Bio::EnsEMBL::FeaturePair Class Reference

Inheritance diagram for Bio::EnsEMBL::FeaturePair:

Public Member Functions
public Bio::EnsEMBL::FeaturePair	new ()
public String	hseqname ()
public Int	hstart ()
public Int	hend ()
public	hstrand ()
public Bio::EnsEMBL::Slice	hslice ()
public String	hseq_region_name ()
public Boolean	hseq_region_strand ()
public Int	hseq_region_start ()
public Int	hseq_region_end ()
public Float	score ()
public Float	percent_id ()
public String	species ()
public String	hspecies ()
public String	coverage ()
public String	hcoverage ()
public String	external_db_id ()
public String	db_name ()
public String	db_display_name ()
public Float	p_value ()
public String	hdescription ()
public String	display_id ()
public Int	identical_matches ()
public Int	positive_matches ()
public Int	group_id ()
public Int	level_id ()
public void	invert ()
public	extra_data ()
public	type ()
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

Synopsis

my $feat = Bio::EnsEMBL::FeaturePair->new(
  -start      => 132_231,
  -end        => 132_321,
  -strand     => -1,
  -slice      => $slice,
  -hstart     => 10,
  -hend       => 100,
  -hstrand    => 1,
  -score      => 100,
  -percent_id => 92.0,
  -hseqname   => 'ALUSX10.1',
  -analysis   => $analysis
);
 
my $hit_start  = $feat->hstart();
my $hit_end    = $feat->hend();
my $hit_strand = $feat->hstrand();
my $analysis   = $feat->analysis();

Description

A sequence feature object where the feature is itself a feature on
another sequence - e.g. a blast hit where residues 1-40 of a protein
sequence SW:HBA_HUMAN has hit to bases 100 - 220 on a genomic sequence
HS120G22.  The genomic sequence coordinates are represented by the
start, end, strand attributes while the protein (hit) coordinates are
represented by the hstart, hend, hstrand attributes.

  $clone = $slice_adpator->fetch_by_region( 'clone', 'HS120G22' );

  $fp = Bio::EnsEMBL::FeaturePair(
    -start      => 100,
    -end        => 220,
    -strand     => 1,
    -slice      => $clone,
    -hstart     => 1,
    -hend       => 40,
    -hstrand    => 1,
    -percent_id => 92.0,
    -score      => 100,
    -hseqname   => 'SW:HBA_HUMAN',
    -species    => 'Homo sapiens',
    -hspecies   => 'Homo sapiens'
  );

Definition at line 56 of file FeaturePair.pm.

Member Function Documentation

coverage()

public String Bio::EnsEMBL::FeaturePair::coverage

(

)

  Arg [1]    : number (percentage) $coverage (optional)
  Example    :

$cov = $fp->coverage();

  Description: Getter/Setter for the % of the query covered by the feature
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

db_display_name()

public String Bio::EnsEMBL::FeaturePair::db_display_name

(

)

  Arg [1]    : string  $db_display_name (optional)
  Example    :

$ex_db_display_name = $fp->db_display_name();

  Description: Getter/Setter for the db_display_name attribute 
               The preferred display name for the external database. 
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : At Risk

Code:

db_name()

public String Bio::EnsEMBL::FeaturePair::db_name

(

)

  Arg [1]    : string  $external_db_name (optional)
  Example    :

$ex_db_name = $fp->dbname();

  Description: Getter/Setter for the external_db_name attribute, name of external database
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : At Risk

Code:

display_id()

public String Bio::EnsEMBL::FeaturePair::display_id

(

)

  Arg [1]    : none
  Example    :

print $fp->display_id();

  Description: This method returns a string that is considered to be
               the 'display' identifier.  For feature pairs this is the 
               hseqname if it is available otherwise it is an empty string.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

Code:

external_db_id()

public String Bio::EnsEMBL::FeaturePair::external_db_id

(

)

  Arg [1]    : int  $external_db_id (optional)
  Example    :

$ex_db = $fp->external_db_id();

  Description: Getter/Setter for the external_db_id taregt source database feature
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : At Risk

Code:

extra_data()

public Bio::EnsEMBL::FeaturePair::extra_data

(

)

Undocumented method

Code:

group_id()

public Int Bio::EnsEMBL::FeaturePair::group_id

(

)

 
  Arg [1]    : int $group_id
  Example    :

none

  Description: get/set for attribute group_id
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

hcoverage()

public String Bio::EnsEMBL::FeaturePair::hcoverage

(

)

  Arg [1]    : number (percentage) $hcoverage (optional)
  Example    :

$hcov = $fp->hcoverage();

  Description: Getter/Setter for the % of the target covered by the feature
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

hdescription()

public String Bio::EnsEMBL::FeaturePair::hdescription

(

)

  Arg [1]    : String (optional)
  Example    :

$des = $fp->hdescription()

  Description: Getter Setter for optional description of this feature
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

hend()

public Int Bio::EnsEMBL::FeaturePair::hend

(

)

  Arg [1]    : string $hend (optional)
  Example    :

$hend = $fp->hend();

  Description: Getter/Setter for the end coordinate on the hit sequence
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

hseq_region_end()

public Int Bio::EnsEMBL::FeaturePair::hseq_region_end

(

)

  Arg [1]    : none
  Example    :

print $feature->hseq_region_end();

  Description: Convenience method which returns the absolute end of this
               feature on the hseq_region, as opposed to the relative (hslice)
               position.

               Returns undef if this feature is not on a hslice.
  Returntype : int or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

hseq_region_name()

public String Bio::EnsEMBL::FeaturePair::hseq_region_name

(

)

  Arg [1]    : none
  Example    :

print $feature->hseq_region_name();

  Description: Gets the name of the hseq_region which this feature is on.
               Returns undef if this Feature is not on a hslice.
  Returntype : string or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

hseq_region_start()

public Int Bio::EnsEMBL::FeaturePair::hseq_region_start

(

)

  Arg [1]    : none
  Example    :

print $feature->hseq_region_start();

  Description: Convenience method which returns the absolute start of this
               feature on the hseq_region, as opposed to the relative (hslice) 
               position.

               Returns undef if this feature is not on a hslice.
  Returntype : int or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

hseq_region_strand()

public Boolean Bio::EnsEMBL::FeaturePair::hseq_region_strand

(

)

  Arg [1]    : none
  Example    :

print $feature->hseq_region_strand();

  Description: Returns the strand of the hseq_region which this feature is on 
               (i.e. feature_strand * slice_strand)
               Returns undef if this Feature is not on a hslice.
  Returntype : 1,0,-1 or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

hseqname()

public String Bio::EnsEMBL::FeaturePair::hseqname

(

)

  Arg [1]    : string $hseqname (optional)
  Example    :

$hseqname = $fp->hseqname();

  Description: Getter/Setter for the name of the hit sequence
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

hslice()

public Bio::EnsEMBL::Slice Bio::EnsEMBL::FeaturePair::hslice

(

)

  Arg [1]    : (optional) Bio::EnsEMBL::Slice $slice
  Example    :

$hseqname = $featurepair->hslice()->seq_region_name();

  Description: Getter/Setter for the Slice that is associated with this 
               hit feature.  The slice represents the underlying sequence that this
               feature is on.  Note that this method call is analagous to the
               old SeqFeature methods contig(), entire_seq(), attach_seq(),
               etc.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : thrown if an invalid argument is passed
  Caller     : general
  Status     : Stable

Code:

hspecies()

public String Bio::EnsEMBL::FeaturePair::hspecies

(

)

 Arg [1]    : string $genus_species_name (optional)
              e.g. Homo_sapiens or Mus_musculus
 Example    :

$hspecies = $fp->hspecies

 Description: get/set on the species of feature2
 Returntype : string
 Execeptions: none
 Caller     : general
 Status     : Stable

Code:

hstart()

public Int Bio::EnsEMBL::FeaturePair::hstart

(

)

  Arg [1]    : string $hstart (optional)
  Example    :

$hstart = $fp->hstart();

  Description: Getter/Setter for the start coordinate on the hit sequence
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

hstrand()

public Bio::EnsEMBL::FeaturePair::hstrand

(

)

  Arg [1]    : int $hstrand (optional)
  Example    :

$hstrand = $fp->hstrand

  Description: Getter/Setter for the orientation of the hit on the hit sequence
  Returntype : 0,1,-1
  Exceptions : thrown 
  Caller     : general
  Status     : Stable

Code:

identical_matches()

public Int Bio::EnsEMBL::FeaturePair::identical_matches

(

)

 Arg [1]    : int $identical_matches (optional)
 Example    :

 Description: get/set on the number of identical matches
 Returntype : int
 Execeptions: none
 Caller     : general
  Status     : Stable

Code:

invert()

public void Bio::EnsEMBL::FeaturePair::invert

(

)

  Arg [1]    : (optional) Bio::EnsEMBL::Slice $newslice
  Example    :

$feature->invert();

  Description: This method is used to swap the hit and query sides of this
               feature in place.  A new slice may optionally provided which
               this feature will be placed on.  If no slice is provided the
               feature slice will be set to undef.
  Returntype : none
  Exceptions : none
  Caller     : pipeline (BlastMiniGenewise)

Code:

level_id()

public Int Bio::EnsEMBL::FeaturePair::level_id

(

)

 
  Arg [1]    : int $level_id
  Example    :

none

  Description: get/set for attribute level_id
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::FeaturePair Bio::EnsEMBL::FeaturePair::new

(

)

  Arg [HSTART]    : int - The start of the hit region (optional)
  Arg [HEND]      : int - The end of the hit region (optional)
  Arg [HSTRAND]   : (0,1,-1) - The strand of the hit region (optional)
  Arg [PERCENT_ID]: float -  The precentage identity of the hit (optional)
  Arg [SCORE]     : float -  The score of the hit (optional)
  Arg [HSEQNAME]  : string - The name of the hit sequence (optional)
  Arg [P_VALUE]   : float -  The pvalue or evalue (optional)
  Arg [SPECIES]   : string - The species the query sequence is from (optional)
  Arg [HSPECIES]  : string - The species the hit sequence is from (optional)
  Arg [COVERAGE]  : string - The % of the query that this feature pair covers
  Arg [HCOVERAGE] : string - The % of the target this this feature pair covers
  Arg [EXTRA_DATA]: HashRef - Additional data, specified as name, value attribute pairs (optional)
  Arg [...]       : Named superclass constructor args (Bio::EnsEMBL::Feature)
  Example    :

$feat = Bio::EnsEMBL::FeaturePair->new(-start    => 132_231,
                                             -end      => 132_321,
                                             -strand   => -1,
                                             -slice    => $slice,
                                             -hstart   => 10,
                                             -hend     => 100,
                                             -hstrand  => 1,
                                             -score    => 100,
                                             -percent_id => 92.0,
                                             -hseqname => 'ALUSX10.1',
                                             -analysis => $analysis);

  Description: Creates a new Bio::EnsEMBL::FeaturePair object
  Returntype : Bio::EnsEMBL::FeaturePair
  Exceptions : throw if start > end
               throw if invalid strand is provided
  Caller     : general
  Status     : Stable

Code:

p_value()

public Float Bio::EnsEMBL::FeaturePair::p_value

(

)

  Arg [1]    : float $p_value (optional)
  Example    :

$eval = $fp->p_value

  Description: Getter Setter for the evalue / pvalue of this feature
  Returntype : float
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

percent_id()

public Float Bio::EnsEMBL::FeaturePair::percent_id

(

)

  Arg [1]    : float $percent_id (optional)
  Example    :

$percent_id = $fp->percent_id();

  Description: Getter/Setter for the percentage identity of this feature pair
  Returntype : float
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

positive_matches()

public Int Bio::EnsEMBL::FeaturePair::positive_matches

(

)

 Arg [1]    : int $positive_matches (optional)
 Example    :

 Description: get/set on the number of positive matches
 Returntype : int
 Execeptions: none
 Caller     : general
  Status     : Stable

Code:

score()

public Float Bio::EnsEMBL::FeaturePair::score

(

)

  Arg [1]    : float $score (optional)
  Example    :

$score = $fp->score();

  Description: Getter/Setter for the score of this feature pair
  Returntype : float
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

species()

public String Bio::EnsEMBL::FeaturePair::species

(

)

 Arg [1]    : string $genus_species_name (optional)
              e.g. Homo_sapiens or Mus_musculus
 Example    :

$species = $fp->species();

 Description: get/set on the species of feature1
 Returntype : string
 Execeptions: none
 Caller     : general
 Status     : Stable

Code:

type()

public Bio::EnsEMBL::FeaturePair::type

(

)

Undocumented method

Code:

---

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

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