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

List of all members.


Class Summary

Synopsis

  my $feat = new Bio::EnsEMBL::DnaPepAlignFeature(
    -slice        =\> $slice,
    -start        =\> 100,
    -end          =\> 120,
    -strand       =\> 1,
    -hseqname     =\> 'SP:RF1231',
    -hstart       =\> 200,
    -hend         =\> 220,
    -analysis     =\> $analysis,
    -cigar_string =\> '10M3D5M2I'
  );

  Alternatively if you have an array of ungapped features

  my $feat =
    new Bio::EnsEMBL::DnaPepAlignFeature( -features =\> \@features );

  Where @features is an array of Bio::EnsEMBL::FeaturePair

  There is a method to manipulate the cigar_string into ungapped features

  my @ungapped_features = $feat-\>ungapped_features();

  This converts the cigar string into an array of Bio::EnsEMBL::FeaturePair

  $analysis is a Bio::EnsEMBL::Analysis object

  Bio::EnsEMBL::Feature methods can be used
  Bio::EnsEMBL::FeaturePair methods can be used

  The cigar_string contains the ungapped pieces that make up the gapped 
  alignment

  It looks like: n Matches [ x Deletes or Inserts m Matches ]*
  but a bit more condensed like "23M4I12M2D1M"
  and evenmore condensed as you can ommit 1s "23M4I12M2DM"


  To make things clearer this is how a blast HSP would be parsed

  \>AK014066
         Length = 146

    Minus Strand HSPs:

    Score = 76 (26.8 bits), Expect = 1.4, P = 0.74
    Identities = 20/71 (28%), Positives = 29/71 (40%), Frame = -1

  Query:   479 GLQAPPPTPQGCRLIPPPPLGLQAPLPTLRAVGSSHHHP*GRQGSSLSSFRSSLASKASA 300
               G  APPP PQG R   P P G + P   L             + + ++  R  +A   +
  Sbjct:     7 GALAPPPAPQG-RWAFPRPTG-KRPATPLHGTARQDRQVRRSEAAKVTGCRGRVAPHVAP 64

  Query:   299 SSPHNPSPLPS 267
                  H P+P P+
  Sbjct:    65 PLTHTPTPTPT 75

  The alignment goes from 267 to 479 in sequence 1 and 7 to 75 in sequence 2 
  and the strand is -1.

  The alignment is made up of the following ungapped pieces :

  sequence 1 start 447 , sequence 2 start 7  , match length 33 , strand -1
  sequence 1 start 417 , sequence 2 start 18 , match length 27 , strand -1
  sequence 1 start 267 , sequence 2 start 27 , match length 137 , strand -1

  These ungapped pieces are made up into the following string (called a cigar 
  string) "33M3I27M3I137M" with start 267 end 479 strand -1 hstart 7 hend 75 
  hstrand 1 and feature type would be DnaPepAlignFeature

Definition at line 80 of file BaseAlignFeature.pm.

Available Methods

protected _deprecated_transform ()
protected Int _hit_unit ()
protected List _parse_cigar ()
protected void _parse_features ()
protected Int _query_unit ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public add_sub_SeqFeature ()
public Int alignment_length ()
public Bio::EnsEMBL::Analysis analysis ()
public String cigar_string ()
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::BaseAlignFeature 
new ()
public
Bio::EnsEMBL::BaseAlignFeature 
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 void reverse_complement ()
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 Int strands_reversed ()
public sub_SeqFeature ()
public Hashref summary_as_hash ()
public Bio::EnsEMBL::Feature transfer ()
public
Bio::EnsEMBL::BaseAlignFeature 
transform ()
public type ()
public List ungapped_features ()
public validate ()
public validate_prot_feature ()

Method Documentation

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

Undocumented method

Code:
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protected Int Bio::EnsEMBL::BaseAlignFeature::_hit_unit ( )
  Args       : none
  Example    : none
  Description: abstract method, overwrite with something that returns
               one or three
  Returntype : int 1,3
  Exceptions : none
  Caller     : internal
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::DnaDnaAlignFeature, Bio::EnsEMBL::DnaPepAlignFeature, and Bio::EnsEMBL::PepDnaAlignFeature.

protected List Bio::EnsEMBL::BaseAlignFeature::_parse_cigar ( )
  Args       : none
  Example    : none
  Description: PRIVATE (internal) method - creates ungapped features from 
               internally stored cigar line
  Returntype : list of Bio::EnsEMBL::FeaturePair
  Exceptions : none
  Caller     : ungapped_features
  Status     : Stable
 
Code:
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protected void Bio::EnsEMBL::BaseAlignFeature::_parse_features ( )
  Arg  1     : listref Bio::EnsEMBL::FeaturePair $ungapped_features
  Example    : none
  Description: creates internal cigarstring and start,end hstart,hend
               entries.
  Returntype : none, fills in values of self
  Exceptions : argument list undergoes many sanity checks - throws under many
               invalid conditions
  Caller     : new
  Status     : Stable
 
Code:
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protected Int Bio::EnsEMBL::BaseAlignFeature::_query_unit ( )
  Args       : none
  Example    : none
  Description: abstract method, overwrite with something that returns
               one or three
  Returntype : int 1,3
  Exceptions : none
  Caller     : internal
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::DnaDnaAlignFeature, Bio::EnsEMBL::DnaPepAlignFeature, and Bio::EnsEMBL::PepDnaAlignFeature.

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 Int Bio::EnsEMBL::BaseAlignFeature::alignment_length ( )
  Arg [1]    : None
  Example    : 
  Description: return the alignment length (including indels) based on the cigar_string
  Returntype : int
  Exceptions : 
  Caller     : 
  Status     : Stable
 
Code:
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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 String Bio::EnsEMBL::BaseAlignFeature::cigar_string ( )
  Arg [1]    : string $cigar_string
  Example    : ( "12MI3M" )
  Description: get/set for attribute cigar_string
               cigar_string describes the alignment. "xM" stands for 
               x matches (mismatches), "xI" for inserts into query sequence 
               (thats the ensembl sequence), "xD" for deletions 
               (inserts in the subject). an "x" that is 1 can be omitted.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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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
 
Code:
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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
 
Code:
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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
 
Code:
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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

Code:
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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

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

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

public Bio::EnsEMBL::BaseAlignFeature Bio::EnsEMBL::BaseAlignFeature::new ( )
  Arg [..]   : List of named arguments. (-cigar_string , -features) defined
               in this constructor, others defined in FeaturePair and 
               SeqFeature superclasses.  Either cigar_string or a list
               of ungapped features should be provided - not both.
  Example    : $baf = new BaseAlignFeatureSubclass(-cigar_string => '3M3I12M');
  Description: Creates a new BaseAlignFeature using either a cigarstring or
               a list of ungapped features.  BaseAlignFeature is an abstract
               baseclass and should not actually be instantiated - rather its
               subclasses should be.
  Returntype : Bio::EnsEMBL::BaseAlignFeature
  Exceptions : thrown if both feature and cigar string args are provided
               thrown if neither feature nor cigar string args are provided
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::FeaturePair.

Reimplemented in Bio::EnsEMBL::DnaDnaAlignFeature.

public Bio::EnsEMBL::BaseAlignFeature Bio::EnsEMBL::BaseAlignFeature::new_fast ( )
  Arg [1]    : hashref $hashref
               A hashref which will be blessed into a PepDnaAlignFeature.
  Example    : none
  Description: This allows for very fast object creation when a large number
               of PepDnaAlignFeatures needs to be created.  This is a bit of
               a hack but necessary when thousands of features need to be
               generated within a couple of seconds for web display. It is
               not recommended that this method be called unless you know what
               you are doing.  It requires knowledge of the internals of this
               class and its superclasses.
  Returntype : Bio::EnsEMBL::BaseAlignFeature
  Exceptions : none
  Caller     : none currently
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Feature.

Reimplemented in Bio::EnsEMBL::DnaPepAlignFeature.

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
 
Code:
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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
 
Code:
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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
 
Code:
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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
 
Code:
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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
 
Code:
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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 void Bio::EnsEMBL::BaseAlignFeature::reverse_complement ( )
  Args       : none
  Example    : none
  Description: reverse complement the FeaturePair,
               modifing strand, hstrand and cigar_string in consequence
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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::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
 
Code:
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Reimplemented in Bio::EnsEMBL::DensityFeature, Bio::EnsEMBL::Exon, Bio::EnsEMBL::KaryotypeBand, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::Map::QtlFeature, and Bio::EnsEMBL::ProteinFeature.

public Int Bio::EnsEMBL::BaseAlignFeature::strands_reversed ( )
 
  Arg [1]    : int $strands_reversed
  Example    : none
  Description: get/set for attribute strands_reversed
               0 means that strand and hstrand are the original strands obtained
                 from the alignment program used
               1 means that strand and hstrand have been flipped as compared to
                 the original result provided by the alignment program used.
                 You may want to use the reverse_complement method to restore the
                 original strandness.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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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::BaseAlignFeature Bio::EnsEMBL::BaseAlignFeature::transform ( )
  Arg  1     : String $coordinate_system_name
  Arg [2]    : String $coordinate_system_version
  Example    : $feature = $feature->transform('contig');
               $feature = $feature->transform('chromosome', 'NCBI33');
  Description: Moves this AlignFeature to the given coordinate system.
               If the feature cannot be transformed to the destination 
               coordinate system undef is returned instead.
  Returntype : Bio::EnsEMBL::BaseAlignFeature;
  Exceptions : wrong parameters
  Caller     : general
  Status     : Medium Risk
             : deprecation needs to be removed at some time
 
Code:
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Reimplemented from Bio::EnsEMBL::Feature.

Reimplemented in Bio::EnsEMBL::PepDnaAlignFeature.

public Bio::EnsEMBL::FeaturePair::type ( ) [inherited]

Undocumented method

Code:
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public List Bio::EnsEMBL::BaseAlignFeature::ungapped_features ( )
  Args       : none
  Example    : @ungapped_features = $align_feature->get_feature
  Description: converts the internal cigar_string into an array of
               ungapped feature pairs
  Returntype : list of Bio::EnsEMBL::FeaturePair
  Exceptions : cigar_string not set internally
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::FeaturePair::validate ( ) [inherited]
  Description:

Deprecated:
do not use
 
Code:
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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: