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Bio::EnsEMBL::RepeatMaskedSlice Class Reference
Inheritance diagram for Bio::EnsEMBL::RepeatMaskedSlice:

List of all members.


Class Summary

Synopsis

  $sa = $db-\>get_SliceAdaptor();

  $slice =
    $sa-\>fetch_by_region( 'chromosome', 'X', 1_000_000, 2_000_000 );

  $repeat_masked_slice = $slice-\>get_repeatmasked_seq();

  # get repeat masked sequence:
  my $dna = $repeat_masked_slice-\>seq();
  $dna = $repeat_masked_slice-\>subseq( 1, 1000 );

Description

This is a specialised Bio::EnsEMBL::Slice class that is used to retrieve
repeat masked genomic sequence rather than normal genomic sequence.
 

Definition at line 28 of file RepeatMaskedSlice.pm.

Available Methods

protected _calculate_a ()
protected _constrain_to_region ()
protected _get_StructuralVariationFeatureAdaptor ()
protected _get_VariationFeatureAdaptor ()
protected void _mask_features ()
public accession_number ()
public
Bio::EnsEMBL::DBSQL::SliceAdaptor 
adaptor ()
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 Int end ()
public Bio::EnsEMBL::Slice expand ()
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 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 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_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 Hash get_generic_features ()
public Reference get_MarkerFeatures_by_Name ()
public
Bio::EnsEMBL::RepeatMaskedSlice 
get_repeatmasked_seq ()
public Int get_seq_region_id ()
public get_tiling_path ()
public has_MapSet ()
public id ()
public Bio::EnsEMBL::Slice invert ()
public Int is_circular ()
public Int is_reference ()
public Int is_toplevel ()
public Int length ()
public moltype ()
public String name ()
public
Bio::EnsEMBL::RepeatMaskedSlice 
new ()
public Bio::EnsEMBL::Slice new_fast ()
public Hash not_default_masking_cases ()
public old_get_all_DASFeatures ()
public primary_id ()
public List project ()
public List project_to_slice ()
public Reference repeat_mask_logic_names ()
public String seq ()
public Int seq_region_length ()
public String seq_region_name ()
public Bio::EnsEMBL::Slice seq_region_Slice ()
public Boolean soft_mask ()
public Int start ()
public Int strand ()
public Bio::EnsEMBL::Slice sub_Slice ()
public String subseq ()
public Hashref summary_as_hash ()

Method Documentation

protected Bio::EnsEMBL::Slice::_calculate_a ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

protected Bio::EnsEMBL::Slice::_constrain_to_region ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

protected Bio::EnsEMBL::Slice::_get_StructuralVariationFeatureAdaptor ( ) [inherited]

Undocumented method

Code:
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protected Bio::EnsEMBL::Slice::_get_VariationFeatureAdaptor ( ) [inherited]

Undocumented method

Code:
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protected void Bio::EnsEMBL::Slice::_mask_features ( ) [inherited]
  Arg [1]    : reference to a string $dnaref
  Arg [2]    : array_ref $repeats
               reference to a list Bio::EnsEMBL::RepeatFeature
               give the list of coordinates to replace with N or with
               lower case
  Arg [3]    : int $soft_masking_enable (optional)
  Arg [4]    : hash reference $not_default_masking_cases (optional, default is {})
               The values are 0 or 1 for hard and soft masking respectively
               The keys of the hash should be of 2 forms
               "repeat_class_" . $repeat_consensus->repeat_class,
                e.g. "repeat_class_SINE/MIR"
               "repeat_name_" . $repeat_consensus->name
                e.g. "repeat_name_MIR"
               depending on which base you want to apply the not default masking either
               the repeat_class or repeat_name. Both can be specified in the same hash
               at the same time, but in that case, repeat_name setting has priority over
               repeat_class. For example, you may have hard masking as default, and
               you may want soft masking of all repeat_class SINE/MIR,
               but repeat_name AluSp (which are also from repeat_class SINE/MIR).
               Your hash will be something like {"repeat_class_SINE/MIR" => 1,
                                                 "repeat_name_AluSp" => 0}
  Example    : none
  Description: replaces string positions described in the RepeatFeatures
               with Ns (default setting), or with the lower case equivalent
               (soft masking).  The reference to a dna string which is passed
               is changed in place.
  Returntype : none
  Exceptions : none
  Caller     : seq
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::accession_number ( ) [inherited]
  Description: Included for Bio::PrimarySeqI interface compliance (1.2)
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::DBSQL::SliceAdaptor Bio::EnsEMBL::Slice::adaptor ( ) [inherited]
  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::SliceAdaptor $adaptor
  Example    : $adaptor = $slice->adaptor();
  Description: Getter/Setter for the slice object adaptor used
               by this slice for database interaction.
  Returntype : Bio::EnsEMBL::DBSQL::SliceAdaptor
  Exceptions : thorws if argument passed is not a SliceAdaptor
  Caller     : general
  Status     : Stable
 
Code:
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public void Bio::EnsEMBL::Slice::add_synonym ( ) [inherited]
  Args[0]    : synonym.
  Example    : $slice->add_synonym("alt_name");
  Description: add an alternative name for this slice
  Returntype : none
  Exception  : none
  Caller     : general
  Status     : At Risk
 
Code:
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public Bio::EnsEMBL::Slice::alphabet ( ) [inherited]
  Description: Included for Bio::PrimarySeqI interface compliance (1.2)
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public String Bio::EnsEMBL::Slice::assembly_exception_type ( ) [inherited]
  Example     : $self->assembly_exception_type(); 
  Description : Returns the type of slice this is. If it is reference then you
                will get 'REF' back. Otherwise you will get the first
                element from get_all_AssemblyExceptionFeatures(). If no
                assembly exception exists you will get an empty string back.
  Returntype  : String
  Exceptions  : None
  Caller      : Public
  Status      : Beta
 
Code:
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public Bio::EnsEMBL::Slice::assembly_type ( ) [inherited]
  Description:

Deprecated:
use version instead
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::calculate_pi ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::calculate_theta ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Int Bio::EnsEMBL::Slice::centrepoint ( ) [inherited]
  Arg [1]    : none
  Example    : $cp = $slice->centrepoint();
  Description: Returns the mid position of this slice relative to the
               start of the sequence region that it was created on.
               Coordinates are inclusive and start at 1.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Int Bio::EnsEMBL::Slice::chr_end ( ) [inherited]
  Description:

Deprecated:
use end() instead Returntype : int Exceptions : none Caller : SliceAdaptor, general
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::chr_name ( ) [inherited]
  Description:

Deprecated:
use seq_region_name() instead
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::chr_start ( ) [inherited]
  Description:

Deprecated:
use start() instead
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::Slice::coord_system ( ) [inherited]
  Arg [1]    : none
  Example    : print $slice->coord_system->name();
  Description: Returns the coordinate system that this slice is on.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::Slice::coord_system_name ( ) [inherited]
  Arg [1]    : none
  Example    : print $slice->coord_system_name()
  Description: Convenience method.  Gets the name of the coord_system which
               this slice is on.
               Returns undef if this Slice does not have an attached
               CoordSystem.
  Returntype: string or undef
  Exceptions: none
  Caller    : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Slice::dbID ( ) [inherited]
  Description:

Deprecated:
use SliceAdaptor::get_seq_region_id instead
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::desc ( ) [inherited]
Description: Included for Bio::PrimarySeqI interface compliance (1.2)
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::display_id ( ) [inherited]
  Description: Included for Bio::PrimarySeqI interface compliance (1.2)
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Int Bio::EnsEMBL::Slice::end ( ) [inherited]
  Arg [1]    : none
  Example    : $end = $slice->end();
  Description: Returns the end position of this slice relative to the
               start of the sequence region that it was created on.
               Coordinates are inclusive and start at 1.  Negative coordinates
               or coordinates exceeding the length of the sequence region are
               permitted.  End is always greater than or equal to start
               regardless of the orientation of the slice.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Slice Bio::EnsEMBL::Slice::expand ( ) [inherited]
  Arg [1]    : (optional) int $five_prime_expand
               The number of basepairs to shift this slices five_prime
               coordinate by.  Positive values make the slice larger,
               negative make the slice smaller.
               coordinate left.
               Default = 0.
  Arg [2]    : (optional) int $three_prime_expand
               The number of basepairs to shift this slices three_prime
               coordinate by. Positive values make the slice larger,
               negative make the slice smaller.
               Default = 0.
  Arg [3]    : (optional) bool $force_expand
               if set to 1, then the slice will be contracted even in the case
               when shifts $five_prime_expand and $three_prime_expand overlap.
               In that case $five_prime_expand and $three_prime_expand will be set
               to a maximum possible number and that will result in the slice
               which would have only 2pbs.
               Default = 0.
  Arg [4]    : (optional) int* $fpref
               The reference to a number of basepairs to shift this slices five_prime
               coordinate by. Normally it would be set to $five_prime_expand.
               But in case when $five_prime_expand shift can not be applied and
               $force_expand is set to 1, then $$fpref will contain the maximum possible
               shift
  Arg [5]    : (optional) int* $tpref
               The reference to a number of basepairs to shift this slices three_prime
               coordinate by. Normally it would be set to $three_prime_expand.
               But in case when $five_prime_expand shift can not be applied and
               $force_expand is set to 1, then $$tpref will contain the maximum possible
               shift
  Example    : my $expanded_slice      = $slice->expand( 1000, 1000);
               my $contracted_slice    = $slice->expand(-1000,-1000);
               my $shifted_right_slice = $slice->expand(-1000, 1000);
               my $shifted_left_slice  = $slice->expand( 1000,-1000);
               my $forced_contracted_slice    = $slice->expand(-1000,-1000, 1, \$five_prime_shift, \$three_prime_shift);
  Description: Returns a slice which is a resized copy of this slice.  The
               start and end are moved outwards from the center of the slice
               if positive values are provided and moved inwards if negative
               values are provided. This slice remains unchanged.  A slice
               may not be contracted below 1bp but may grow to be arbitrarily
               large.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : warning if an attempt is made to contract the slice below 1bp
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::get_all_AffyFeatures ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_AssemblyExceptionFeatures ( ) [inherited]
  Arg [1]    : string $set (optional)
  Example    : $slice->get_all_AssemblyExceptionFeatures();
  Description: Retreives all misc features which overlap this slice. If
               a set code is provided only features which are members of
               the requested set are returned.
  Returntype : listref of Bio::EnsEMBL::AssemblyExceptionFeatures
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_Attributes ( ) [inherited]
  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 this slice''s seq_region.
               Optionally just get Attrubutes for given code.
  Returntype : listref Bio::EnsEMBL::Attribute
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Reference Bio::EnsEMBL::Slice::get_all_compara_DnaAlignFeatures ( ) [inherited]
  Arg [1]    : string $qy_species
               The name of the species to retrieve similarity features from
  Arg [2]    : string $qy_assembly
               The name of the assembly to retrieve similarity features from
  Arg [3]    : string $type
               The type of the alignment to retrieve similarity features from
  Arg [4]    : <optional> compara dbadptor to use.
  Example    : $fs = $slc->get_all_compara_DnaAlignFeatures('Mus musculus',
							    'MGSC3',
							    'WGA');
  Description: Retrieves a list of DNA-DNA Alignments to the species specified
               by the $qy_species argument.
               The compara database must be attached to the core database
               for this call to work correctly.  As well the compara database
               must have the core dbadaptors for both this species, and the
               query species added to function correctly.
  Returntype : reference to a list of Bio::EnsEMBL::DnaDnaAlignFeatures
  Exceptions : warning if compara database is not available
  Caller     : contigview
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Arrayref Bio::EnsEMBL::Slice::get_all_compara_Syntenies ( ) [inherited]
  Arg [1]    : string $query_species e.g. "Mus_musculus" or "Mus musculus"
  Arg [2]    : string $method_link_type, default is "SYNTENY"
  Arg [3]    : <optional> compara dbadaptor to use.
  Description: gets all the compara syntenyies for a specfic species
  Returns    : arrayref of Bio::EnsEMBL::Compara::SyntenyRegion
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_CopyNumberVariantProbeFeatures ( ) [inherited]
    Arg[1]      : string $source [optional]
    Description : returns all copy number variant probes on this slice. This function will only work
                  correctly if the variation database has been attached to the core database.
                  If $source is set, only CNV probes with that source name will be returned.
                  If $study is set, only CNV probes of that study will be returned.
    ReturnType  : listref of Bio::EnsEMBL::Variation::StructuralVariationFeature
    Exceptions  : none
    Caller      : contigview, snpview, structural_variation_feature
    Status      : At Risk
 
Code:
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public Bio::EnsEMBL::Slice::get_all_CopyNumberVariantProbes ( ) [inherited]
	Description:

Deprecated:
. Use get_all_CopyNumberVariantProbeFeatures instead
 
Code:
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public Hashref Bio::EnsEMBL::Slice::get_all_DAS_Features ( ) [inherited]
  Arg [1]    : none
  Example    : $features = $slice->get_all_DASFeatures;
  Description: Retreives a hash reference to a hash of DAS feature
               sets, keyed by the DNS, NOTE the values of this hash
               are an anonymous array containing:
                (1) a pointer to an array of features;
                (2) a pointer to the DAS stylesheet
  Returntype : hashref of Bio::SeqFeatures
  Exceptions : ?
  Caller     : webcode
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::get_all_DASFactories ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::get_all_DASFeatures ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::get_all_DASFeatures_dsn ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_DitagFeatures ( ) [inherited]
  Arg [1]    : (optional) string ditag type
  Arg [1]    : (optional) string logic_name
  Example    : @dna_dna_align_feats = @{$slice->get_all_DitagFeatures};
  Description: Retrieves the DitagFeatures of a specific type which overlap
               this slice with. If type is not defined, all features are
               retrieved.
  Returntype : listref of Bio::EnsEMBL::DitagFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_DnaAlignFeatures ( ) [inherited]
  Arg [1]    : (optional) string $logic_name
               The name of the analysis performed on the dna align features
               to obtain.
  Arg [2]    : (optional) float $score
               The mimimum score of the features to retrieve
  Arg [3]    : (optional) string $dbtype
               The name of an attached database to retrieve the features from
               instead, e.g. 'otherfeatures'.
  Arg [4]    : (optional) float hcoverage
               The minimum hcoverage od the featurs to retrieve
  Example    : @dna_dna_align_feats = @{$slice->get_all_DnaAlignFeatures};
  Description: Retrieves the DnaDnaAlignFeatures which overlap this slice with
               logic name $logic_name and with score above $score.  If
               $logic_name is not defined features of all logic names are
               retrieved.  If $score is not defined features of all scores are
               retrieved.
  Returntype : listref of Bio::EnsEMBL::DnaDnaAlignFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Reference Bio::EnsEMBL::Slice::get_all_Exons ( ) [inherited]
  Arg [1]    : none
  Example    : @exons = @{$slice->get_all_Exons};
  Description: Gets all exons which overlap this slice.  Note that these exons
               will not be associated with any transcripts, so this may not
               be terribly useful.
  Returntype : reference to a list of Bio::EnsEMBL::Exons
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice, and Bio::EnsEMBL::IndividualSlice.

public Listref Bio::EnsEMBL::Slice::get_all_ExternalFeatures ( ) [inherited]
  Arg [1]    : (optional) string $track_name
               If specified only features from ExternalFeatureAdaptors with
               the track name $track_name are retrieved.
               If not set, all features from every ExternalFeatureAdaptor are
               retrieved.
  Example    : @x_features = @{$slice->get_all_ExternalFeatures}
  Description: Retrieves features on this slice from external feature adaptors
  Returntype : listref of Bio::SeqFeatureI implementing objects in slice
               coordinates
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_Genes ( ) [inherited]
  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.  This assumes that the db has
               been added to the DBAdaptor under this name (using the
               DBConnection::add_db_adaptor method).
  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).
  Arg [4]    : (optional) string $source
               The source of the genes to retrieve.
  Arg [5]    : (optional) string $biotype
               The biotype of the genes to retrieve.
  Example    : @genes = @{$slice->get_all_Genes};
  Description: Retrieves all genes that overlap this slice.
  Returntype : listref of Bio::EnsEMBL::Genes
  Exceptions : none
  Caller     : none
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice, and Bio::EnsEMBL::IndividualSlice.

public Listref Bio::EnsEMBL::Slice::get_all_Genes_by_source ( ) [inherited]
  Arg [1]    : string source
  Arg [2]    : (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_source('ensembl')};
  Description: Retrieves genes that overlap this slice of source $source.
  Returntype : listref of Bio::EnsEMBL::Genes
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_Genes_by_type ( ) [inherited]
  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.
  Returntype : listref of Bio::EnsEMBL::Genes
  Exceptions : none
  Caller     : genebuilder, general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::get_all_genotyped_SNPs ( ) [inherited]
  Description   :

Deprecated:
. Use get_all_genotyped_VariationFeatures insted
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_genotyped_VariationFeatures ( ) [inherited]
    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.
    ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
    Exceptions : none
    Caller     : contigview, snpview, ldview
    Status     : At Risk
               : Variation database is under development.
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_Haplotypes ( ) [inherited]
  Arg [1]    : (optional) boolean $lite_flag
               if true lightweight haplotype objects are used
  Example    : @haplotypes = $slice->get_all_Haplotypes;
  Description: Retrieves all of the haplotypes on this slice.  Only works
               if the haplotype adaptor has been attached to the core adaptor
               via $dba->add_db_adaptor('haplotype', $hdba);
  Returntype : listref of Bio::EnsEMBL::External::Haplotype::Haplotypes
  Exceptions : warning is Haplotype database is not available
  Caller     : contigview, general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_IndividualSlice ( ) [inherited]
    Args        : none
    Example     : my $individualSlice = $slice->get_by_Population($population);
    Description : Gets the specific Slice for all the individuls in the population
    ReturnType  : listref of Bio::EnsEMB::IndividualSlice
    Exceptions  : none
    Caller      : general
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_KaryotypeBands ( ) [inherited]
  Arg [1]    : none
  Example    : @kary_bands = @{$slice->get_all_KaryotypeBands};
  Description: Retrieves the karyotype bands which this slice overlaps.
  Returntype : listref oif Bio::EnsEMBL::KaryotypeBands
  Exceptions : none
  Caller     : general, contigview
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Variation::LDFeatureContainer Bio::EnsEMBL::Slice::get_all_LD_values ( ) [inherited]
    Arg [1]     : (optional) Bio::EnsEMBL::Variation::Population $population
    Description : returns all LD values on this slice. This function will only work correctly if the variation
                  database has been attached to the core database. If the argument is passed, will return the LD information
                  in that population
    ReturnType  : Bio::EnsEMBL::Variation::LDFeatureContainer
    Exceptions  : none
    Caller      : contigview, snpview
     Status     : At Risk
                : Variation database is under development.
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::get_all_MapFrags ( ) [inherited]
  Description:

Deprecated:
use get_all_MiscFeatures instead
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::CircularSlice.

public Reference Bio::EnsEMBL::Slice::get_all_MarkerFeatures ( ) [inherited]
  Arg [1]    : (optional) string logic_name
               The logic name of the marker features to retrieve
  Arg [2]    : (optional) int $priority
               Lower (exclusive) priority bound of the markers to retrieve
  Arg [3]    : (optional) int $map_weight
               Upper (exclusive) priority bound of the markers to retrieve
  Example    : my @markers = @{$slice->get_all_MarkerFeatures(undef,50, 2)};
  Description: Retrieves all markers which lie on this slice fulfilling the
               specified map_weight and priority parameters (if supplied).
  Returntype : reference to a list of Bio::EnsEMBL::MarkerFeatures
  Exceptions : none
  Caller     : contigview, general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_MiscFeatures ( ) [inherited]
  Arg [1]    : string $set (optional)
  Arg [2]    : string $database (optional)
  Example    : $slice->get_all_MiscFeatures('cloneset');
  Description: Retreives all misc features which overlap this slice. If
               a set code is provided only features which are members of
               the requested set are returned.
  Returntype : listref of Bio::EnsEMBL::MiscFeatures
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::get_all_OligoFeatures ( ) [inherited]
  Description:

Deprecated:
, use functionality provided by the Ensembl Functional Genomics API instead.
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::get_all_OligoFeatures_by_type ( ) [inherited]
  Description:

Deprecated:
, use functionality provided by the Ensembl Functional Genomics API instead.
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_PredictionTranscripts ( ) [inherited]
  Arg [1]    : (optional) string $logic_name
               The name of the analysis used to generate the prediction
               transcripts obtained.
  Arg [2]    : (optional) boolean $load_exons
               If set to true will force loading of all PredictionExons
               immediately rather than loading them on demand later.  This
               is faster if there are a large number of PredictionTranscripts
               and the exons will be used.
  Example    : @transcripts = @{$slice->get_all_PredictionTranscripts};
  Description: Retrieves the list of prediction transcripts which overlap
               this slice with logic_name $logic_name.  If logic_name is
               not defined then all prediction transcripts are retrieved.
  Returntype : listref of Bio::EnsEMBL::PredictionTranscript
  Exceptions : warning if slice does not have attached adaptor
  Caller     : none
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_ProteinAlignFeatures ( ) [inherited]
  Arg [1]    : (optional) string $logic_name
               The name of the analysis performed on the protein align features
               to obtain.
  Arg [2]    : (optional) float $score
               The mimimum score of the features to retrieve
  Arg [3]    : (optional) string $dbtype
               The name of an attached database to retrieve features from
               instead.
  Arg [4]    : (optional) float hcoverage
               The minimum hcoverage od the featurs to retrieve
  Example    : @dna_pep_align_feats = @{$slice->get_all_ProteinAlignFeatures};
  Description: Retrieves the DnaPepAlignFeatures which overlap this slice with
               logic name $logic_name and with score above $score.  If
               $logic_name is not defined features of all logic names are
               retrieved.  If $score is not defined features of all scores are
               retrieved.
  Returntype : listref of Bio::EnsEMBL::DnaPepAlignFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_QtlFeatures ( ) [inherited]
  Args       : none
  Example    : none
  Description: returns overlapping QtlFeatures
  Returntype : listref Bio::EnsEMBL::Map::QtlFeature
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_RepeatFeatures ( ) [inherited]
  Arg [1]    : (optional) string $logic_name
               The name of the analysis performed on the repeat features
               to obtain.
  Arg [2]    : (optional) string/array $repeat_type
               Limits features returned to those of the specified 
               repeat_type. Can specify a single value or an array reference
               to limit by more than one
  Arg [3]    : (optional) string $db
               Key for database e.g. core/vega/cdna/....
  Example    : @repeat_feats = @{$slice->get_all_RepeatFeatures(undef,'Type II Transposons')};
  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.
  Returntype : listref of Bio::EnsEMBL::RepeatFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_SearchFeatures ( ) [inherited]
  Arg [1]    : scalar $ticket_ids
  Example    : $slice->get_all_SearchFeatures('BLA_KpUwwWi5gY');
  Description: Retreives all search features for stored blast
               results for the ticket that overlap this slice
  Returntype : listref of Bio::EnsEMBL::SeqFeatures
  Exceptions : none
  Caller     : general (webby!)
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_SimilarityFeatures ( ) [inherited]
  Arg [1]    : (optional) string $logic_name
               the name of the analysis performed on the features to retrieve
  Arg [2]    : (optional) float $score
               the lower bound of the score of the features to be retrieved
  Example    : @feats = @{$slice->get_all_SimilarityFeatures};
  Description: Retrieves all dna_align_features and protein_align_features
               with analysis named $logic_name and with score above $score.
               It is probably faster to use get_all_ProteinAlignFeatures or
               get_all_DnaAlignFeatures if a sepcific feature type is desired.
               If $logic_name is not defined features of all logic names are
               retrieved.  If $score is not defined features of all scores are
               retrieved.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_SimpleFeatures ( ) [inherited]
  Arg [1]    : (optional) string $logic_name
               The name of the analysis performed on the simple features
               to obtain.
  Arg [2]    : (optional) float $score
               The mimimum score of the features to retrieve
  Example    : @simple_feats = @{$slice->get_all_SimpleFeatures};
  Description: Retrieves the SimpleFeatures which overlap this slice with
               logic name $logic_name and with score above $score.  If
               $logic_name is not defined features of all logic names are
               retrieved.  If $score is not defined features of all scores are
               retrieved.
  Returntype : listref of Bio::EnsEMBL::SimpleFeatures
  Exceptions : warning if slice does not have attached adaptor
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::get_all_SNPs ( ) [inherited]
 Description:

Deprecated:
. Use get_all_VariationFeatures insted
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::get_all_SNPs_transcripts ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Listref Bio::EnsEMBL::Slice::get_all_somatic_VariationFeatures ( ) [inherited]
    Args        : $filter [optional]
    Description : Returns all somatic variation features on this slice. This function will only 
                  work correctly if the variation database has been attached to the core database.
    ReturnType  : listref of Bio::EnsEMBL::Variation::VariationFeature
    Exceptions  : none
    Status      : At Risk
                : Variation database is under development.
 
Code:
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public Listref Bio::EnsEMBL::Slice::get_all_somatic_VariationFeatures_with_annotation ( ) [inherited]
    Arg [1]     : $variation_feature_source [optional]
    Arg [2]     : $annotation_source [optional]
    Arg [3]     : $annotation_name [optional]
    Description : returns all somatic variation features on this slice associated with a phenotype.
                  (see get_all_VariationFeatures_with_annotation for further documentation)
    ReturnType  : listref of Bio::EnsEMBL::Variation::VariationFeature
    Exceptions  : none
    Status      : At Risk
                : Variation database is under development.
 
Code:
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public Listref Bio::EnsEMBL::Slice::get_all_StructuralVariationFeatures ( ) [inherited]
    Arg[1]      : string $source [optional]
		Arg[2]      : int $include_evidence [optional]
    Description : returns all structural variation features on this slice. This function will only work
                  correctly if the variation database has been attached to the core database.
                  If $source is set, only structural variation features with that source name will be 
									returned. By default, it only returns structural variant features which are not labelled 
									as "CNV_PROBE".
									If $include_evidence is set (i.e. $include_evidence=1), structural variation features from 
							    both structural variation (SV) and their supporting structural variations (SSV) will be 
							    returned. By default, it only returns features from structural variations (SV). 
							    from structural variations.
    ReturnType  : listref of Bio::EnsEMBL::Variation::StructuralVariationFeature
    Exceptions  : none
    Caller      : contigview, snpview, structural_variation_features
    Status      : At Risk
 
Code:
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public Listref Bio::EnsEMBL::Slice::get_all_StructuralVariationFeatures_by_VariationSet ( ) [inherited]
    Arg [1]     : Bio::EnsEMBL:Variation::VariationSet $set
    Description :returns all structural variation features on this slice associated with a 
                 given set.
                 This function will only work correctly if the variation database has been
                 attached to the core database. 
    ReturnType : listref of Bio::EnsEMBL::Variation::StructuralVariationFeature
    Exceptions : none
    Caller     : contigview, snpview
    Status     : At Risk
 
Code:
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public Bio::EnsEMBL::Slice::get_all_StructuralVariations ( ) [inherited]
		Description:

Deprecated:
. Use get_all_StructuralVariationFeatures instead
 
Code:
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public Bio::EnsEMBL::Slice::get_all_supercontig_Slices ( ) [inherited]
  Description:

Deprecated:
use get_tiling_path("NTcontig") instead
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Reference Bio::EnsEMBL::Slice::get_all_synonyms ( ) [inherited]
  Args       : none.
  Example    : my @alternative_names = @{$slice->get_all_synonyms()};
  Description: get a list of alternative names for this slice
  Returntype : reference to list of SeqRegionSynonym objects.
  Exception  : none
  Caller     : general
  Status     : At Risk
 
Code:
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public Reference Bio::EnsEMBL::Slice::get_all_Transcripts ( ) [inherited]
  Arg [1]    : (optional) boolean $load_exons
               If set to true exons will not be lazy-loaded but will instead
               be loaded right away.  This is faster if the exons are
               actually going to be used right away.
  Arg [2]    : (optional) string $logic_name
               the logic name of the type of features to obtain
  Arg [3]    : (optional) string $db_type
  Example    : @transcripts = @{$slice->get_all_Transcripts)_};
  Description: Gets all transcripts which overlap this slice.  If you want to
               specify a particular analysis or type, then you are better off
               using get_all_Genes or get_all_Genes_by_type and iterating
               through the transcripts of each gene.
  Returntype : reference to a list of Bio::EnsEMBL::Transcripts
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice, and Bio::EnsEMBL::IndividualSlice.

public Listref Bio::EnsEMBL::Slice::get_all_VariationFeatures ( ) [inherited]
    Args        : $filter [optional] (

Deprecated:

) Description : Returns all germline variation features on this slice. This function will only work correctly if the variation database has been attached to the core database. If (the

parameter) $filter is "genotyped" return genotyped SNPs only, otherwise return all germline variations. ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature Exceptions : none Caller : contigview, snpview Status : At Risk : Variation database is under development.

 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice, and Bio::EnsEMBL::StrainSlice.

public Listref Bio::EnsEMBL::Slice::get_all_VariationFeatures_by_Population ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Variation::Population
  Arg [2]	 : $minimum_frequency (optional)
  Example    : $pop = $pop_adaptor->fetch_by_dbID(659);
               @vfs = @{$slice->get_all_VariationFeatures_by_Population(
                 $pop,$slice)};
  Description: Retrieves all variation features in a slice which are stored for
			   a specified population. If $minimum_frequency is supplied, only
			   variations with a minor allele frequency (MAF) greater than
			   $minimum_frequency will be returned.
  Returntype : listref of Bio::EnsEMBL::Variation::VariationFeature
  Exceptions : throw on incorrect argument
  Caller     : general
  Status     : At Risk
 
Code:
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public Listref Bio::EnsEMBL::Slice::get_all_VariationFeatures_by_VariationSet ( ) [inherited]
    Arg [1]     : Bio::EnsEMBL:Variation::VariationSet $set
    Description :returns all variation features on this slice associated with a given set.
                 This function will only work correctly if the variation database has been
                 attached to the core database. 
    ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
    Exceptions : none
    Caller     : contigview, snpview
    Status     : At Risk
               : Variation database is under development.
 
Code:
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public Listref Bio::EnsEMBL::Slice::get_all_VariationFeatures_with_annotation ( ) [inherited]
    Arg [1]     : $variation_feature_source [optional]
    Arg [2]     : $annotation_source [optional]
    Arg [3]     : $annotation_name [optional]
    Description : returns all germline variation features on this slice associated with a phenotype.
                  This function will only work correctly if the variation database has been
                  attached to the core database.
                  If $variation_feature_source is set only variations from that source
                  are retrieved.
                  If $annotation_source is set only variations whose annotations come from
                  $annotation_source will be retrieved.
                  If $annotation_name is set only variations with that annotation will be retrieved.
                  $annotation_name can be a phenotype's internal dbID.
    ReturnType  : listref of Bio::EnsEMBL::Variation::VariationFeature
    Exceptions  : none
    Caller      : contigview, snpview
    Status      : At Risk
                : Variation database is under development.
 
Code:
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public Hashref Bio::EnsEMBL::Slice::get_base_count ( ) [inherited]
  Arg [1]    : none
  Example    : $c_count = $slice->get_base_count->{'c'};
  Description: Retrieves a hashref containing the counts of each bases in the
               sequence spanned by this slice.  The format of the hash is :
               { 'a' => num,
                 'c' => num,
                 't' => num,
                 'g' => num,
                 'n' => num,
                 '%gc' => num }
               All bases which are not in the set [A,a,C,c,T,t,G,g] are
               included in the 'n' count.  The 'n' count could therefore be
               inclusive of ambiguity codes such as 'y'.
               The %gc is the ratio of GC to AT content as in:
               total(GC)/total(ACTG) * 100
               This function is conservative in its memory usage and scales to
               work for entire chromosomes.
  Returntype : hashref
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMB::IndividualSlice Bio::EnsEMBL::Slice::get_by_Individual ( ) [inherited]
    Arg[1]      : Bio::EnsEMBL::Variation::Individual $individual
    Example     : my $individualSlice = $slice->get_by_Individual($individual);
    Description : Gets the specific Slice for the individual
    ReturnType  : Bio::EnsEMB::IndividualSlice
    Exceptions  : none
    Caller      : general
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMB::StrainSlice Bio::EnsEMBL::Slice::get_by_strain ( ) [inherited]
    Arg[1]      : string $strain
    Example     : my $strainSlice = $slice->get_by_strain($strain);
    Description : Gets the specific Slice for the strain
    ReturnType  : Bio::EnsEMB::StrainSlice
    Exceptions  : none
    Caller      : general
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::get_Chromosome ( ) [inherited]
  Description:

Deprecated:
use this instead: $slice_adp->fetch_by_region('chromosome', $slice->seq_region_name)
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Hash Bio::EnsEMBL::Slice::get_generic_features ( ) [inherited]
  Arg [1]    : (optional) List of names of generic feature types to return.
               If no feature names are given, all generic features are
               returned.
  Example    : my %features = %{$slice->get_generic_features()};
  Description: Gets generic features via the generic feature adaptors that
               have been added via DBAdaptor->add_GenricFeatureAdaptor (if
               any)
  Returntype : Hash of named features.
  Exceptions : none
  Caller     : none
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Reference Bio::EnsEMBL::Slice::get_MarkerFeatures_by_Name ( ) [inherited]
  Arg [1]    : string marker Name
               The name (synonym) of the marker feature(s) to retrieve
  Example    : my @markers = @{$slice->get_MarkerFeatures_by_Name('z1705')};
  Description: Retrieves all markers with this ID
  Returntype : reference to a list of Bio::EnsEMBL::MarkerFeatures
  Exceptions : none
  Caller     : contigview, general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::RepeatMaskedSlice Bio::EnsEMBL::Slice::get_repeatmasked_seq ( ) [inherited]
  Arg [1]    : listref of strings $logic_names (optional)
  Arg [2]    : int $soft_masking_enable (optional)
  Arg [3]    : hash reference $not_default_masking_cases (optional, default is {})
               The values are 0 or 1 for hard and soft masking respectively
               The keys of the hash should be of 2 forms
               "repeat_class_" . $repeat_consensus->repeat_class,
                e.g. "repeat_class_SINE/MIR"
               "repeat_name_" . $repeat_consensus->name
                e.g. "repeat_name_MIR"
               depending on which base you want to apply the not default
               masking either the repeat_class or repeat_name. Both can be
               specified in the same hash at the same time, but in that case,
               repeat_name setting has priority over repeat_class. For example,
               you may have hard masking as default, and you may want soft
               masking of all repeat_class SINE/MIR, but repeat_name AluSp
               (which are also from repeat_class SINE/MIR).
               Your hash will be something like {"repeat_class_SINE/MIR" => 1,
                                                 "repeat_name_AluSp" => 0}
  Example    : $rm_slice = $slice->get_repeatmasked_seq();
               $softrm_slice = $slice->get_repeatmasked_seq(['RepeatMask'],1);
  Description: Returns Bio::EnsEMBL::Slice that can be used to create repeat
               masked sequence instead of the regular sequence.
               Sequence returned by this new slice will have repeat regions
               hardmasked by default (sequence replaced by N) or
               or soft-masked when arg[2] = 1 (sequence in lowercase)
               Will only work with database connection to get repeat features.
  Returntype : Bio::EnsEMBL::RepeatMaskedSlice
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Int Bio::EnsEMBL::Slice::get_seq_region_id ( ) [inherited]
  Arg [1]    : none
  Example    : my $seq_region_id = $slice->get_seq_region_id();
  Description: Gets the internal identifier of the seq_region that this slice
               is on. Note that this function will not work correctly if this
               slice does not have an attached adaptor. Also note that it may
               be better to go through the SliceAdaptor::get_seq_region_id
               method if you are working with multiple databases since is
               possible to work with slices from databases with different
               internal seq_region identifiers.
  Returntype : int or undef if slices does not have attached adaptor
  Exceptions : warning if slice is not associated with a SliceAdaptor
  Caller     : assembly loading scripts, general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Slice::get_tiling_path ( ) [inherited]
  Description:

Deprecated:
use project instead
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::has_MapSet ( ) [inherited]
  Description:

Deprecated:
use get_all_MiscFeatures instead
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::id ( ) [inherited]
  Description: Included for Bio::PrimarySeqI interface compliance (0.7)
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Slice::invert ( ) [inherited]
  Arg [1]    : none
  Example    : $inverted_slice = $slice->invert;
  Description: Creates a copy of this slice on the opposite strand and
               returns it.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Int Bio::EnsEMBL::Slice::is_circular ( ) [inherited]
  Arg        : none
  Example    : my $circ = $slice->is_circular()
  Description: Returns 1 if slice is a circular slice else 0
  Returntype : int
  Caller     : general
  Status     : At Risk
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Int Bio::EnsEMBL::Slice::is_reference ( ) [inherited]
  Arg        : none
  Example    : my $reference = $slice->is_reference()
  Description: Returns 1 if slice is a reference  slice else 0
  Returntype : int
  Caller     : general
  Status     : At Risk
 
Code:
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public Int Bio::EnsEMBL::Slice::is_toplevel ( ) [inherited]
  Arg        : none
  Example    : my $top = $slice->is_toplevel()
  Description: Returns 1 if slice is a toplevel slice else 0
  Returntype : int
  Caller     : general
  Status     : At Risk
 
Code:
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public Int Bio::EnsEMBL::Slice::length ( ) [inherited]
  Arg [1]    : none
  Example    : $length = $slice->length();
  Description: Returns the length of this slice in basepairs
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::moltype ( ) [inherited]
Description: Included for Bio::PrimarySeqI interface compliance (0.7)
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public String Bio::EnsEMBL::Slice::name ( ) [inherited]
  Arg [1]    : none
  Example    : my $results = $cache{$slice->name()};
  Description: Returns the name of this slice. The name is formatted as a colon
               delimited string with the following attributes:
               coord_system:version:seq_region_name:start:end:strand
               Slices with the same name are equivalent and thus the name can
               act as a hash key.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::RepeatMaskedSlice Bio::EnsEMBL::RepeatMaskedSlice::new ( )
  Arg [-REPEAT_MASK] : The logic name of the repeats to be used for masking.
                      If not provided, all repeats in the database are used.
  Arg [...]  : Named superclass arguments. See Bio::EnsEMBL::Slice.
  Example    : my $slice = Bio::EnsEMBL::RepeatMaskedSlice->new
                  (-START  => $start,
                   -END    => $end,
                   -STRAND => $strand,
                   -SEQ_REGION_NAME => $seq_region,
                   -SEQ_REGION_LENGTH => $seq_region_length,
                   -COORD_SYSTEM  => $cs,
                   -ADAPTOR => $adaptor,
                   -REPEAT_MASK => ['repeat_masker'],
                   -SOFT_MASK => 1,
                   -NOT_DEFAULT_MASKING_CASES => {"repeat_class_SINE/MIR" => 1,
                                                  "repeat_name_AluSp" => 0});
  Description: Creates a Slice which behaves exactly as a normal slice but
               that returns repeat masked sequence from the seq method.
  Returntype : Bio::EnsEMBL::RepeatMaskedSlice
  Exceptions : none
  Caller     : RawComputes (PredictionTranscript creation code).
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Slice::new_fast ( ) [inherited]
  Arg [1]    : hashref to be blessed
  Description: Construct a new Bio::EnsEMBL::Slice using the hashref.
  Exceptions : none
  Returntype : Bio::EnsEMBL::Slice
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Hash Bio::EnsEMBL::RepeatMaskedSlice::not_default_masking_cases ( )
  Arg [1]    : hash reference $not_default_masking_cases (optional, default is {})
               The values are 0 or 1 for hard and soft masking respectively
               The keys of the hash should be of 2 forms
               "repeat_class_" . $repeat_consensus->repeat_class,
                e.g. "repeat_class_SINE/MIR"
               "repeat_name_" . $repeat_consensus->name
                e.g. "repeat_name_MIR"
               depending on which base you want to apply the not default masking either 
               the repeat_class or repeat_name. Both can be specified in the same hash
               at the same time, but in that case, repeat_name setting has priority over 
               repeat_class. For example, you may have hard masking as default, and 
               you may want soft masking of all repeat_class SINE/MIR,
               but repeat_name AluSp (which are also from repeat_class SINE/MIR)
  Example    : $rm_slice->not_default_masking_cases({"repeat_class_SINE/MIR" => 1,
                                                     "repeat_name_AluSp" => 0});
  Description: Getter/Setter which is used to escape some repeat class or name from the default 
               masking in place. 
  Returntype : hash reference
  Exceptions : none
  Caller     : seq() and subseq() methods
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Slice::old_get_all_DASFeatures ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Bio::EnsEMBL::Slice::primary_id ( ) [inherited]
  Description: Included for Bio::PrimarySeqI interface compliance (1.2)
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public List Bio::EnsEMBL::Slice::project ( ) [inherited]
  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(),
            $clone->strand(), "\\n";
    }
  Description: Returns the results of 'projecting' this slice onto another
               coordinate system.  Projecting to a coordinate system that
               the slice is assembled from is analagous to retrieving a tiling
               path.  This method may also be used to 'project up' to a higher
               level coordinate system, however.
               This method returns a listref of triplets [start,end,slice]
               which represents the projection.  The start and end defined the
               region of this slice which is made up of the third value of
               the triplet: a slice in the requested coordinate system.
  Returntype : list reference of Bio::EnsEMBL::ProjectionSegment objects which
               can also be used as [$start,$end,$slice] triplets
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public List Bio::EnsEMBL::Slice::project_to_slice ( ) [inherited]
  Arg [1]    : Slice to project to.
  Example    : my $chr_projection = $clone_slice->project_to_slice($chrom_slice);
                foreach my $segment ( @$chr_projection ){
                  $chr_slice = $segment->to_Slice();
                  print $clone_slice->seq_region_name(). ':'. $segment->from_start(). '-'.
                        $segment->from_end(). ' -> '.$chr_slice->seq_region_name(). ':'. $chr_slice->start().
	                '-'.$chr_slice->end().
                         $chr_slice->strand(). " length: ".($chr_slice->end()-$chr_slice->start()+1). "\\n";
                }
  Description: Projection of slice to another specific slice. Needed for where we have multiple mappings
               and we want to state which one to project to.
  Returntype : list reference of Bio::EnsEMBL::ProjectionSegment objects which
               can also be used as [$start,$end,$slice] triplets.
  Exceptions : none
  Caller     : none
  Status     : At Risk
 
Code:
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Reimplemented in Bio::EnsEMBL::CircularSlice.

public Reference Bio::EnsEMBL::RepeatMaskedSlice::repeat_mask_logic_names ( )
  Arg [1]    : reference to list of strings $logic_names (optional)
  Example    : $rm_slice->repeat_mask_logic_name(['repeat_masker']);
  Description: Getter/Setter for the logic_names of the repeats that are used
               to mask this slices sequence.
  Returntype : reference to list of strings
  Exceptions : none
  Caller     : seq() method
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::RepeatMaskedSlice::seq ( )
  Arg [1]    : none
  Example    : print $rmslice->seq(), "\\n";
  Description: Retrieves the entire repeat masked sequence for this slice.
               See also the Bio::EnsEMBL::Slice implementation of this 
               method.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public Int Bio::EnsEMBL::Slice::seq_region_length ( ) [inherited]
  Arg [1]    : none
  Example    : $seq_region_length = $slice->seq_region_length();
  Description: Returns the length of the entire seq_region that this slice is
               on. For example if this slice is on a chromosome this will be
               the length (in basepairs) of the entire chromosome.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::Slice::seq_region_name ( ) [inherited]
  Arg [1]    : none
  Example    : $seq_region = $slice->seq_region_name();
  Description: Returns the name of the seq_region that this slice is on. For
               example if this slice is in chromosomal coordinates the
               seq_region_name might be 'X' or '10'.
               This function was formerly named chr_name, but since slices can
               now be on coordinate systems other than chromosomal it has been
               changed.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Slice Bio::EnsEMBL::Slice::seq_region_Slice ( ) [inherited]
  Arg [1]    : none
  Example    : $slice = $slice->seq_region_Slice();
  Description: Returns a slice which spans the whole seq_region which this slice
               is on.  For example if this is a slice which spans a small region
               of chromosome X, this method will return a slice which covers the
               entire chromosome X. The returned slice will always have strand
               of 1 and start of 1.  This method cannot be used if the sequence
               of the slice has been set manually.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : warning if called when sequence of Slice has been set manually.
  Caller     : general
  Status     : Stable
 
Code:
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public Boolean Bio::EnsEMBL::RepeatMaskedSlice::soft_mask ( )
  Arg [1]    : boolean $soft_mask (optional)
  Example    : $rm_slice->soft_mask(0);
  Description: Getter/Setter which is used to turn on/off softmasking of the
               sequence returned by seq.
  Returntype : boolean
  Exceptions : none
  Caller     : seq() method
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Slice::start ( ) [inherited]
  Arg [1]    : none
  Example    : $start = $slice->start();
  Description: Returns the start position of this slice relative to the
               start of the sequence region that it was created on.
               Coordinates are inclusive and start at 1.  Negative coordinates
               or coordinates exceeding the length of the sequence region are
               permitted.  Start is always less than or equal to end
               regardless of the orientation of the slice.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Slice::strand ( ) [inherited]
  Arg [1]    : none
  Example    : $strand = $slice->strand();
  Description: Returns the orientation of this slice on the seq_region it has
               been created on
  Returntype : int (either 1 or -1)
  Exceptions : none
  Caller     : general, invert
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Slice Bio::EnsEMBL::Slice::sub_Slice ( ) [inherited]
  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 : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::IndividualSlice, and Bio::EnsEMBL::StrainSlice.

public String Bio::EnsEMBL::RepeatMaskedSlice::subseq ( )
  Arg [1]    : none
  Example    : print $rmslice->subseq(1, 1000);
  Description: Retrieves a repeat masked sequence from a specified subregion
               of this slice.  See also the Bio::EnsEMBL::Slice 
               implementation of this method.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Slice.

public Hashref Bio::EnsEMBL::Slice::summary_as_hash ( ) [inherited]
  Example       : $slice_summary = $slice->summary_as_hash();
  Description   : Retrieves a textual summary of this slice.
  Returns       : hashref of descriptive strings
 
Code:
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The documentation for this class was generated from the following file: