Bio::EnsEMBL::IntronSupportingEvidence Class Reference

Inheritance diagram for Bio::EnsEMBL::IntronSupportingEvidence:

Public Member Functions
public Bio::EnsEMBL::IntronSupportEvidence	new ()
public void	set_values_from_Intron ()
public Boolean	is_splice_canonical ()
public Bio::EnsEMBL::Intron	get_Intron ()
public String	hit_name ()
public Number	score ()
public String	score_type ()
public Boolean	has_linked_transcripts ()
public Boolean	equals ()
public Bio::EnsEMBL::Exon	find_previous_Exon ()
public Bio::EnsEMBL::Exon	find_next_Exon ()
Public Member Functions inherited from Bio::EnsEMBL::Feature
public Bio::EnsEMBL::Feature	new ()
public Int	start ()
public Int	end ()
public Int	strand ()
public void	move ()
public Int	length ()
public Bio::EnsEMBL::Analysis	analysis ()
public Bio::EnsEMBL::Slice	slice ()
public Boolean Or Undef	equals ()
public Bio::EnsEMBL::Feature	transform ()
public Bio::EnsEMBL::Feature	transfer ()
public Listref	project_to_slice ()
public Listref	project ()
public String	seqname ()
public String	display_id ()
public String	version ()
public Bio::EnsEMBL::Slice	feature_Slice ()
public String	seq_region_name ()
public Int	seq_region_length ()
public Boolean	seq_region_strand ()
public Int	seq_region_start ()
public Int	seq_region_end ()
public String	coord_system_name ()
public String	seq ()
public Listref	get_all_alt_locations ()
public Boolean	overlaps ()
public Boolean	overlaps_local ()
public List	get_overlapping_Genes ()
public Bio::EnsEMBL::Gene	get_nearest_Gene ()
public String	feature_so_acc ()
public String	feature_so_term ()
public Hashref	summary_as_hash ()
public String	species ()
public	sub_SeqFeature ()
public	add_sub_SeqFeature ()
public	flush_sub_SeqFeature ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

Description

Formalises an Intron with information about why it is a believed Intron. This 
serves as a parallel object to Bio::EnsEMBL::Intron which you can use 
to populate values in this field from. They are different objects though
due to Intron's non-existence as a DB data structure.

Synopsis

#Example setups a ISE from the first two Exons
my ($five_prime_exon, $three_prime_exon) = @{$transcript->get_all_Exons()}[0..1];
my $intron = Bio::EnsEMBL::Intron->new($five_prime_exon, $three_prime_exon);

Definition at line 23 of file IntronSupportingEvidence.pm.

Member Function Documentation

equals()

public Boolean Bio::EnsEMBL::IntronSupportingEvidence::equals

(

)

  Arg [1]     : Bio::EnsEMBL::IntronSupportEvidence Object to compare to
  Example     :

$ise->equals($another_ise);

  Description : Asserts if the given IntronSupportEvidence instance was equal to this
  Returntype  : Boolean
  Exceptions  : None

Code:

find_next_Exon()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::IntronSupportingEvidence::find_next_Exon

(

)

  Arg [1]     : Bio::EnsEMBL::Transcript Transcript to search for the Exons from
  Example     :

$ise->find_next_Exon($transcript);

  Description : Loops through those Exons available from the Transcript and
                attempts to find one which was the 3' flanking exon. If the
                object has already been persisted we will use dbIDs to
                find the Exons
  Returntype  : Bio::EnsEMBL::Exon
  Exceptions  : None

Code:

find_previous_Exon()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::IntronSupportingEvidence::find_previous_Exon

(

)

  Arg [1]     : Bio::EnsEMBL::Transcript Transcript to search for the Exons from
  Example     :

$ise->find_previous_Exon($transcript);

  Description : Loops through those Exons available from the Transcript and
                attempts to find one which was the 5' flanking exon. If the
                object has already been persisted we will use dbIDs to
                find the Exons
  Returntype  : Bio::EnsEMBL::Exon
  Exceptions  : None

Code:

get_Intron()

public Bio::EnsEMBL::Intron Bio::EnsEMBL::IntronSupportingEvidence::get_Intron

(

)

  Arg [1]     : Bio::EnsEMBL::Transcript
  Example     :

my $intron = $ise->intron($transcript);

  Description : Provides access to an Intron object by using a given transcript 
                object and its associcated array of Exons.
  Returntype  : Bio::EnsEMBL::Intron
  Exceptions  : None

Code:

has_linked_transcripts()

public Boolean Bio::EnsEMBL::IntronSupportingEvidence::has_linked_transcripts

(

)

  Example     :

$ise->has_linked_transcripts();

  Description : Returns true if we have transcripts linked to this ISE
  Returntype  : Boolean
  Exceptions  : Thrown if we do not have an attached adaptor

Code:

hit_name()

public String Bio::EnsEMBL::IntronSupportingEvidence::hit_name

(

)

  Arg [1]     : String name of the hit
  Example     :

$ise->hit_name('hit');

  Description : Getter/setter for hit name i.e. an identifier for the alignments
  Returntype  : String
  Exceptions  : None

Code:

is_splice_canonical()

public Boolean Bio::EnsEMBL::IntronSupportingEvidence::is_splice_canonical

(

)

  Arg [1]     : Boolean
  Example     :

$ise->is_splice_canonical(1);

  Description : Getter/setter for is_splice_canonical. Splice canonical 
                indicates those Introns which have a splice junction which 
                is structured as expected 
  Returntype  : Boolean
  Exceptions  :

Code:

new()

public Bio::EnsEMBL::IntronSupportEvidence Bio::EnsEMBL::IntronSupportingEvidence::new

(

)

  Arg [-ANALYSIS]     : Bio::EnsEMBL::Analysis The analysis this intron is linked to
  Arg [-START]        : int - start postion of the IntronSupportingEvidence
  Arg [-END]          : int - end position of the IntronSupportingEvidence
  Arg [-STRAND]       : int - strand the IntronSupportingEvidence is on
  Arg [-SLICE]        : Bio::EnsEMBL::Slice - the slice the IntronSupportingEvidence is on
  Arg [-INTRON]       : Bio::EnsEMBL::Intron Intron the evidence is based 
                        on. Useful if you are not specifying the location 
                        parameters as we will take them from this 
  Arg [-HIT_NAME]     : String The name of the hit
  Arg [-SCORE]        : Double The score associated with the supporting evidence
  Arg [-SCORE_TYPE]   : String The type of score we are representing
  Example             :

Bio::EnsEMBL::IntronSupportingEvidence->new(
                         -ANALYSIS => $analysis, -INTRON => $intron, 
                         -SCORE => 100, -SCORE_TYPE => 'DEPTH');

  Description         : Returns a new instance of this object
  Returntype          : Bio::EnsEMBL::IntronSupportEvidence
  Exceptions          : Thrown if data is not as requested

Code:

score()

public Number Bio::EnsEMBL::IntronSupportingEvidence::score

(

)

  Arg [1]     : Number; the score associated with this feature
  Example     :

$ise->score(100);

  Description : Getter/setter for score
  Returntype  : Number
  Exceptions  : None

Code:

score_type()

public String Bio::EnsEMBL::IntronSupportingEvidence::score_type

(

)

  Arg [1]     : String the enum type. Currently only allowed NONE or DEPTH
  Example     :

$ise->score_type('DEPTH');

  Description : Gets and sets the type of score this instance represents
  Returntype  : String
  Exceptions  : Thrown if given an unsupported type of data

Code:

set_values_from_Intron()

public void Bio::EnsEMBL::IntronSupportingEvidence::set_values_from_Intron

(

)

  Arg [1]     : Bio::EnsEMBL::Intron The intron to base this object on
  Example     :

$ise->set_values_from_Intron($intron);

  Description : Sets the start, end, strand and slice of this ISE instance
                using values from the given Intron object.
  Returntype  : None
  Exceptions  : Thrown if data is not as requested

Code:

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

• ensembl/modules/Bio/EnsEMBL/IntronSupportingEvidence.pm