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Bio::EnsEMBL::Funcgen::ProbeFeature Class Reference
Inheritance diagram for Bio::EnsEMBL::Funcgen::ProbeFeature:

List of all members.


Class Summary

Synopsis

use Bio::EnsEMBL::Funcgen::ProbeFeature;

my $feature = Bio::EnsEMBL::Funcgen::ProbeFeature-\>new(
    -PROBE         =\> $probe,
    -MISMATCHCOUNT =\> 0,
    -SLICE         =\> $chr_1_slice,
    -START         =\> 1_000_000,
    -END           =\> 1_000_024,
    -STRAND        =\> -1,
    -ANALYSIS      =\> $analysis,
    -CIGAR_STRING  =\> '1U2M426D2M1m21M',
); 

Description

An ProbeFeature object represents the genomic placement of an Probe
object. The data are stored in the probe_feature table.
 

Definition at line 33 of file ProbeFeature.pm.

Available Methods

protected _deprecated_transform ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public void add_DBEntry ()
public void add_status ()
public add_sub_SeqFeature ()
public Bio::EnsEMBL::Analysis analysis ()
public ARRAYREF associated_feature_types ()
public Str cigar_string ()
public contig ()
public String coord_system_name ()
public Int dbID ()
public String display_id ()
public Int end ()
public Boolean Or Undef equals ()
public Bio::EnsEMBL::Slice feature_Slice ()
public flush_sub_SeqFeature ()
public Reference get_all_alt_locations ()
public get_all_DAS_Features ()
public Listref get_all_DBEntries ()
public Listref get_all_Gene_DBEntries ()
public LISTREF get_all_states ()
public Listref get_all_Transcript_DBEntries ()
public Arrayref get_all_UnmappedObjects ()
public Bio::EnsEMBL::Gene get_nearest_Gene ()
public List get_overlapping_Genes ()
public Float get_result_by_Analysis_ExperimentalChips ()
public get_result_by_ResultSet ()
public List get_results_by_channel_id ()
public BOOLEAN has_status ()
public id ()
public is_displayable ()
public Boolean is_stored ()
public Int length ()
public Int mismatchcount ()
public void move ()
public
Bio::EnsEMBL::Funcgen::ProbeFeature 
new ()
public
Bio::EnsEMBL::Funcgen::ProbeFeature 
new_fast ()
public Boolean overlaps ()
public Bio::EnsEMBL::Funcgen::Probe probe ()
public Int probe_id ()
public String probeset ()
public probeset_id ()
public List project ()
public List project_to_slice ()
public Undef seq ()
public Int seq_region_end ()
public Unsigned seq_region_length ()
public String seq_region_name ()
public Int seq_region_start ()
public Boolean seq_region_strand ()
public String seqname ()
public Bio::EnsEMBL::Slice slice ()
public String species ()
public Int start ()
public Int strand ()
public sub_SeqFeature ()
public Hashref summary_as_hash ()
public Bio::EnsEMBL::Feature transfer ()
public Bio::EnsEMBL::Feature transform ()

Method Documentation

public void Bio::EnsEMBL::Funcgen::Storable::add_DBEntry ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBEntry $dbe
               The dbEntry to be added
  Example    : my $dbe = Bio::EnsEMBL::DBEntry->new(...);
               $transcript->add_DBEntry($dbe);
  Description: Associates a DBEntry with this object. Note that adding
               DBEntries will prevent future lazy-loading of DBEntries for this
               storable (see get_all_DBEntries).
  Returntype : none
  Exceptions : thrown on incorrect argument type
  Caller     : general
  Status     : Stable
 
Code:
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public void Bio::EnsEMBL::Funcgen::Storable::add_status ( ) [inherited]
  Example    : $ec->add_state('DISPLAYABLE');
  Description: Adds a state to a new or previously stored Storable
  Returntype : None
  Exceptions : Throws if no status supplied
  Caller     : general
  Status     : At risk
 
Code:
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public ARRAYREF Bio::EnsEMBL::Funcgen::Storable::associated_feature_types ( ) [inherited]
  Example    : my @associated_ftypes = @{$feature->associated_feature_types()};
  Description: Getter/Setter for other associated FeatureTypes.
  Returntype : ARRAYREF of Bio::EnsEMBL::Funcgen:FeatureType objects
  Exceptions : None
  Caller     : General
  Status     : At risk
 
Code:
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public Str Bio::EnsEMBL::Funcgen::ProbeFeature::cigar_string ( )
  Arg [1]    : str - Cigar line alignment annotation (M = Align & Seq match, m = Align matcht & Seq mismatch, D = Deletion in ProbeFeature wrt genome, U = Unknown at time of alignment)
  Example    : my $cg = $feature->cigar_string();
  Description: Getter and setter for number of the cigar line attribute for this feature.
  Returntype : str
  Exceptions : None
  Caller     : General
  Status     : High Risk
 
Code:
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public Listref Bio::EnsEMBL::Funcgen::Storable::get_all_DBEntries ( ) [inherited]
  Arg[1]     : string - External DB name e.g. ensembl_core_Gene
  Arg[2]     : string - External DB type 
  Example    : my @dbentries = @{ $set_feature->get_all_DBEntries };
  Description: Retrieves DBEntries (xrefs) for this SetFeature.  
               This does _not_ include the corresponding translations 
               DBEntries (see get_all_DBLinks).
               This method will attempt to lazy-load DBEntries from a
               database if an adaptor is available and no DBEntries are present
               on the SetFeature (i.e. they have not already been added or 
               loaded).
  Returntype : Listref of Bio::EnsEMBL::DBEntry objects
  Exceptions : none
  Caller     : general, get_all_DBLinks
  Status     : Stable - at risk move to storable
 
Code:
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public Listref Bio::EnsEMBL::Funcgen::Storable::get_all_Gene_DBEntries ( ) [inherited]
  Example    : my @gene_dbentries = @{ $storable->get_all_Gene_DBEntries };
  Description: Retrieves Ensembl Gene DBEntries (xrefs) for this Storable.  
               This does _not_ include the corresponding translations 
               DBEntries (see get_all_DBLinks).
               This method will attempt to lazy-load DBEntries from a
               database if an adaptor is available and no DBEntries are present
               on the transcript (i.e. they have not already been added or 
               loaded).
  Returntype : Listref of Bio::EnsEMBL::DBEntry objects
  Exceptions : none
  Caller     : general
  Status     : at risk
 
Code:
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public LISTREF Bio::EnsEMBL::Funcgen::Storable::get_all_states ( ) [inherited]
  Example    : my @ec_states = @{$experimental_chip->get_all_states()};
  Description: Retrieves all states from DB and merges with current states array
  Returntype : LISTREF
  Exceptions : None
  Caller     : general
  Status     : At risk
 
Code:
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public Listref Bio::EnsEMBL::Funcgen::Storable::get_all_Transcript_DBEntries ( ) [inherited]
  Arg[0]     : optional - Bio::EnsEMBL::Transcript to filter DBEntries on.
  Example    : my @transc_dbentries = @{ $set_feature->get_all_Transcript_DBEntries };
  Description: Retrieves ensembl Transcript DBEntries (xrefs) for this Storable.  
               This does _not_ include the corresponding translations 
               DBEntries (see get_all_DBLinks).
               This method will attempt to lazy-load DBEntries from a
               database if an adaptor is available and no DBEntries are present
               on the Storable (i.e. they have not already been added or 
               loaded).
  Returntype : Listref of Bio::EnsEMBL::DBEntry objects
  Exceptions : none
  Caller     : general
  Status     : at risk
 
Code:
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public Arrayref Bio::EnsEMBL::Funcgen::Storable::get_all_UnmappedObjects ( ) [inherited]
  Example    : my @uos = @{$storable->get_all_UnmappedObjects };
  Description: Retrieves UnamappedObjects for this Storable.
  Returntype : arrayref of Bio::EnsEMBL::UnmappedObject objects
  Exceptions : none
  Caller     : general
  Status     : At risk - move to Bio::Ensembl::Storable?
 
Code:
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public Float Bio::EnsEMBL::Funcgen::ProbeFeature::get_result_by_Analysis_ExperimentalChips ( )
  Arg [1]    : Bio::EnsEMBL::Analysis
  Arg [2]    : listref - Bio::EnsEMBL::Funcgen::ExperimentalChip
  Example    : my $result = $feature->get_result_by_Analysis_ExperimentalChips($anal, \@echips);
  Description: Getter of results attribute for a given Analysis and set of ExperimentalChips
  Returntype : float
  Exceptions : Throws is no Analysis or ExperimentalChips are not passed?
  Caller     : General
  Status     : High Risk
 
Code:
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public Bio::EnsEMBL::Funcgen::ProbeFeature::get_result_by_ResultSet ( )

Undocumented method

Code:
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public List Bio::EnsEMBL::Funcgen::ProbeFeature::get_results_by_channel_id ( )
  Arg [1]    : int - channel_id (mandatory)
  Arg [2]    : string - Analysis name e.g. RawValue, VSN (optional)
  Example    : my @results = $feature->results();
  Description: Getter, setter and lazy loader of results attribute for
               ProbeFeature objects.
  Returntype : List ref to arrays containing ('score', 'Analysis logic_name');
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public BOOLEAN Bio::EnsEMBL::Funcgen::Storable::has_status ( ) [inherited]
  Arg [1]    : string - status e.g. IMPORTED, DISPLAYABLE
  Example    : if($experimental_chip->has_status('IMPORTED'){ ... skip import ... };
  Description: Tests whether storable has a given status
  Returntype : BOOLEAN
  Exceptions : Throws if not status is provided
  Caller     : general
  Status     : At risk
 
Code:
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public Bio::EnsEMBL::Funcgen::Storable::is_displayable ( ) [inherited]

Undocumented method

Code:
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public Int Bio::EnsEMBL::Funcgen::ProbeFeature::mismatchcount ( )
  Arg [1]    : int - number of mismatches
  Example    : my $mismatches = $feature->mismatchcount();
  Description: Getter and setter for number of mismatches for this feature.
  Returntype : int
  Exceptions : None
  Caller     : General
  Status     : High Risk
 
Code:
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public Bio::EnsEMBL::Funcgen::ProbeFeature Bio::EnsEMBL::Funcgen::ProbeFeature::new ( )
  Arg [-PROBE]        : Bio::EnsEMBL::Funcgen::Probe - probe
        A ProbeFeature must have a probe. This probe must already be stored if
		you plan to store the feature.
  Arg [-MISMATCHCOUNT]: int
        Number of mismatches over the length of the probe. 
  Arg [-SLICE]        : Bio::EnsEMBL::Slice
        The slice on which this feature is.
  Arg [-START]        : int
        The start coordinate of this feature relative to the start of the slice
		it is sitting on. Coordinates start at 1 and are inclusive.
  Arg [-END]          : int
        The end coordinate of this feature relative to the start of the slice
		it is sitting on. Coordinates start at 1 and are inclusive.
  Arg [-STRAND]       : int
        The orientation of this feature. Valid values are 1, -1 and 0.
  Arg [-dbID]         : (optional) int
        Internal database ID.
  Arg [-ADAPTOR]      : (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
        Database adaptor.
  Example    : my $feature = Bio::EnsEMBL::Funcgen::ProbeFeature->new(
				   -PROBE         => $probe,
				   -MISMATCHCOUNT => 0,
				   -SLICE         => $chr_1_slice,
				   -START         => 1_000_000,
				   -END           => 1_000_024,
				   -STRAND        => -1,
				   -ANALYSIS      => $analysis,
                   -CIGARLINE     => '15M2m3d4M', 
                   #Can represent transcript alignment as gapped genomic alignments
                   #D(eletions) representing introns
                   #Lowercase m's showing sequence mismatches
			   ); 
  Description: Constructor for ProbeFeature objects.
  Returntype : Bio::EnsEMBL::Funcgen::ProbeFeature
  Exceptions : None
  Caller     : General
  Status     : At risk
 
Code:
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Reimplemented from Bio::EnsEMBL::Feature.

public Bio::EnsEMBL::Funcgen::ProbeFeature Bio::EnsEMBL::Funcgen::ProbeFeature::new_fast ( )
  Args       : Hashref with all internal attributes set
  Example    : none
  Description: Quick and dirty version of new. Only works if the code is very
               disciplined. 
  Returntype : Bio::EnsEMBL::Funcgen::ProbeFeature
  Exceptions : None
  Caller     : General
  Status     : At Risk
 
Code:
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Reimplemented from Bio::EnsEMBL::Feature.

public Bio::EnsEMBL::Funcgen::Probe Bio::EnsEMBL::Funcgen::ProbeFeature::probe ( )
  Arg [1]    : Bio::EnsEMBL::Funcgen::Probe - probe
  Example    : my $probe = $feature->probe();
  Description: Getter, setter and lazy loader of probe attribute for
               ProbeFeature objects. Features are retrieved from the database
			   without attached probes, so retrieving probe information for a
			   feature will involve another query.
  Returntype : Bio::EnsEMBL::Funcgen::Probe
  Exceptions : None
  Caller     : General
  Status     : at risk
 
Code:
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public Int Bio::EnsEMBL::Funcgen::ProbeFeature::probe_id ( )
  Example    : my $probe_id = $pfeature->probe_id();
  Description: Getter for the probe db id of the ProbeFeature
  Returntype : int
  Exceptions : None
  Caller     : General
  Status     : at risk
 
Code:
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public String Bio::EnsEMBL::Funcgen::ProbeFeature::probeset ( )
  Arg [1]    : (optional) string - probeset
  Example    : my $probeset = $feature->probeset();
  Description: Getter and setter for the probeset for this feature. Shortcut
               for $feature->probe->probeset(), which should be used instead.
			   Probeset is not persisted if set with this method.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
             : Use $feature->probe->probeset() because this may be removed
 
Code:
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public Bio::EnsEMBL::Funcgen::ProbeFeature::probeset_id ( )

Undocumented method

Code:
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The documentation for this class was generated from the following file: