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

List of all members.


Class Summary

Synopsis

use Bio::EnsEMBL::Funcgen::Array;

my $array = Bio::EnsEMBL::Funcgen::Array-\>new(
        -NAME        =\> 'Array-1',
        -FORMAT      =\> 'Tiled',
        -SIZE        =\> '1',
        -VENDOR      =\> 'Nimblegen',
        -DESCRIPTION =\> $desc,
        -TYPE        =\> 'OLIGO',
        -CLASS       =\> 'VENDOR_FORMAT'
);

my $db_adaptor = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor-\>new(...);
my $array_adaptor = $db_adaptor-\>get_ArrayAdaptor();
my $array = $array_adaptor-\>fetch_by_name($array_name)

Description

An Array object represents a nucleotide (OLIGO, PCR etc.) microarray. The data
(currently the name, format, size, species, vendor and description) are stored
in the array table.
 

Definition at line 34 of file Array.pm.

Available Methods

public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public void add_ArrayChip ()
public void add_DBEntry ()
public void add_status ()
public ARRAYREF associated_feature_types ()
public String class ()
public Int dbID ()
public String description ()
public String format ()
public get_all_DAS_Features ()
public Listref get_all_DBEntries ()
public Listref get_all_Gene_DBEntries ()
public Arrayref get_all_Probe_dbIDs ()
public Listref get_all_Probes ()
public Listref get_all_ProbeSets ()
public LISTREF get_all_states ()
public Listref get_all_Transcript_DBEntries ()
public Arrayref get_all_UnmappedObjects ()
public Listref get_array_chip_ids ()
public Hashref get_ArrayChip_by_design_id ()
public Arrays get_ArrayChips ()
public List get_design_ids ()
public BOOLEAN has_status ()
public is_displayable ()
public Boolean is_stored ()
public String name ()
public Bio::EnsEMBL::Funcgen::Array new ()
public String probe_count ()
public Int size ()
public String type ()
public String vendor ()

Method Documentation

public void Bio::EnsEMBL::Funcgen::Array::add_ArrayChip ( )
  Arg [1]    : mandatory - Bio::EnsEMBL::Funcgen::ArrayChip
  Example    : $array->add_ArrayChip($array_chip);
  Description: Setter for array chips
  Returntype : None
  Exceptions : Throws if arg not a Bio::EnsEMBL::Funcgen::ArrayChip, or Array not stored
  Caller     : General
  Status     : Ar risk
 
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::Array::class ( )
  Arg [1]    : (optional) string - the class of the array
  Example    : my $class = $array->class('AFFY_UTR');
  Description: Getter, setter of class attribute for
               Array objects e.g. AFFY_UTR, AFFY_ST
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public String Bio::EnsEMBL::Funcgen::Array::description ( )
  Arg [1]    : (optional) string - the description of the array
  Example    : my $size = $array->description();
  Description: Getter, setter of description attribute for
               Array objects. 
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public String Bio::EnsEMBL::Funcgen::Array::format ( )
  Arg [1]    : (optional) string - the format of the array
  Example    : my $format = $array->format();
  Description: Getter, setter of format attribute for
               Array objects e.g. Tiled, Targetted etc...
  Returntype : string
  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 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 Arrayref Bio::EnsEMBL::Funcgen::Array::get_all_Probe_dbIDs ( )
  Args       : None
  Example    : my @dbids = @{$array->get_all_Probe_dbIDs};
  Description: Returns an array ref of all the Probe database IDs for this array
  Returntype : arrayref of ints
  Exceptions : None
  Caller     : General
  Status     : At Risk
 
Code:
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public Listref Bio::EnsEMBL::Funcgen::Array::get_all_Probes ( )
  Args       : None
  Example    : my $probes = $array->get_all_Probes();
  Description: Returns all probes on an array. Needs a database connection.
  Returntype : Listref of Bio::EnsEMBL::Funcgen::Probe objects
  Exceptions : None
  Caller     : General
  Status     : At Risk
 
Code:
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public Listref Bio::EnsEMBL::Funcgen::Array::get_all_ProbeSets ( )
  Args       : None
  Example    : my $probesets = $array->get_all_ProbeSets();
  Description: Returns all probesets on an array. Needs a database connection.
  Returntype : Listref of Bio::EnsEMBL::Funcgen::ProbeSets objects
  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 Listref Bio::EnsEMBL::Funcgen::Array::get_array_chip_ids ( )
  Example    : my @ac_ids = @{$array->get_array_chip_ids()};
  Description: Returns all array_chip_ids for this array.
  Returntype : Listref of array_chip ids
  Exceptions : Throws if none retrieved
  Caller     : General
  Status     : At Risk
 
Code:
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public Hashref Bio::EnsEMBL::Funcgen::Array::get_ArrayChip_by_design_id ( )
  Arg [1]    : (mandatory) int - design_id
  Example    : my %ac = %{$array->get_ArrayChip_by_design_id('1234')};
  Description: Getter for array_chip hashes
  Returntype : Hashref
  Exceptions : Throws exception if no design_id defined, warns if not part of array
  Caller     : General
  Status     : At risk
 
Code:
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public Arrays Bio::EnsEMBL::Funcgen::Array::get_ArrayChips ( )
  Example    : my @achips = @{$array->get_ArrayChips()};
  Description: Getter, setter and lazy loader of array_chip hashes
  Returntype : Arrays of ArrayChip objects
  Exceptions : Throws exception if none found for array_id
  Caller     : General
  Status     : High Risk - migrate to ArrayChip.pm
 
Code:
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public List Bio::EnsEMBL::Funcgen::Array::get_design_ids ( )
  Example    : my @design_ids = @{$array->get_design_ids()};
  Description: Returns a the design_ids for each array_chip contained within this array
  Returntype : list
  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 String Bio::EnsEMBL::Funcgen::Array::name ( )
  Arg [1]    : (optional) string - the name of this array
  Example    : my $name = $array->name();
  Description: Getter, setter of the name attribute for Array
               objects.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public Bio::EnsEMBL::Funcgen::Array Bio::EnsEMBL::Funcgen::Array::new ( )
  Arg [-NAME]        : string - the name of this array
  Arg [-VENDOR]      : string - the vendor of this array (AFFY, NIMBLEGEN etc)
  Arg [-TYPE]        : string - type of array e.g. OLIGO, PCR
  Arg [-FORMAT]      : string - the format of this array (TILED, TARGETTED, GENE etc)
  Arg [-DESCRIPTION] : strin - description of the array
#array_chips is array of hashes or design_id and name, dbID will be populated on store, this should be a simple object!
  Example    : my $array = Bio::EnsEMBL::Funcgen::Array->new(
								  -NAME        => 'Array-1',
								  -FORMAT      => 'Tiled',
								  -SIZE        => '1',
								  -VENDOR      => 'Nimblegen',
                                  -TYPE        => 'OLIGO',
								  -DESCRIPTION => $desc,
                                  -CLASS       => 'VENDOR_FORMAT',#e.g. AFFY_UTR, ILLUMINA_WG
								 );
  Description: Creates a new Bio::EnsEMBL::Funcgen::Array object.
  Returntype : Bio::EnsEMBL::Funcgen::Array
  Exceptions : None ? should throw if mandatort params not set/valid
  Caller     : General
  Status     : At risk
 
Code:
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Reimplemented from Bio::EnsEMBL::Funcgen::Storable.

public String Bio::EnsEMBL::Funcgen::Array::probe_count ( )
  Example    : my $num_probes = $array->probe_count();
  Description: Return number of probes on array
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : At Risk
 
Code:
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public Int Bio::EnsEMBL::Funcgen::Array::size ( )
  Arg [1]    : (optional) int - the number of ? in the array
  Example    : my $size = $array->size();
  Description: Getter of size attribute for Array objects. This
               simply counts the constituent ArrayChips
  Returntype : int
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public String Bio::EnsEMBL::Funcgen::Array::type ( )
  Arg [1]    : (optional) string - the type of this array
  Example    : $array->type('OLIGO');
  Description: Getter, setter of the type attribute for Array
               objects.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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public String Bio::EnsEMBL::Funcgen::Array::vendor ( )
  Arg [1]    : (optional) string - the name of the array vendor
  Example    : my $vendor = $array->vendor();
  Description: Getter, setter of vendor attribute for
               Array objects.
  Returntype : string
  Exceptions : None
  Caller     : General
  Status     : Medium Risk
 
Code:
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The documentation for this class was generated from the following file: