sub hseq_region_start { my $self = shift; my $slice = $self->{'hslice'}; return undef if(!$slice); if($slice->strand == 1) { return undef if(!defined($self->{'hstart'})); return $slice->start() + $self->{'hstart'} - 1; } else { return undef if(!defined($self->{'hend'})); return $slice->end() - $self->{'hend'} + 1; } }

Class Summary
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.
Available Methods | |
protected | _deprecated_transform () |
public Bio::EnsEMBL::DBSQL::BaseAdaptor | adaptor () |
public | add_sub_SeqFeature () |
public Bio::EnsEMBL::Analysis | analysis () |
public | contig () |
public String | coord_system_name () |
public String | coverage () |
public String | db_display_name () |
public String | db_name () |
public Int | dbID () |
public String | display_id () |
public Int | end () |
public Boolean Or Undef | equals () |
public String | external_db_id () |
public | extra_data () |
public | feature1 () |
public | feature2 () |
public Bio::EnsEMBL::Slice | feature_Slice () |
public | flush_sub_SeqFeature () |
public Reference | get_all_alt_locations () |
public | get_all_DAS_Features () |
public Bio::EnsEMBL::Gene | get_nearest_Gene () |
public List | get_overlapping_Genes () |
public | gffstring () |
public Int | group_id () |
public String | hcoverage () |
public Int | hend () |
public | hend_phase () |
public | hphase () |
public Int | hseq_region_end () |
public String | hseq_region_name () |
public Int | hseq_region_start () |
public Boolean | hseq_region_strand () |
public String | hseqname () |
public Bio::EnsEMBL::Slice | hslice () |
public String | hspecies () |
public Int | hstart () |
public | hstrand () |
public | id () |
public Int | identical_matches () |
public void | invert () |
public Boolean | is_stored () |
public Int | length () |
public Int | level_id () |
public void | move () |
public Bio::EnsEMBL::FeaturePair | new () |
public Bio::EnsEMBL::Feature | new_fast () |
public Boolean | overlaps () |
public Float | p_value () |
public Float | percent_id () |
public Int | positive_matches () |
public List | project () |
public List | project_to_slice () |
public Float | score () |
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 | set_featurepair_fields () |
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 () |
public | type () |
public | validate () |
public | validate_prot_feature () |
Method Documentation
protected Bio::EnsEMBL::Feature::_deprecated_transform | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor Example : none Description: get/set for this objects Adaptor Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor Exceptions : none Caller : general, set from adaptor on store Status : Stable

public Bio::EnsEMBL::Feature::add_sub_SeqFeature | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Analysis Bio::EnsEMBL::Feature::analysis | ( | ) | [inherited] |
Arg [1] : (optional) Bio::EnsEMBL::Analysis $analysis Example : $feature->analysis(new Bio::EnsEMBL::Analysis(...)) Description: Getter/Setter for the analysis that is associated with this feature. The analysis describes how this feature was derived. Returntype : Bio::EnsEMBL::Analysis Exceptions : thrown if an invalid argument is passed Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::DensityFeature.
public Bio::EnsEMBL::Feature::contig | ( | ) | [inherited] |
Undocumented method

public String Bio::EnsEMBL::Feature::coord_system_name | ( | ) | [inherited] |
Arg [1] : none Example : print $feature->coord_system_name() Description: Gets the name of the coord_system which this feature is on. Returns undef if this Feature is not on a slice. Returntype : string or undef Exceptions : none Caller : general Status : Stable

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

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

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

public Int Bio::EnsEMBL::Storable::dbID | ( | ) | [inherited] |
Arg [1] : int $dbID Example : none Description: getter/setter for the database internal id Returntype : int Exceptions : none Caller : general, set from adaptor on store Status : Stable

Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.
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

Reimplemented from Bio::EnsEMBL::Feature.
public Int Bio::EnsEMBL::Feature::end | ( | ) | [inherited] |
Arg [1] : (optional) int $end Example : $end = $feat->end(); Description: Getter/Setter for the end of this feature relative to the start of the slice that it is on. Note that negative values, of values exceeding the length of the slice are permitted. End must be greater than or equal to start regardless of the strand. Coordinate values start at 1 and are inclusive. Returntype : int Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::SplicingEventFeature, and Bio::EnsEMBL::SplicingTranscriptPair.
public Boolean Or Undef Bio::EnsEMBL::Feature::equals | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::Feature object Example : if ($featureA->equals($featureB)) { ... } Description : Compares two features using various criteria. The test for eqality goes through the following list and terminates at the first true match:
1. If the two features are the same object, they are equal. 2. If they are of different types (e.g., transcript and gene), they are *not* equal. 3. If they both have dbIDs: if these are the same, then they are equal, otherwise not. 4. If they both have slices and analysis objects: if the analysis dbIDs are the same and the seq_region_id are the same, along with seq_region_start and seq_region_end, then they are equal, otherwise not.
If none of the above is able to determine equality, undef is returned.
Return type : tri-Boolean (0, 1, undef = "unknown")
Exceptions : Thrown if a non-feature is passed as the argument.

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Gene, and Bio::EnsEMBL::Transcript.
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

public Bio::EnsEMBL::FeaturePair::extra_data | ( | ) |
Undocumented method

public Bio::EnsEMBL::FeaturePair::feature1 | ( | ) |
Description:
- Deprecated:
- use start(), end(), strand(), slice(), etc. methods instead

public Bio::EnsEMBL::FeaturePair::feature2 | ( | ) |
public Bio::EnsEMBL::Slice Bio::EnsEMBL::Feature::feature_Slice | ( | ) | [inherited] |
Args : none Example : $slice = $feature->feature_Slice() Description: This is a convenience method to return a slice that covers the Area of this feature. The feature start will be at 1 on it, and it will have the length of this feature. Returntype : Bio::EnsEMBL::Slice or undef if this feature has no attached Slice. Exceptions : warning if Feature does not have attached slice. Caller : web drawing code Status : Stable

public Bio::EnsEMBL::Feature::flush_sub_SeqFeature | ( | ) | [inherited] |
Undocumented method

public Reference Bio::EnsEMBL::Feature::get_all_alt_locations | ( | ) | [inherited] |
Arg [1] : none Example : @features = @{$feature->get_all_alt_locations()}; foreach $f (@features) { print $f->slice->seq_region_name,' ',$f->start, $f->end,"\\n"; }
Description: Retrieves shallow copies of this feature in its alternate locations. A feature can be considered to have multiple locations when it sits on a alternative structural haplotype or when it is on a pseudo autosomal region. Most features will just return a reference to an empty list though. The features returned by this method will be on a slice which covers the entire alternate region.
Currently this method does not take into account alternate locations on the alternate locations (e.g. a reference sequence may have multiple alternate haplotypes. Asking for alternate locations of a feature on one of the alternate haplotypes will give you back the reference location, but not locations on the other alternate haplotypes).
Returntype : reference to list of features of the same type of this feature. Exceptions : none Caller : general Status : Stable

public Bio::EnsEMBL::Storable::get_all_DAS_Features | ( | ) | [inherited] |
Undocumented method

Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.
public Bio::EnsEMBL::Gene Bio::EnsEMBL::Feature::get_nearest_Gene | ( | ) | [inherited] |
Description: Get all the nearest gene to the feature Returntype : Bio::EnsEMBL::Gene Caller : general Status : UnStable

public List Bio::EnsEMBL::Feature::get_overlapping_Genes | ( | ) | [inherited] |
Description: Get all the genes that overlap this feature. Returntype : list ref of Bio::EnsEMBL::Gene Caller : general Status : UnStable

public Bio::EnsEMBL::FeaturePair::gffstring | ( | ) |
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

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

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

public Bio::EnsEMBL::FeaturePair::hend_phase | ( | ) |
public Bio::EnsEMBL::FeaturePair::hphase | ( | ) |
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

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

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

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

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

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

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

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

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

public Bio::EnsEMBL::Feature::id | ( | ) | [inherited] |
Undocumented method

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

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)

public Boolean Bio::EnsEMBL::Storable::is_stored | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::DBSQL::DBConnection : or Bio::EnsEMBL::DBSQL::DBAdaptor Example : do_something if($object->is_stored($db)); Description: Returns true if this object is stored in the provided database. This works under the assumption that if the adaptor and dbID are set and the database of the adaptor shares the port, dbname and hostname with the provided database, this object is stored in that database. Returntype : 1 or 0 Exceptions : throw if dbID is set but adaptor is not throw if adaptor is set but dbID is not throw if incorrect argument is passed Caller : store methods Status : Stable

public Int Bio::EnsEMBL::Feature::length | ( | ) | [inherited] |
Arg [1] : none Example : $length = $feat->length(); Description: Returns the length of this feature Returntype : Integer Exceptions : Throws if end < start and the feature is not on a circular slice Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::Intron, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Upstream.
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

public void Bio::EnsEMBL::Feature::move | ( | ) | [inherited] |
Arg [1] : int start Arg [2] : int end Arg [3] : (optional) int strand Example : None Description: Sets the start, end and strand in one call rather than in 3 seperate calls to the start(), end() and strand() methods. This is for convenience and for speed when this needs to be done within a tight loop. Returntype : none Exceptions : Thrown is invalid arguments are provided Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::KaryotypeBand, and Bio::EnsEMBL::Map::QtlFeature.
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 [...] : 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

Reimplemented from Bio::EnsEMBL::Feature.
Reimplemented in Bio::EnsEMBL::BaseAlignFeature, Bio::EnsEMBL::DnaDnaAlignFeature, and Bio::EnsEMBL::ProteinFeature.
public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::new_fast | ( | ) | [inherited] |
Arg [1] : hashref to be blessed Description: Construct a new Bio::EnsEMBL::Feature using the hashref. Exceptions : none Returntype : Bio::EnsEMBL::Feature Caller : general, subclass constructors Status : Stable

Reimplemented in Bio::EnsEMBL::AssemblyExceptionFeature, Bio::EnsEMBL::BaseAlignFeature, Bio::EnsEMBL::DensityFeature, Bio::EnsEMBL::DnaPepAlignFeature, Bio::EnsEMBL::MiscFeature, Bio::EnsEMBL::RepeatFeature, and Bio::EnsEMBL::SimpleFeature.
public Boolean Bio::EnsEMBL::Feature::overlaps | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::Feature $f The other feature you want to check overlap with this feature for. Description: This method does a range comparison of this features start and end and compares it with another features start and end. It will return true if these ranges overlap and the features are on the same seq_region. Returntype : TRUE if features overlap, FALSE if they don't Exceptions : warning if features are on different seq_regions Caller : general Status : Stable

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

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

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

public List Bio::EnsEMBL::Feature::project | ( | ) | [inherited] |
Arg [1] : string $name The name of the coordinate system to project this feature onto Arg [2] : string $version (optional) The version of the coordinate system (such as 'NCBI34') to project this feature onto Example : my $clone_projection = $feature->project('clone');
foreach my $seg (@$clone_projection) { my $clone = $seg->to_Slice(); print "Features current coords ", $seg->from_start, '-', $seg->from_end, " project onto clone coords " . $clone->seq_region_name, ':', $clone->start, '-', $clone->end, $clone->strand, "\\n"; } Description: Returns the results of 'projecting' this feature onto another coordinate system. This is useful to see where a feature would lie in a coordinate system in which it crosses a boundary.
This method returns a reference to a list of Bio::EnsEMBL::ProjectionSegment objects. ProjectionSegments are blessed arrays and can also be used as triplets [from_start,from_end,to_Slice]. The from_start and from_end are the coordinates relative to the feature start. For example, if a feature is current 100-200bp on a slice then the triplets returned might be: [1,50,$slice1], [51,101,$slice2]
The to_Slice is a slice spanning the region on the requested coordinate system that this feature projected to.
If the feature projects entirely into a gap then a reference to an empty list is returned.
Returntype : list reference of Bio::EnsEMBL::ProjectionSegments which can also be used as [$start,$end,$slice] triplets Exceptions : slice does not have an adaptor Caller : general Status : Stable

public List Bio::EnsEMBL::Feature::project_to_slice | ( | ) | [inherited] |
Arg [1] : slice to project to
Example : my $clone_projection = $feature->project_to_slice($slice);
foreach my $seg (@$clone_projection) { my $clone = $seg->to_Slice(); print "Features current coords ", $seg->from_start, '-', $seg->from_end, " project onto clone coords " . $clone->seq_region_name, ':', $clone->start, '-', $clone->end, $clone->strand, "\\n"; } Description: Returns the results of 'projecting' this feature onto another slcie . This is useful to see where a feature would lie in a coordinate system in which it crosses a boundary.
This method returns a reference to a list of Bio::EnsEMBL::ProjectionSegment objects. ProjectionSegments are blessed arrays and can also be used as triplets [from_start,from_end,to_Slice]. The from_start and from_end are the coordinates relative to the feature start. For example, if a feature is current 100-200bp on a slice then the triplets returned might be: [1,50,$slice1], [51,101,$slice2]
The to_Slice is a slice spanning the region on the requested coordinate system that this feature projected to.
If the feature projects entirely into a gap then a reference to an empty list is returned.
Returntype : list reference of Bio::EnsEMBL::ProjectionSegments which can also be used as [$start,$end,$slice] triplets Exceptions : slice does not have an adaptor Caller : general Status : At Risk

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

public Undef Bio::EnsEMBL::Feature::seq | ( | ) | [inherited] |
Args : none Example : my $dna_sequence = $simple_feature->seq(); Description: Returns the dna sequence from the attached slice and attached database that overlaps with this feature. Returns undef if there is no slice or no database. Returns undef if this feature is unstranded (i.e. strand=0). Returntype : undef or string Exceptions : warning if this feature is not stranded Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::Exon, and Bio::EnsEMBL::Transcript.
public Int Bio::EnsEMBL::Feature::seq_region_end | ( | ) | [inherited] |
Arg [1] : none Example : print $feature->seq_region_end(); Description: Convenience method which returns the absolute end of this feature on the seq_region, as opposed to the relative (slice) position.
Returns undef if this feature is not on a slice. Returntype : int or undef Exceptions : none Caller : general Status : Stable

public Unsigned Bio::EnsEMBL::Feature::seq_region_length | ( | ) | [inherited] |
Arg [1] : none Example : print $feature->seq_region_length(); Description: Returns the length of the seq_region which this feature is on Returns undef if this Feature is not on a slice. Returntype : unsigned int or undef Exceptions : none Caller : general Status : Stable

public String Bio::EnsEMBL::Feature::seq_region_name | ( | ) | [inherited] |
Arg [1] : none Example : print $feature->seq_region_name(); Description: Gets the name of the seq_region which this feature is on. Returns undef if this Feature is not on a slice. Returntype : string or undef Exceptions : none Caller : general Status : Stable

public Int Bio::EnsEMBL::Feature::seq_region_start | ( | ) | [inherited] |
Arg [1] : none Example : print $feature->seq_region_start(); Description: Convenience method which returns the absolute start of this feature on the seq_region, as opposed to the relative (slice) position.
Returns undef if this feature is not on a slice. Returntype : int or undef Exceptions : none Caller : general Status : Stable

public Boolean Bio::EnsEMBL::Feature::seq_region_strand | ( | ) | [inherited] |
Arg [1] : none Example : print $feature->seq_region_strand(); Description: Returns the strand of the seq_region which this feature is on (i.e. feature_strand * slice_strand) Returns undef if this Feature is not on a slice. Returntype : 1,0,-1 or undef Exceptions : none Caller : general Status : Stable

public String Bio::EnsEMBL::Feature::seqname | ( | ) | [inherited] |
Arg [1] : (optional) $seqname Example : $seqname = $feat->seqname(); Description: Getter/Setter for the name of the sequence that this feature is on. Normally you can get away with not setting this value and it will default to the name of the slice on which this feature is on. It is useful to set this value on features which do not ordinarily sit on features such as ProteinFeatures which sit on peptides. Returntype : string Exceptions : none Caller : general Status : Stable

public Bio::EnsEMBL::FeaturePair::set_featurepair_fields | ( | ) |
public Bio::EnsEMBL::Slice Bio::EnsEMBL::Feature::slice | ( | ) | [inherited] |
Arg [1] : (optional) Bio::EnsEMBL::Slice $slice Example : $seqname = $feature->slice()->name(); Description: Getter/Setter for the Slice that is associated with this 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

Reimplemented in Bio::EnsEMBL::Exon, and Bio::EnsEMBL::Map::DitagFeature.
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

Reimplemented from Bio::EnsEMBL::Feature.
public Int Bio::EnsEMBL::Feature::start | ( | ) | [inherited] |
Arg [1] : (optional) int $start The start of this feature relative to the start of the slice that it is on. Example : $start = $feat->start() Description: Getter/Setter for the start of this feature relative to the start of the slice it is on. Note that negative values, or values exceeding the length of the slice are permitted. Start must be less than or equal to the end regardless of the strand. Coordinate values start at 1 and are inclusive. Returntype : int Exceptions : none Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::SplicingEventFeature, and Bio::EnsEMBL::SplicingTranscriptPair.
public Int Bio::EnsEMBL::Feature::strand | ( | ) | [inherited] |
Arg [1] : (optional) int $strand Example : $feat->strand(-1); Description: Getter/Setter for the strand of this feature relative to the slice it is on. 0 is an unknown or non-applicable strand. -1 is the reverse (negative) strand and 1 is the forward (positive) strand. No other values are permitted. Returntype : int Exceptions : thrown if an invalid strand argument is passed Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::DensityFeature, Bio::EnsEMBL::Exon, Bio::EnsEMBL::KaryotypeBand, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::Map::QtlFeature, and Bio::EnsEMBL::ProteinFeature.
public Bio::EnsEMBL::Feature::sub_SeqFeature | ( | ) | [inherited] |
Undocumented method

public Hashref Bio::EnsEMBL::Feature::summary_as_hash | ( | ) | [inherited] |
Example : $feature_summary = $feature->summary_as_hash(); Description : Retrieves a textual summary of this Feature. Should be overidden by subclasses for specific tweaking Returns : hashref of arrays of descriptive strings Status : Intended for internal use

Reimplemented in Bio::EnsEMBL::Gene, and Bio::EnsEMBL::Transcript.
public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::transfer | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::Slice $slice The slice to transfer this feature to Example : $feature = $feature->transfer($slice); next if(!defined($feature)); Description: Returns a copy of this feature which has been shifted onto another slice.
If the new slice is in a different coordinate system the feature is transformed first and then placed on the slice. If the feature would be split across a coordinate system boundary or mapped to a gap undef is returned instead.
If the feature cannot be placed on the provided slice because it maps to an entirely different location, undef is returned instead.
Returntype : Bio::EnsEMBL::Feature (or undef) Exceptions : throw on incorrect argument throw if feature does not have attached slice Caller : general, transform() Status : Stable

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Gene, Bio::EnsEMBL::PredictionExon, Bio::EnsEMBL::PredictionTranscript, and Bio::EnsEMBL::Transcript.
public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::transform | ( | ) | [inherited] |
Arg [1] : string $coord_system The coord system to transform this feature to. Arg [2] : string $version (optional) The version of the coord system to transform this feature to. Example : $feature = $feature->transform('contig'); next if(!defined($feature)); Description: Returns a copy of this feature, but converted to a different coordinate system. The converted feature will be placed on a slice which spans an entire sequence region of the new coordinate system. If the requested coordinate system is the same coordinate system it is simply placed on a slice which spans the entire seq_region (as opposed to the original slice which may have only partially covered the seq_region).
If a feature spans a boundary in the new coordinate system, undef is returned instead.
For example, transforming an exon in contig coordinates to one in chromosomal coodinates will place the exon on a slice of an entire chromosome. Returntype : Bio::EnsEMBL::Feature (or undef) Exceptions : thrown if an invalid coordinate system is provided warning if Feature is not attached to a slice Caller : general, transfer() Status : Stable

Reimplemented in Bio::EnsEMBL::BaseAlignFeature, Bio::EnsEMBL::Exon, Bio::EnsEMBL::Gene, Bio::EnsEMBL::PepDnaAlignFeature, Bio::EnsEMBL::PredictionExon, Bio::EnsEMBL::PredictionTranscript, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Upstream.
public Bio::EnsEMBL::FeaturePair::type | ( | ) |
Undocumented method

public Bio::EnsEMBL::FeaturePair::validate | ( | ) |
public Bio::EnsEMBL::FeaturePair::validate_prot_feature | ( | ) |
The documentation for this class was generated from the following file:
- Bio/EnsEMBL/FeaturePair.pm