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Bio-EnsEMBL-112.0.0_58
River stage zero No dependents
/ Bio::EnsEMBL::FeaturePair

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::FeaturePair - Stores sequence Features which are themselves hits to other sequence features.

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'
  );

METHODS

new

  Arg [HSTART]    : int - The start of the hit region (optional)
  Arg [HEND]      : int - The end of the hit region (optional)
  Arg [HSTRAND]   : (0,1,-1) - The strand of the hit region (optional)
  Arg [PERCENT_ID]: float -  The precentage identity of the hit (optional)
  Arg [SCORE]     : float -  The score of the hit (optional)
  Arg [HSEQNAME]  : string - The name of the hit sequence (optional)
  Arg [P_VALUE]   : float -  The pvalue or evalue (optional)
  Arg [SPECIES]   : string - The species the query sequence is from (optional)
  Arg [HSPECIES]  : string - The species the hit sequence is from (optional)
  Arg [COVERAGE]  : string - The % of the query that this feature pair covers
  Arg [HCOVERAGE] : string - The % of the target this this feature pair covers
  Arg [EXTRA_DATA]: HashRef - Additional data, specified as name, value attribute pairs (optional)
  Arg [...]       : Named superclass constructor args (Bio::EnsEMBL::Feature)
  Example    : $feat = Bio::EnsEMBL::FeaturePair->new(-start    => 132_231,
                                              -end      => 132_321,
                                              -strand   => -1,
                                              -slice    => $slice,
                                              -hstart   => 10,
                                              -hend     => 100,
                                              -hstrand  => 1,
                                              -score    => 100,
                                              -percent_id => 92.0,
                                              -hseqname => 'ALUSX10.1',
                                              -analysis => $analysis);
  Description: Creates a new Bio::EnsEMBL::FeaturePair object
  Returntype : Bio::EnsEMBL::FeaturePair
  Exceptions : throw if start > end
               throw if invalid strand is provided
  Caller     : general
  Status     : Stable

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

hdescription

  Arg [1]    : String (optional)
  Example    : $des = $fp->hdescription()
  Description: Getter Setter for optional description of this feature
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

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

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

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

group_id

  Arg [1]    : int $group_id
  Example    : none
  Description: get/set for attribute group_id
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

level_id

  Arg [1]    : int $level_id
  Example    : none
  Description: get/set for attribute level_id
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

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)