Inheritance diagram for Bio::EnsEMBL::DnaDnaAlignFeature:

Public Member Functions
public Bio::EnsEMBL::DnaDnaAlignFeature	new ()

protected Int	_hit_unit ()

protected Int	_query_unit ()

public Bio::EnsEMBL::DnaDnaAlignFeature	restrict_between_positions ()

public Array	alignment_strings ()

protected Array	_ensembl_alignment_strings ()

public A	get_SimpleAlign ()

protected A	_ensembl_SimpleAlign ()

public Listref	get_all_Attributes ()

public void	add_Attributes ()

public Bio::EnsEMBL::DnaDnaAlignFeature	transfer ()

Public Member Functions inherited from Bio::EnsEMBL::BaseAlignFeature
public Bio::EnsEMBL::BaseAlignFeature	new ()

public String	cigar_string ()

public String	align_type ()

public Int	alignment_length ()

protected Int	_ensembl_cigar_alignment_length ()

public List	ungapped_features ()

public Int	strands_reversed ()

public void	reverse_complement ()

protected void	_ensembl_reverse_complement ()

public Bio::EnsEMBL::BaseAlignFeature	transform ()

protected List	_parse_ensembl_cigar ()

protected	_parse_cigar ()

protected void	_parse_features ()

protected	_parse_ensembl_features ()

protected Int	_hit_unit ()

protected Int	_query_unit ()

protected Int	_mdtag_alignment_length ()

protected Array	_get_mdz_chunks ()

protected Array	_get_mdz_alignment_length ()

protected String	_get_mdz_chunk_type ()

protected Array	_mdz_alignment_string ()

Public Member Functions inherited from Bio::EnsEMBL::FeaturePair
public Bio::EnsEMBL::FeaturePair	new ()

public String	hseqname ()

public Int	hstart ()

public Int	hend ()

public	hstrand ()

public Bio::EnsEMBL::Slice	hslice ()

public String	hseq_region_name ()

public Boolean	hseq_region_strand ()

public Int	hseq_region_start ()

public Int	hseq_region_end ()

public Float	score ()

public Float	percent_id ()

public String	species ()

public String	hspecies ()

public String	coverage ()

public String	hcoverage ()

public String	external_db_id ()

public String	db_name ()

public String	db_display_name ()

public Float	p_value ()

public String	hdescription ()

public String	display_id ()

public Int	identical_matches ()

public Int	positive_matches ()

public Int	group_id ()

public Int	level_id ()

public void	invert ()

public	extra_data ()

public	type ()

Public Member Functions inherited from Bio::EnsEMBL::Feature
public Bio::EnsEMBL::Feature	new ()

public Int	start ()

public Int	end ()

public Int	strand ()

public void	move ()

public Int	length ()

public Bio::EnsEMBL::Analysis	analysis ()

public Bio::EnsEMBL::Slice	slice ()

public Boolean Or Undef	equals ()

public Bio::EnsEMBL::Feature	transform ()

public Bio::EnsEMBL::Feature	transfer ()

public Listref	project_to_slice ()

public Listref	project ()

public String	seqname ()

public String	display_id ()

public String	version ()

public Bio::EnsEMBL::Slice	feature_Slice ()

public String	seq_region_name ()

public Int	seq_region_length ()

public Boolean	seq_region_strand ()

public Int	seq_region_start ()

public Int	seq_region_end ()

public String	coord_system_name ()

public String	seq ()

public Listref	get_all_alt_locations ()

public Boolean	overlaps ()

public Boolean	overlaps_local ()

public List	get_overlapping_Genes ()

public Bio::EnsEMBL::Gene	get_nearest_Gene ()

public String	feature_so_acc ()

public String	feature_so_term ()

public Hashref	summary_as_hash ()

public String	species ()

public	sub_SeqFeature ()

public	add_sub_SeqFeature ()

public	flush_sub_SeqFeature ()

Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()

public Instance	new_fast ()

public Int	dbID ()

public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()

public Boolean	is_stored ()

public	get_all_DAS_Features ()

Detailed Description

Synopsis

See BaseAlignFeature

Definition at line 15 of file DnaDnaAlignFeature.pm.

Member Function Documentation

◆ _ensembl_alignment_strings()

protected Array Bio::EnsEMBL::DnaDnaAlignFeature::_ensembl_alignment_strings ( )

  Arg [1]    : list of string $flags
  Description: Allows to rebuild the alignment string of both the seq and hseq sequence
               using the cigar_string information for ensembl cigar strings
  Returntype : array reference containing 2 strings
               the first corresponds to seq
               the second corresponds to hseq
  Exceptions :
  Caller     :
  Status     : Stable

Code:

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◆ _ensembl_SimpleAlign()

protected A Bio::EnsEMBL::DnaDnaAlignFeature::_ensembl_SimpleAlign ( )

  Arg [1]    : list of string $flags
  Description: Internal method to build alignment string
               for ensembl type cigar strings
               using the cigar_string information and the slice and hslice objects
  Returntype : a Bio::SimpleAlign object
  Exceptions :
  Caller     :
  Status     : Stable

Code:

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◆ _hit_unit()

protected Int Bio::EnsEMBL::DnaDnaAlignFeature::_hit_unit ( )

  Arg [1]    : none
  Description: PRIVATE implementation of abstract superclass method.  Returns
               1 as the 'unit' used for the hit sequence. 
  Returntype : int
  Exceptions : none
  Caller     : Bio::EnsEMBL::BaseAlignFeature
  Status     : Stable

Code:

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◆ _query_unit()

protected Int Bio::EnsEMBL::DnaDnaAlignFeature::_query_unit ( )

  Arg [1]    : none
  Description: PRIVATE implementation of abstract superclass method Returns
               1 as the 'unit' used for the hit sequence.
  Returntype : int
  Exceptions : none
  Caller     : Bio::EnsEMBL::BaseAlignFeature
  Status     : Stable

Code:

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◆ add_Attributes()

public void Bio::EnsEMBL::DnaDnaAlignFeature::add_Attributes ( )

  Arg [1-N]  : list of Bio::EnsEMBL::Attribute's @attribs
               Attribute(s) to add
  Example    :

my $attrib = Bio::EnsEMBL::Attribute->new(...);

$gene->add_Attributes($attrib);

  Description: Adds an Attribute to the feature.
  Returntype : none
  Exceptions : throw on incorrect arguments
  Caller     : general
  Status     : Stable

Code:

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◆ alignment_strings()

public Array Bio::EnsEMBL::DnaDnaAlignFeature::alignment_strings ( )

  Arg [1]    : list of string $flags
               FIX_SEQ = does not introduce gaps (dashes) in seq aligned sequence
                         and delete the corresponding insertions in hseq aligned sequence
               FIX_HSEQ = does not introduce gaps (dashes) in hseq aligned sequence
                         and delete the corresponding insertions in seq aligned sequence
               NO_SEQ = return the seq aligned sequence as an empty string
               NO_HSEQ = return the hseq aligned sequence as an empty string
               This 2 last flags would save a bit of time as doing so no querying to the core
               database in done to get the sequence.
  Example    :

$daf->alignment_strings or
              $daf->alignment_strings("FIX_HSEQ") or
              $daf->alignment_strings("NO_SEQ","FIX_SEQ")

  Description: Allows to rebuild the alignment string of both the seq and hseq sequence
               using the cigar_string information and the slice and hslice objects
  Returntype : array reference containing 2 strings
               the first corresponds to seq
               the second corresponds to hseq
  Exceptions : 
  Caller     : 
  Status     : Stable

Code:

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◆ get_all_Attributes()

public Listref Bio::EnsEMBL::DnaDnaAlignFeature::get_all_Attributes ( )

  Arg [1]    : (optional) String $attrib_code
               The code of the attribute type to retrieve values for
  Example    :

my ($description) = @{ $feature->get_all_Attributes('description') };

my @attributes = @{ $feature->get_all_Attributes };

  Description: Gets a list of Attributes of this gene.
               Optionally just get Attributes for given code.
  Returntype : Listref of Bio::EnsEMBL::Attribute
  Exceptions : 
  Caller     : general
  Status     : Stable

Code:

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◆ get_SimpleAlign()

public A Bio::EnsEMBL::DnaDnaAlignFeature::get_SimpleAlign ( )

  Arg [1]    : list of string $flags
               translated = by default, the sequence alignment will be on nucleotide. With translated flag
                            the aligned sequences are translated.
               uc = by default aligned sequences are given in lower cases. With uc flag, the aligned 
                    sequences are given in upper cases.
  Example    :

$daf->get_SimpleAlign or
              $daf->get_SimpleAlign("translated") or
              $daf->get_SimpleAlign("translated","uc")

  Description: Allows to rebuild the alignment string of both the seq and hseq sequence
               using the cigar_string information and the slice and hslice objects
  Returntype : a Bio::SimpleAlign object
  Exceptions : 
  Caller     : 
  Status     : Stable

Code:

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◆ new()

public Bio::EnsEMBL::DnaDnaAlignFeature Bio::EnsEMBL::DnaDnaAlignFeature::new ( )

  Arg [..]   : List of named arguments. defined
               in this constructor, others defined in BaseFeaturePair and 
               SeqFeature superclasses.  
  Example    :

$daf = new DnaDnaAlignFeature(-cigar_string => '3M3I12M');

  Description: Creates a new DnaDnaAlignFeature using either a cigarstring or
               a list of ungapped features.  
  Returntype : Bio::EnsEMBL::DnaDnaAlignFeature
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ restrict_between_positions()

public Bio::EnsEMBL::DnaDnaAlignFeature Bio::EnsEMBL::DnaDnaAlignFeature::restrict_between_positions ( )

  Arg [1]    : int $start
  Arg [2]    : int $end
  Arg [3]    : string $flags
               SEQ = $start and $end apply to the seq sequence
                     i.e. start and end methods
               HSEQ = $start and $end apply to the hseq sequence
                      i.e. hstart and hend methods
  Example    :

$daf->restrict_between_positions(150,543,"SEQ")

  Description: Build a new DnaDnaAlignFeature object that fits within
               the new specified coordinates and sequence reference, cutting
               any pieces hanging upstream and downstream.
  Returntype : Bio::EnsEMBL::DnaDnaAlignFeature object
  Exceptions : 
  Caller     : 
  Status     : Stable

Code:

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sub restrict_between_positions {
  my ($self,$start,$end,$seqref) = @_;
 
  unless (defined $start && $start =~ /^\d+$/) {
    $self->throw("The first argument is not defined or is not an integer");
  }
  unless (defined $end && $end =~ /^\d+$/) {
    $self->throw("The second argument is not defined or is not an integer");
  }
  unless (defined $seqref &&
          ($seqref eq "SEQ" || $seqref eq "HSEQ")) {
    $self->throw("The third argument is not defined or is not equal to 'SEQ' or 'HSEQ'");
  }
 
# symbolic method references should be forbidden!
# need to be rewrite at some stage.
 
  my ($start_method1,$end_method1,$strand_method1,$start_method2,$end_method2,$strand_method2) =
    qw(start end strand hstart hend hstrand);
 
  if ($seqref eq "HSEQ") {
    ($start_method1,$end_method1,$strand_method1,$start_method2,$end_method2,$strand_method2) =
    qw(hstart hend hstrand start end strand);
  }
 
  my @restricted_features;
 
  foreach my $ungapped_feature ($self->ungapped_features) {
 
    if ($ungapped_feature->$start_method1() > $end ||
        $ungapped_feature->$end_method1() < $start) {
 
      next;
 
    } elsif ($ungapped_feature->$end_method1() <= $end &&
             $ungapped_feature->$start_method1() >= $start) {
 
      push @restricted_features, $ungapped_feature;
 
    } else {
 
      if ($ungapped_feature->$strand_method1() eq $ungapped_feature->$strand_method2()) {
 
        if ($ungapped_feature->$start_method1() < $start) {
 
          my $offset = $start - $ungapped_feature->$start_method1();
          $ungapped_feature->$start_method1($start);
          $ungapped_feature->$start_method2($ungapped_feature->$start_method2() + $offset);
 
        }
        if ($ungapped_feature->$end_method1() > $end) {
 
          my $offset = $ungapped_feature->$end_method1() - $end;
          $ungapped_feature->$end_method1($end);
          $ungapped_feature->$end_method2($ungapped_feature->$end_method2() - $offset);
 
        }
      } else {
 
        if ($ungapped_feature->$start_method1() < $start) {
 
          my $offset = $start - $ungapped_feature->$start_method1();
          $ungapped_feature->$start_method1($start);
          $ungapped_feature->$end_method2($ungapped_feature->$end_method2() - $offset);
 
        }
        if ($ungapped_feature->$end_method1() > $end) {
 
          my $offset = $ungapped_feature->$end_method1() - $end;
          $ungapped_feature->$end_method1($end);
          $ungapped_feature->$start_method2($ungapped_feature->$start_method2() + $offset);
 
        }
      }
      
      push @restricted_features, $ungapped_feature;
    }
  }
 
  if (scalar @restricted_features) {
    my $DnaDnaAlignFeature = new Bio::EnsEMBL::DnaDnaAlignFeature('-features' =>\@restricted_features);
    if (defined $self->slice) {
      $DnaDnaAlignFeature->slice($self->slice);
    }
    if (defined $self->hslice) {
      $DnaDnaAlignFeature->hslice($self->hslice);
    }
    return $DnaDnaAlignFeature;
  } else {
    return undef;
  }
}

◆ transfer()

public Bio::EnsEMBL::DnaDnaAlignFeature Bio::EnsEMBL::DnaDnaAlignFeature::transfer ( )

  Arg [1]    : Bio::EnsEMBL::Slice $destination_slice
  Example    :

my $new_feature = $feature->transfer($slice);

  Description: Moves this feature to given target slice coordinates.
               Returns a new feature.
  Returntype : Bio::EnsEMBL::DnaDnaAlignFeature
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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

ensembl/modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm

Public Member Functions

Detailed Description

Synopsis

Member Function Documentation

◆ _ensembl_alignment_strings()

◆ _ensembl_SimpleAlign()

◆ _hit_unit()

◆ _query_unit()

◆ add_Attributes()

◆ alignment_strings()

◆ get_all_Attributes()

◆ get_SimpleAlign()

◆ new()

◆ restrict_between_positions()

◆ transfer()