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

List of all members.


Class Summary

Synopsis

use Bio::EnsEMBL::Funcgen::Probe;

#

my $probe = Bio::EnsEMBL::Funcgen::Probe-\>new(
        -PROBE_SET     =\> $probe_set,
        -NAME          =\> 'Probe-1',
        -ARRAY         =\> $array,
        -ARRAY_CHIP_ID =\> $ac_dbid,
        -CLASS         =\> "EXPERIMENTAL",
);

Description

An Probe object represents an probe on a microarray. The data (currently the 
name, probe_set_id, length, pair_index and class) are stored
in the oligo_probe table.
For Affy arrays, a probe can be part of more than one array, but only part of
one probeset. On each Affy array the probe has a slightly different name. For
example, two different complete names for the same probe might be
DrosGenome1:AFFX-LysX-5_at:535:35; and Drosophila_2:AFFX-LysX-5_at:460:51;. In
the database, these two probes will have the same oligo_probe_id. Thus the same
Affy probe can have a number of different names and complete names depending on
which array it is on.
 

Definition at line 38 of file Probe.pm.

Available Methods

public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public void add_Analysis_CoordSystem_score ()
public void add_Analysis_score ()
public void add_array_chip_probename ()
public void add_DBEntry ()
public void add_status ()
public ARRAYREF associated_feature_types ()
public String class ()
public Int dbID ()
public String description ()
public Int feature_count ()
public Listref get_all_Arrays ()
public Listref get_all_complete_names ()
public get_all_DAS_Features ()
public Listref get_all_DBEntries ()
public ARRAYREF get_all_design_scores ()
public Listref get_all_Gene_DBEntries ()
public Listref get_all_ProbeFeatures ()
public Listref get_all_probenames ()
public LISTREF get_all_states ()
public Listref get_all_Transcript_DBEntries ()
public Arrayref get_all_UnmappedObjects ()
public String get_complete_name ()
public Hashref get_names_Arrays ()
public String get_probename ()
public String get_score_by_Analysis ()
public void get_score_by_Analysis_CoordSystem ()
public BOOLEAN has_status ()
public is_displayable ()
public Boolean is_stored ()
public Int length ()
public Bio::EnsEMBL::Probe new ()
public Bio::EnsEMBL::Funcgen::Probe new_fast ()
public
Bio::EnsEMBL::Funcgen::ProbeSet 
probeset ()

Method Documentation

public void Bio::EnsEMBL::Funcgen::Probe::add_Analysis_CoordSystem_score ( )
  Arg [1]    : Bio::EnsEMBL::Analysis
  Arg [2]    : Bio::EnsEMBL::CoordSystem
  Arg [3]    : string - analysis score (as string a precision may differ between analyses)??
  Example    : $probe->add_Analysis_CoordSystem_score($analysis, $coord_sys, $score);
  Description: Setter for coord system dependant probe analysis attributes from an array design
  Returntype : None
  Exceptions : throws if args are not met or valid
  Caller     : General
  Status     : at risk
 
Code:
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public void Bio::EnsEMBL::Funcgen::Probe::add_Analysis_score ( )
  Arg [1]    : Bio::EnsEMBL::Analysis
  Arg [2]    : string - analysis score (as string a precision may differ between analyses)??
  Example    : $probe->add_Analysis_score($analysis, $score);
  Description: Setter for probe analysis attributes from an array design
  Returntype : None
  Exceptions : throws if args are not met or valid
  Caller     : General
  Status     : at risk
 
Code:
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public void Bio::EnsEMBL::Funcgen::Probe::add_array_chip_probename ( )
  Arg [1]    : int - db ID of array_chip
  Arg [2]    : string - probe name
  Arg [3]    : Bio::EnsEMBL::Funcgen::Array
  Example    : $probe->add_array_chip_probename($ac_dbid, $probename, $array);
  Description: Adds a probe name / array pair to a probe, allowing incremental
               generation of a probe.
  Returntype : None
  Exceptions : None
  Caller     : General,
               Probe->new(),
               ProbeAdaptor->_obj_from_sth(),
			   AffyProbeAdaptor->_obj_from_sth()
  Status     : Medium Risk - Change to take ArrayChip object.
 
Code:
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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 String Bio::EnsEMBL::Funcgen::Probe::class ( )
  Arg [1]    : (optional) string - class
  Example    : my $class = $probe->class();
  Description: Getter and setter of class attribute for Probe
               objects e.g. CONTROL, EXPERIMENTAL
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public String Bio::EnsEMBL::Funcgen::Probe::description ( )
  Arg [1]    : (optional) string - description
  Example    : my $pdesc = $probe->description();
  Description: Getter and setter of description attribute for Probe
               objects.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : At Risk
 
Code:
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public Int Bio::EnsEMBL::Funcgen::Probe::feature_count ( )
  Arg[0]     : recount flag
  Example    : my $num_features = $probe->feature_count();
  Description: Counts the number of ProbeFeatures associated with this Probe
  Returntype : int
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public Listref Bio::EnsEMBL::Funcgen::Probe::get_all_Arrays ( )
  Args       : None
  Example    : my $arrays = $probe->get_all_Arrays();
  Description: Returns all arrays that this probe is part of. Only works if the
               probe was retrieved from the database or created using
			   add_Array_probename (rather than add_arrayname_probename).
  Returntype : Listref of Bio::EnsEMBL::Funcgen::Array objects
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public Listref Bio::EnsEMBL::Funcgen::Probe::get_all_complete_names ( )
  Args       : None
  Example    : my @compnames = @{$probe->get_all_complete_names()};
  Description: Retrieves all complete names for this probe. The complete name
               is a concatenation of the array name, the probeset name and the
			   probe name.
  Returntype : Listref of strings
  Exceptions : None
  Caller     : General
  Status     : Medium 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 ARRAYREF Bio::EnsEMBL::Funcgen::Probe::get_all_design_scores ( )
  Arg [1]    : Boolean - No fetch flag, to fetch design scores from DB, used in adaptor
               To avoid testing DB for each probe when no design scores have been added.
  Example    : my @anal_score_coordsets = @{$probe->get_all_design_scores()};
  Description: Gets all design scores as analysis_id, score and optionally coord_system_id
  Returntype : ARRAYREF
  Exceptions : throws if no fetch flag is not defined and adaptor or probe is not defined and or stored.
  Caller     : General
  Status     : at risk
 
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::Probe::get_all_ProbeFeatures ( )
  Args       : None
  Example    : my $features = $probe->get_all_ProbeFeatures();
  Description: Get all features produced by this probe. The probe needs to be
               database persistent.
  Returntype : Listref of Bio::EnsEMBL:Funcgen::ProbeFeature objects
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public Listref Bio::EnsEMBL::Funcgen::Probe::get_all_probenames ( )
  Arg [1]    : Optional - list of array names, defaults to all available
  Example    : my @probenames = @{$probe->get_all_probenames()};
  Description: Retrieves all names for this probe. Only makes sense for probes
               that are part of a probeset (i.e. Affy probes), in which case
			   get_all_complete_names() would be more appropriate.
  Returntype : Listref of strings
  Exceptions : None
  Caller     : General
  Status     : Medium 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 String Bio::EnsEMBL::Funcgen::Probe::get_complete_name ( )
  Arg [1]    : string - array name
  Example    : my $compname = $probe->get_complete_name('Array-1');
  Description: For a given array, retrieve the complete name for this probe.
  Returntype : string
  Exceptions : Throws if the array name not specified or not known for this probe
  Caller     : General
  Status     : Medium Risk
 
Code:
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public Hashref Bio::EnsEMBL::Funcgen::Probe::get_names_Arrays ( )
  Args       : None
  Example    : my %name_array_pairs = %{$probe->get_names_Arrays};
  Description: Returns Array name hash
  Returntype : hashref of probe name Bio::EnsEMBL::Funcgen::Array pairs 
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public String Bio::EnsEMBL::Funcgen::Probe::get_probename ( )
  Arg [1]    : string - array name
  Example    : my $probename = $probe->get_probename('Array-1');
  Description: For a given array, retrieve the name for this probe.
  Returntype : string
  Exceptions : Throws if the array name is required but not specified
               Warns if probe has more than one name for the given array.
  Caller     : General
  Status     : Medium Risk
 
Code:
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public String Bio::EnsEMBL::Funcgen::Probe::get_score_by_Analysis ( )
  Arg [1]    : Bio::EnsEMBL::Analysis
  Example    : my $anal_score = $probe->get_analysis_score($analysis);
  Description: Setter for probe analysis attributes from an array design
  Returntype : string
  Exceptions : throws if args are not met or valid
  Caller     : General
  Status     : at risk
 
Code:
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public void Bio::EnsEMBL::Funcgen::Probe::get_score_by_Analysis_CoordSystem ( )
  Arg [1]    : Bio::EnsEMBL::Analysis
  Arg [2]    : Bio::EnsEMBL::CoordSystem
  Arg [3]    : string - analysis score (as string a precision may differ between analyses)??
  Example    : $probe->add_analysis($analysis, $coord_sys, $score);
  Description: Setter for coord system dependant probe analysis attributes from an array design
  Returntype : None
  Exceptions : throws if args are not met or valid
  Caller     : General
  Status     : at 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
 
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public Bio::EnsEMBL::Funcgen::Storable::is_displayable ( ) [inherited]

Undocumented method

Code:
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public Int Bio::EnsEMBL::Funcgen::Probe::length ( )
  Arg [1]    : (optional) int - probe length
  Example    : my $probelength = $probe->length();
  Description: Getter and setter of length attribute for Probe
               objects.
  Returntype : int
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public Bio::EnsEMBL::Probe Bio::EnsEMBL::Funcgen::Probe::new ( )
  Arg [-NAME]          : string - probe name
        Used when the probe is on one array.
  Arg [-NAMES]         : Listref of strings - probe names
        Used when the probe is on multiple arrays.
  Arg [-ARRAY]          : Bio::EnsEMBL::Funcgen::Array
        Used when the probe is on one array.
  Arg [-ARRAYS]         : Listref of Bio::EnsEMBL::Funcgen::Array
        Used when the probe is on multiple arrays.
  Arg [-ARRAY_CHIP_ID]  : int - array_chip db ID
        Used when the probe is on one array.
  Arg [-ARRAY_CHIP_IDS]  : Listref of ints - array_chip dbIDs
        Used when the probe is on multiple array chips
  Arg [-NAMES]          : Listref of ints - arary_chip db IDs
        Used when the probe is on multiple arrays.
  Arg [-PROBE_SET]      : Bio::EnsEMBL::ProbeSet
        Each probe is part of one(and only one) probeset, if not probe set
        then probeset = probe i.e. probe_set size = 1
  Arg [-LENGTH]         : int - probe length
        Will obviously be the same for all probes if same probe
		is on multiple arrays.
  Arg [-CLASS]          : string - probe class e.g. CONTROL, EXPERIMENTAL
        Will be the same for all probes if same probe is on
		multiple arrays.
  Arg [-DESCRIPTION]    : (optional) string - description
  Example    : my $probe = Bio::EnsEMBL::Probe->new(
                   -NAME          => 'Probe-1',
				   -PROBE_SET     => $probe_set,
                   -ARRAY         => $array,
                   -ARRAY_CHIP_ID => $array_chip_id,
				   -LENGTH        => 25,
                   -CLASS         => 'EXPERIMENTAL',
                   -DESCRIPTION   => 'Some useful description',
               );
  Description: Creates a new Bio::EnsEMBL::Probe object.
  Returntype : Bio::EnsEMBL::Probe
  Exceptions : Throws if not supplied with probe name(s) and array(s)
  Caller     : General
  Status     : Medium Risk
 
Code:
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Reimplemented from Bio::EnsEMBL::Funcgen::Storable.

public Bio::EnsEMBL::Funcgen::Probe Bio::EnsEMBL::Funcgen::Probe::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. Cannot add array chip probe names unless we recreate
               the data structure in the caller.
  Returntype : Bio::EnsEMBL::Funcgen::Probe
  Exceptions : None
  Caller     : General
  Status     : At Risk
 
Code:
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public Bio::EnsEMBL::Funcgen::ProbeSet Bio::EnsEMBL::Funcgen::Probe::probeset ( )
  Arg [1]    : (optional) Bio::EnsEMBL::Funcgen::ProbeSet
  Example    : my $probe_set = $probe->probeset();
  Description: Getter and setter of probe_set attribute for Probe objects.
  Returntype : Bio::EnsEMBL::Funcgen::ProbeSet
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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The documentation for this class was generated from the following file: