces
  Arg[6]     : int $strict_order_of_exons
  Example    : my $compiled_genes = $align_slice->compile_mapped_Genes($mapped_genes,
                       100, 1000, 100000, 1, 0);
  Description: This method compiles all the pieces of gene mapped before into a list
               of Bio::EnsEMBL::Gene objects. It tries to merge pieces of the same
               exon, link them according to their original transcript and finally
               group the transcripts in Bio::EnsEMBL::Gene objects. Merging and
               linking of Exons is done according to some rules that can be changed
               with the parameters.
  Parameters:  They are sent as is to _separate_in_incompatible_sets_of_Exons() and
               _merge_Exons() methods. Please refer to them elsewhere in this
               document.
  Returntype : listref of Bio::EnsEMBL::Gene objects. (overrides $mapped_genes)
  Exceptions : none
  Caller     : $object->methodname
 
Code:
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protected Bio::EnsEMBL::Gene Bio::EnsEMBL::Compara::AlignSlice::Slice::_get_mapped_Gene ( )
  Arg[1]     : Bio::EnsEMBL::Gene $original_gene
  Arg[2]     : Bio::EnsEMBL::Compara::GenomicAlign $genomic_align
  Example    : my $mapped_gene = $align_slice->get_mapped_Gene($orignal_gene, $genomic_align);
  Description: returns a new Bio::EnsEMBL::Gene object. Mapping is based on exons.
               The object returned contains Bio::EnsEMBL::Transcripts objects. Those
               mapped transcripts contain Bio::EnsEMBL::Compara::AlignSlice::Exon objects.
               If no exon can be mapped, the returned object will contain an empty array of
               transcripts. Since mapped objects are not stored in the DB, they have no dbID
               and no adaptor.
  Returntype : Bio::EnsEMBL::Gene object. (new object)
  Exceptions : returns undef if no part of $original_gene can be mapped using this
               $genomic_align. This method assumes that the slices of all the exons got
               from that gene have the same coordinates as the gene slice. It will throw
               if this is not true.
  Caller     : get_all_Genes
 
Code:
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protected Int Bio::EnsEMBL::Compara::AlignSlice::Slice::_map_position_using_cigar_line ( )
  Arg[1]     : string $cigar_line
  Arg[2]     : int $original_position
  Arg[3]     : int $original_length
  Arg[4]     : bool $start
  Example    : my $mapped_start_position = _map_position_using_cigar_line(
                   "16M4I", 10, 20, 1);
  Example    : my $mapped_end_position = _map_position_using_cigar_line(
                   "16M4I", 10, 20, 1);
  Description: This method is used to locate the start or the end position of
               a Translation on the Bio::EnsEMBL::Compara::AlignSlice::Exon object
               using the cigar_line of the object. As the Bio::EnsEMBL::Compara::
               AlignSlice::Exon object may result from the fusion of the same
               Bio::EnsEMBL::Exon object several times, this method returns the
               best mapping among all the available possibilities. When the original
               position maps on an insertion in the Bio::EnsEMBL::Compara::
               AlignSlice::Exon object, the resulting mapped start position is the
               next one to the latest mapped one.
  Returntype : int $mapped_position
  Exceptions : returns 0 when the end position cannot be mapped.
  Exceptions : returns a number larger than the length of the Bio::EnsEMBL::Compara::
               AlignSlice::Exon when the start position cannot be mapped.
 
Code:
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protected Lisref Bio::EnsEMBL::Compara::AlignSlice::Slice::_merge_Exons ( )
  Arg[1]     : listref of Bio::EnsEMBL::Compara::AlignSlice::Exon $set_of_exons
  Arg[2]     : int $max_repetition_length
  Arg[3]     : int $max_gap_length
  Arg[4]     : int $strict_order_of_exon_pieces
  Example    : my $merged_exons = _merge_Exons($exons_to_be_merged, 100, 1000, 1);
  Description: Takes a list of Bio::EnsEMBL::Compara::AlignSlice::Exon objects and
               tries to merge them according to exon stable_id and some rules that can
               be tunned using some optional parameters. This method can overwrite some
               of the exon in the $set_of_exons.
  Parameters:  MAX_REPETITION_LENGTH. In principle you want to merge together pieces
                   of an exon which do not overlap (the beginning and the end of the
                   exon). With this flag you can to set up what amount of the original
                   exon is allowed on two aligned exons to be merged.
               MAX_GAP_LENGTH. If the distance between two pieces of exons in the
                   aligned slice is larger than this parameter, they will not be
                   merged. Setting this parameter to -1 will
                   avoid any merging event.
               STRICT_ORDER_OF_EXON_PIECES. This flag allows you to decide whether two
                   pieces of an exon should be merged or not if they are not in the
                   right order, for instance if the end of the original exon will
                   appear before the start on the merged exon.
  Returntype : lisref of Bio::EnsEMBL::Compara::AlignSlice::Exon objects.
  Exceptions : none
  Caller     : methodname
 
Code:
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protected Listref Bio::EnsEMBL::Compara::AlignSlice::Slice::_method_returning_simple_features ( )
  Args[1]     : method_name
  Description : This Slice is made of several Bio::EnsEMBL::Slices mapped on it. This
                method go through all of them, calls method_name and maps teh result on
                this Bio::EnsEMBL::Compara::AlignSlice::Slice object.
  ReturnType  : listref of Bio::EnsEMBL::Variation::VariationFeature
  Exceptions  : none
  Caller      : contigview, snpview
 
Code:
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protected Listref Bio::EnsEMBL::Compara::AlignSlice::Slice::_separate_in_incompatible_sets_of_Exons ( )
  Arg[1]     : listref of Bio::EnsEMBL::Compara::AlignSlice::Exon $set_of_exons
  Arg[2]     : int $max_repetition_length
  Arg[3]     : int $max_intron_length
  Arg[4]     : int $strict_order_of_exons
  Example    : my $sets_of_exons = _separate_in_incompatible_sets_of_Exons(
                   $set_of_exons, 100, 100000, 0);
  Description: Takes a list of Bio::EnsEMBL::Compara::AlignSlice::Exon and separate
               them in sets of comaptible exons. Compatibility is defined taking into
               account 5 parameters:

  • exons must be in the same strand
  • exons cannot overlap on the align_slice
  • distance between exons cannot be larger than MAX_INTRON_LENGTH
  • two exons with the same stable_id can belong to the same transcript only if they represent diferent parts of the original exon. Some overlapping is allowed (see MAX_REPETITION_LENGTH parameter).
  • exons must be in the same order as in the original transcript if the STRICT_ORDER_OF_EXONS parameter is true. Parameters: MAX_REPETITION_LENGTH. In principle you want to link together pieces of an exon which do not overlap (the beginning and the end of the exon). With this flag you can to set up what amount of the original exon is allowed on two aligned exons to be linked. MAX_INTRON_LENGTH. If the distance between two exons in the aligned slice is larger than this parameter, they will not be linked. STRICT_ORDER_OF_EXONS. This flag allows you to decide whether two exons should be linked or not if they are not in the original order. Returntype : listref of lisrefs of Bio::EnsEMBL::Compara::AlignSlice::Exon objects. Exceptions : none Caller : methodname
 
Code:
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protected Bio::EnsEMBL::Compara::AlignSlice::Slice::_sort_Exons ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::AlignSlice::Slice::add_Slice_Mapper_pair ( )
  Arg[1]     : Bio::EnsEMBL::Slice $slice
  Arg[2]     : Bio::EnsEMBL::Mapper $mapper
  Arg[3]     : integer $start
  Arg[4]     : integer $end
  Arg[5]     : integer $strand
  Example    : $slice->add_Slice_Mapper_pair($slice, $mapper, 124, 542, -1);
  Description: Attaches a pair of Slice and the corresponding Mapper
               to this Bio::EnsEMBL::Compara::AlginSlice::Slice
               object. The Mapper contains the information for
               mapping coordinates from (to) the Slice to (from) the
               Bio::EnsEMBL::Compara::AlignSlice. Start, end and strand
               locates the $slice in the AlignSlice::Slice.
               $start and $end refer to the Coordinate System. If you are using
               a sub_Slice, this method will be using the coordinates of the
               original Bio::EnsEMBL::Compara::AlignSlice::Slice object!
  Returntype : 
  Exceptions : throws if $slice is not a Bio::EnsEMBL::Slice object
  Exceptions : throws if $mapper is not a Bio::EnsEMBL::Mapper object
 
Code:
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public String Bio::EnsEMBL::Compara::AlignSlice::Slice::display_Slice_name ( )
  Arg[1]     : string $name
  Example    : $slice->display_Slice_name("Homo_sapiens");
  Description: getter/setter for the attribute display_Slice_name
  Returntype : string
  Caller     : $object->methodname
 
Code:
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public Bio::EnsEMBL::Compara::AlignSlice::Slice::expand ( )
Expanding a Bio::EnsEMBL::Compara::AlignSlice::Slice object is not supported at the moment.
You could create a new Bio::EnsEMBL::Slice and fetch a new Bio::EnsEMBL::Compara::AlignSlice
from it. On the hand, if you only want to extend the sequence, you could use the subseq method
with a negatve start value or an end value larger than the end of this Slice.
This method returns undef
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public Bio::EnsEMBL::Compara::GenomeDB Bio::EnsEMBL::Compara::AlignSlice::Slice::genome_db ( )
  Arg[1]     : Bio::EnsEMBL::Compara::GenomeDB $genome_db
  Example    : $slice->genome_db($human_gdb);
  Description: getter/setter for the attribute genome_db
  Returntype : Bio::EnsEMBL::Compara::GenomeDB object
  Exceptions : This attribute should never be unset. Several methods
               rely on this attribute.
  Caller     : $object->methodname
 
Code:
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public Listref Bio::EnsEMBL::Compara::AlignSlice::Slice::get_all_Attributes ( )
  Arg [1]    : optional string $attrib_code
               The code of the attribute type to retrieve values for.
  Example    : ($htg_phase) = @{$slice->get_all_Attributes('htg_phase')};
               @slice_attributes    = @{$slice->get_all_Attributes()};
  Description: Gets a list of Attributes of all teh underlying slice''s
               seq_region. Optionally just get Attributes for given code.
               This Slice is made of several Bio::EnsEMBL::Slices mapped
               on it. This method go through all of them, retrieves the
               data and return them in order. There will be one set of
               Attributes by underlying slice.
  Returntype : listref Bio::EnsEMBL::Attribute
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public Ref Bio::EnsEMBL::Compara::AlignSlice::Slice::get_all_constrained_elements ( )
  Arg  1     : (opt) string $method_link_type (default = GERP_CONSTRAINED_ELEMENT)
  Arg  2     : (opt) listref Bio::EnsEMBL::Compara::GenomeDB $species_set
               (default, the set of species from the MethodLinkSpeciesSet used
               to build this AlignSlice)
  Example    : my $constrained_elements =
                    $align_slice->get_all_constrained_elements();
  Description: Retrieve the corresponding constrained elements for these alignments.
               Objects will be mapped on this AlignSlice::Slice, i.e. the
               reference_slice, reference_slice_start, reference_slice_end
               and reference_slice_strand will refer to this AlignSlice::Slice
               object
  Returntype : ref. to an array of Bio::EnsEMBL::Compara::GenomicAlignBlock
               objects.
  Caller     : object::methodname
  Status     : At risk
 
Code:
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public Listref Bio::EnsEMBL::Compara::AlignSlice::Slice::get_all_Genes ( )
  Arg [1]    : (optional) string $logic_name
               The name of the analysis used to generate the genes to retrieve
  Arg [2]    : (optional) string $dbtype
               The dbtype of genes to obtain.
  Arg [3]    : (optional) boolean $load_transcripts
               This option is always disabled for AlingSlices. It only exists for
               compatibility with the Bio::EnsEMBL::Slice objects.
  Example    : @genes = @{$slice->get_all_Genes};
  Description: Retrieves all genes that overlap this slice.
  Returntype : listref of Bio::EnsEMBL::Genes
  Exceptions : none
  Caller     : none
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public Listref Bio::EnsEMBL::Compara::AlignSlice::Slice::get_all_Genes_by_type ( )
  Arg [1]    : string $type
               The biotype of genes wanted.
  Arg [2]    : (optional) string $logic_name
  Arg [3]    : (optional) boolean $load_transcripts
               If set to true, transcripts will be loaded immediately rather
               than being lazy-loaded on request.  This will result in a
               significant speed up if the Transcripts and Exons are going to
               be used (but a slow down if they are not).
  Example    : @genes = @{$slice->get_all_Genes_by_type('protein_coding',
               'ensembl')};
  Description: Retrieves genes that overlap this slice of biotype $type.
               This is primarily used by the genebuilding code when several
               biotypes of genes are used.
               The logic name is the analysis of the genes that are retrieved.
               If not provided all genes will be retrieved instead.
               This methods overwrites the core one since it sends a warning
               message and return an empty array because this AlignSlice::Slice
               object has no adaptor. This implementation calls the
               get_all_Genes methdo elsewhere in this module to fulfil the
               query.
  Returntype : listref of Bio::EnsEMBL::Genes
  Exceptions : none
  Caller     : genebuilder, general
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public Listref Bio::EnsEMBL::Compara::AlignSlice::Slice::get_all_genotyped_VariationFeatures ( )
  Args       : none
  Function   : returns all variation features on this slice that have been genotyped. This
               function will only work correctly if the variation database has been
               attached to the core database.
               This Slice is made of several Bio::EnsEMBL::Slices mapped on it. This
               method go through all of them, retrieves the data and maps them on this
               Bio::EnsEMBL::Compara::AlignSlice::Slice object by changing start, end,
               strand and slice attributes.
  ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
  Exceptions : none
  Caller     : contigview, snpview
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public Listref Bio::EnsEMBL::Compara::AlignSlice::Slice::get_all_RepeatFeatures ( )
  Arg [1]    : (optional) string $logic_name
               The name of the analysis performed on the repeat features
               to obtain.
  Arg [2]    : (optional) string $repeat_type
               Limits features returned to those of the specified repeat_type
  Example    : @repeat_feats = @{$slice->get_all_RepeatFeatures(undef,'LTR')};
  Description: Retrieves the RepeatFeatures which overlap  with
               logic name $logic_name and with score above $score.  If 
               $logic_name is not defined features of all logic names are 
               retrieved.
               This Slice is made of several Bio::EnsEMBL::Slices mapped on it. This
               method go through all of them, retrieves the data and maps them on this
               Bio::EnsEMBL::Compara::AlignSlice::Slice object by changing start, end,
               strand and slice attributes.
  Returntype : listref of Bio::EnsEMBL::RepeatFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public List Bio::EnsEMBL::Compara::AlignSlice::Slice::get_all_Slice_Mapper_pairs ( )
  Arg[1]     : [optional] bool $get_gap_slices
  Example    : $slice_mapper_pairs = $slice->get_all_Slice_Mapper_pairs();
  Description: Returns all pairs of Slices and Mappers attached to this
               Bio::EnsEMBL::Compara::AlignSlice::Slice
               The $get_gap_slice flag is normally used internally to get the
               the gap slices. These are created when the alignment(s)
               underlying the AlignSlice correspond to gaps only in one or more
               species. These are used to tell the difference between gap due to
               lack of alignments and gaps due to the alignments. If you set this
               this flag to true you will get these gap slices back but it is your
               responsability to deal with these gap slices properly.
  Returntype : list ref of hashes which keys are "slice", "mapper", "start",
               "end" and "strand". Each hash corresponds to a pair of Slice
               and Mapper and the coordintes needed to locate the Slice in
               the AlignSlice::Slice.
               start and end refer to the Coordinate System. If you are using
               a sub_Slice, this method will be using the coordinates of the
               original Bio::EnsEMBL::Compara::AlignSlice::Slice object!
  Exceptions : return a ref to an empty list if no pairs have been attached
               so far.
 
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public Listref Bio::EnsEMBL::Compara::AlignSlice::Slice::get_all_underlying_Slices ( )
  Arg  [1]   : int $startBasePair
               relative to start of slice, which is 1.
  Arg  [2]   : int $endBasePair
               relative to start of slice.
  Arg  [3]   : (optional) int $strand
               The strand of the slice to obtain sequence from. Default
               value is 1.
  Description: This Slice is made of several Bio::EnsEMBL::Slices mapped
               on it with gaps inside and regions with no matching
               sequence. This method returns these Slices (or part of
               them) with the original coordinates and the gapped
               sequence attached to them. Additionally, extra Slices
               could be returned in order to fill in gaps between
               underlying Slices.
  Returntype : listref of Bio::EnsEMBL::Slice objects
  Exceptions : end should be at least as big as start
  Caller     : general
 
Code:
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public Listref Bio::EnsEMBL::Compara::AlignSlice::Slice::get_all_VariationFeatures ( )
    Args       : none
    Description :returns all variation features on this slice. This function will only work 
                correctly if the variation database has been attached to the core database.
                This Slice is made of several Bio::EnsEMBL::Slices mapped on it. This
                method go through all of them, retrieves the data and maps them on this
                Bio::EnsEMBL::Compara::AlignSlice::Slice object.
    ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
    Exceptions : none
    Caller     : contigview, snpview
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public Txt Bio::EnsEMBL::Compara::AlignSlice::Slice::get_cigar_line ( )
  Arg        : -none-
  Description: returns a cigar_line describing the gaps in the mapped sequence
               This Slice is made of several Bio::EnsEMBL::Slices mapped
               on it with gaps inside and regions with no matching
               sequence. The resulting cigar line corresponds to the mapping
               of all the nucleotides that can be mapepd. If several Slices map
               on the same positions, the behaviour is undefined.
               The cigar_line includes 3 types of regions: M for matches/mismatches,
               D for alignment gaps (formerly known as deletions) and G for
               gaps between alignment blocks.
  Returntype : txt
  Exceptions :
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::AlignSlice::Slice::get_original_seq_region_position ( )
  Arg  [1]   : int $position
               relative to start of slice, which is 1.
  Description: This Slice is made of several Bio::EnsEMBL::Slices mapped
               on it with gaps inside and regions with no matching
               sequence. This method returns the original seq_region_position
               in the original Slice of the requested position in AlignSlice
               coordinates
  Example    : my ($slice, $seq_region_position) = $as_slice->
                   get_original_seq_region_position(100);
  Returntype : ($slice, $seq_region_position), an array where the first
               element is a Bio::EnsEMBL::Slice and the second one is the
               requested seq_region_position.
  Exceptions : if the position corresponds to a gap, the slice will be a fake GAP
               slice and the position will be the requested one (in AlignSlice
               coordinates)
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::AlignSlice::Slice::invert ( )
Maybe at some point...
This method returns undef
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public Listref Bio::EnsEMBL::Compara::AlignSlice::Slice::map_original_Slice ( )
  Arg  [1]   : Bio::EnsEMBL::Slice $original_slice
  Description: This Slice is made of several Bio::EnsEMBL::Slices mapped
               on it with gaps inside and regions with no matching
               sequence. This method tries to map on this Slice the
               region(s) corresponding to the provided $original_slice
               NB: This method does not know how to project Slices onto
               other coordinate systems. It is your responsability to
               provide an original Slice on the same coordinate system
               as the underlying Bio::EnsEMBL::Slices
  Example    : my $slices = $as_slice->map_original_Slice($orginal_slice);
  Returntype : listref of Bio::EnsEMBL::Compara::AlignSlice::Slice objects
               which are the sub_Slices of this Bio::EnsEMBL::Compara::
               AlignSlice::Slice where the $original_slice maps
  Exceptions :
 
Code:
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public Bio::EnsEMBL::Compara::AlignSlice::Slice::new ( )
  Arg[1]     : 
  Example    : 
  Description: 
  Returntype : 
  Exceptions : 
  Caller     : Bio::EnsEMBL::Compara::AlignSlice->_create_underlying_Slices()
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public List Bio::EnsEMBL::Compara::AlignSlice::Slice::project ( )
  Arg [1]    : string $name
               The name of the coordinate system to project this slice onto
  Arg [2]    : string $version
               The version of the coordinate system (such as 'NCBI34') to
               project this slice onto
  Example    :
    my $clone_projection = $slice->project('clone');
    foreach my $seg (@$clone_projection) {
      my $clone = $segment->to_Slice();
      print $slice->seq_region_name(), ':', $seg->from_start(), '-',
            $seg->from_end(), ' -> ',
            $clone->seq_region_name(), ':', $clone->start(), '-',$clone->end(),
            $clone->strand(), "\\n";
    }
  Description: This Slice is made of several Bio::EnsEMBL::Slices mapped on it. This
               method go through all of them, porject them and maps the projections
               on this Bio::EnsEMBL::Compara::AlignSlice::Slice object.
               The original 'project' method returns the results of 'projecting'
               a slice onto another coordinate system.  Projecting to a coordinate
               system that the slice is assembled from is analagous to retrieving a tiling
               path. The original method may also be used to 'project up' to a higher
               level coordinate system, however.
               This method returns a listref of triplets [start,end,slice]
               which represents the projection.  The start and end defined the
               region of this slice which is made up of the third value of
               the triplet: a slice in the requested coordinate system.
               Because of the gaps in the mapping of the Bio::EnsEMBL::Slices
               the lenght of the slice returned in the tripet may be different
               than the distance defined by the start and end of the
               Bio::EnsEMBL::ProjectionSegment object.
  Returntype : list reference of Bio::EnsEMBL::ProjectionSegment objects which
               can also be used as [$start,$end,$slice] triplets
  Exceptions : none
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public String Bio::EnsEMBL::Compara::AlignSlice::Slice::seq ( )
  Arg [1]    : none
  Example    : print "SEQUENCE = ", $slice->seq();
  Description: Returns the sequence of the region represented by this
               slice formatted as a string.
               This Slice is made of several Bio::EnsEMBL::Slices mapped
               on it with gaps inside and regions with no matching
               sequence. The resulting string might contain gaps and/or
               dots as padding characters. If several Slices map on the
               same positions, the last one will override the positions.
  Returntype : string
  Exceptions : none
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::AlignSlice::Slice::sub_Slice ( )
  Arg   1    : int $start
  Arg   2    : int $end
  Arge [3]   : int $strand
  Example    : none
  Description: Makes another Slice that covers only part of this slice
               If a slice is requested which lies outside of the boundaries
               of this function will return undef.  This means that
               behaviour will be consistant whether or not the slice is
               attached to the database (i.e. if there is attached sequence
               to the slice).  Alternatively the expand() method or the
               SliceAdaptor::fetch_by_region method can be used instead.
  Returntype : Bio::EnsEMBL::Slice or undef if arguments are wrong
  Exceptions : return undef if $start and $end define a region outside
               of actual Slice.
  Caller     : general
  Status     : Testing
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public Txt Bio::EnsEMBL::Compara::AlignSlice::Slice::subseq ( )
  Arg  [1]   : int $startBasePair
               relative to start of slice, which is 1.
  Arg  [2]   : int $endBasePair
               relative to start of slice.
  Arg  [3]   : (optional) int $strand
               The strand of the slice to obtain sequence from. Default
               value is 1.
  Description: returns string of dna sequence
               This Slice is made of several Bio::EnsEMBL::Slices mapped
               on it with gaps inside and regions with no matching
               sequence. The resulting string might contain gaps and/or
               dots as padding characters. If several Slices map on the
               same positions, the last one will override the positions.
  Returntype : txt
  Exceptions : end should be at least as big as start
               strand must be set
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.


The documentation for this class was generated from the following file:
  • Bio/EnsEMBL/Compara/AlignSlice/Slice.pm