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Bio::EnsEMBL::ProteinFeature Class Reference
Inheritance diagram for Bio::EnsEMBL::ProteinFeature:

List of all members.


Class Summary

Synopsis

  my $feature = Bio::EnsEMBL::ProteinFeature-\>new(
    -start    =\> $start,
    -end      =\> $end,
    -hstart   =\> $hit_start,
    -hend     =\> $hit_end,
    -hseqname =\> $hit_name
  );

Description

ProteinFeature objects represent domains or other features of interest
on a peptide sequence.
 

Definition at line 23 of file ProteinFeature.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 String idesc ()
public String interpro_ac ()
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 String translation_id ()
public type ()
public validate ()
public validate_prot_feature ()

Method Documentation

protected Bio::EnsEMBL::Feature::_deprecated_transform ( ) [inherited]

Undocumented method

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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
 
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public Bio::EnsEMBL::Feature::add_sub_SeqFeature ( ) [inherited]

Undocumented method

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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
 
Code:
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Reimplemented in Bio::EnsEMBL::DensityFeature.

public Bio::EnsEMBL::Feature::contig ( ) [inherited]

Undocumented method

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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
 
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public String Bio::EnsEMBL::FeaturePair::coverage ( ) [inherited]
  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
 
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public String Bio::EnsEMBL::FeaturePair::db_display_name ( ) [inherited]
  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
 
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public String Bio::EnsEMBL::FeaturePair::db_name ( ) [inherited]
  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
 
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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
 
Code:
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Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

public String Bio::EnsEMBL::FeaturePair::display_id ( ) [inherited]
  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:
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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
 
Code:
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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.
 
Code:
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Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Gene, and Bio::EnsEMBL::Transcript.

public String Bio::EnsEMBL::FeaturePair::external_db_id ( ) [inherited]
  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
 
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public Bio::EnsEMBL::FeaturePair::extra_data ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::FeaturePair::feature1 ( ) [inherited]
  Description:

Deprecated:
use start(), end(), strand(), slice(), etc. methods instead
 
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public Bio::EnsEMBL::FeaturePair::feature2 ( ) [inherited]
  Description:

Deprecated:
use hstart(), hend(), hstrand() etc. methods instead
 
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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
 
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public Bio::EnsEMBL::Feature::flush_sub_SeqFeature ( ) [inherited]

Undocumented method

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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
 
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public Bio::EnsEMBL::Storable::get_all_DAS_Features ( ) [inherited]

Undocumented method

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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
 
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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
 
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public Bio::EnsEMBL::FeaturePair::gffstring ( ) [inherited]
  Description:

Deprecated:
do not use
 
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public Int Bio::EnsEMBL::FeaturePair::group_id ( ) [inherited]
 
  Arg [1]    : int $group_id
  Example    : none
  Description: get/set for attribute group_id
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::FeaturePair::hcoverage ( ) [inherited]
  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
 
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public Int Bio::EnsEMBL::FeaturePair::hend ( ) [inherited]
  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
 
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public Bio::EnsEMBL::FeaturePair::hend_phase ( ) [inherited]
  Description:

Deprecated:
do not use
 
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public Bio::EnsEMBL::FeaturePair::hphase ( ) [inherited]
  Description:

Deprecated:
do not use
 
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public Int Bio::EnsEMBL::FeaturePair::hseq_region_end ( ) [inherited]
  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
 
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public String Bio::EnsEMBL::FeaturePair::hseq_region_name ( ) [inherited]
  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
 
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public Int Bio::EnsEMBL::FeaturePair::hseq_region_start ( ) [inherited]
  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
 
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public Boolean Bio::EnsEMBL::FeaturePair::hseq_region_strand ( ) [inherited]
  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
 
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public String Bio::EnsEMBL::FeaturePair::hseqname ( ) [inherited]
  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
 
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public Bio::EnsEMBL::Slice Bio::EnsEMBL::FeaturePair::hslice ( ) [inherited]
  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
 
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public String Bio::EnsEMBL::FeaturePair::hspecies ( ) [inherited]
 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
 
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public Int Bio::EnsEMBL::FeaturePair::hstart ( ) [inherited]
  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:
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public Bio::EnsEMBL::FeaturePair::hstrand ( ) [inherited]
  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
 
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public Bio::EnsEMBL::Feature::id ( ) [inherited]

Undocumented method

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public Int Bio::EnsEMBL::FeaturePair::identical_matches ( ) [inherited]
 Arg [1]    : int $identical_matches (optional)
 Example    : 
 Description: get/set on the number of identical matches
 Returntype : int
 Execeptions: none
 Caller     : general
  Status     : Stable
 
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public String Bio::EnsEMBL::ProteinFeature::idesc ( )
  Arg [1]    : (optional) string The interpro description
  Example    : print $protein_feature->idesc();
  Description: Getter/Setter for the interpro description of this protein
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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public String Bio::EnsEMBL::ProteinFeature::interpro_ac ( )
  Arg [1]    : (optional) string The interpro accession
  Example    : print $protein_feature->interpro_ac();
  Description: Getter/Setter for the interpro accession of this protein
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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public void Bio::EnsEMBL::FeaturePair::invert ( ) [inherited]
  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)
 
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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
 
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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
 
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Reimplemented in Bio::EnsEMBL::Intron, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Upstream.

public Int Bio::EnsEMBL::FeaturePair::level_id ( ) [inherited]
 
  Arg [1]    : int $level_id
  Example    : none
  Description: get/set for attribute level_id
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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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
 
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Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::KaryotypeBand, and Bio::EnsEMBL::Map::QtlFeature.

public Bio::EnsEMBL::FeaturePair Bio::EnsEMBL::ProteinFeature::new ( )
  Arg [IDESC]           : (optional) string An interpro description
  Arg [INTERPRO_AC]     : (optional) string An interpro accession
  Arg [TRANSLATION_ID]  : (optional) integer A translation dbID
  Arg [...]             : named arguments to FeaturePair superclass
  Example    :
    $pf =
      Bio::EnsEMBL::ProteinFeature->new( -IDESC       => $idesc,
                                         -INTERPRO_AC => $iac,
                                         @fp_args );
  Description: Instantiates a Bio::EnsEMBL::ProteinFeature
  Returntype : Bio::EnsEMBL::FeaturePair
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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Reimplemented from Bio::EnsEMBL::FeaturePair.

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
 
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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
 
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public Float Bio::EnsEMBL::FeaturePair::p_value ( ) [inherited]
  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
 
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public Float Bio::EnsEMBL::FeaturePair::percent_id ( ) [inherited]
  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
 
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public Int Bio::EnsEMBL::FeaturePair::positive_matches ( ) [inherited]
 Arg [1]    : int $positive_matches (optional)
 Example    : 
 Description: get/set on the number of positive matches
 Returntype : int
 Execeptions: none
 Caller     : general
  Status     : Stable
 
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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
 
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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
 
Code:
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public Float Bio::EnsEMBL::FeaturePair::score ( ) [inherited]
  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:
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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
 
Code:
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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
 
Code:
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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
 
Code:
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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
 
Code:
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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
 
Code:
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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
 
Code:
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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
 
Code:
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public Bio::EnsEMBL::FeaturePair::set_featurepair_fields ( ) [inherited]
  Description:

Deprecated:
do not use
 
Code:
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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
 
Code:
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Reimplemented in Bio::EnsEMBL::Exon, and Bio::EnsEMBL::Map::DitagFeature.

public String Bio::EnsEMBL::FeaturePair::species ( ) [inherited]
 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:
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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
 
Code:
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Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::SplicingEventFeature, and Bio::EnsEMBL::SplicingTranscriptPair.

public Int Bio::EnsEMBL::ProteinFeature::strand ( )
  Arg [1]    : Ignored
  Description: Overwrites Bio::EnsEMBL::Feature->strand to not allow
             : the strand to be set.
  Returntype : int
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Feature.

public Bio::EnsEMBL::Feature::sub_SeqFeature ( ) [inherited]

Undocumented method

Code:
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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
 
Code:
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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
 
Code:
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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
 
Code:
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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 String Bio::EnsEMBL::ProteinFeature::translation_id ( )
  Arg [1]    : (optional) integer The dbID of the translation
  Example    : print $protein_feature->translation_id();
  Description: Getter/Setter for the translation dbID of this protein
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::FeaturePair::type ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::FeaturePair::validate ( ) [inherited]
  Description:

Deprecated:
do not use
 
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public Bio::EnsEMBL::FeaturePair::validate_prot_feature ( ) [inherited]
  Description:

Deprecated:
do not use
 
Code:
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The documentation for this class was generated from the following file: