Inheritance diagram for Bio::EnsEMBL::PepDnaAlignFeature:

Class Summary

Synopsis

  See BaseAlignFeature

Definition at line 10 of file PepDnaAlignFeature.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	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::PepDnaAlignFeature::_hit_unit ( )

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

Code:

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Reimplemented from Bio::EnsEMBL::BaseAlignFeature.

protected List Bio::EnsEMBL::BaseAlignFeature::_parse_cigar ( ) [inherited]

  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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sub _parse_cigar {
  my ( $self ) = @_;

  my $query_unit = $self->_query_unit();
  my $hit_unit = $self->_hit_unit();

  my $string = $self->{'cigar_string'};

  throw("No cigar string defined in object") if(!defined($string));

  my @pieces = ( $string =~ /(\d*[MDI])/g );
  #print "cigar: ",join ( ",", @pieces ),"\n";

  my @features;
  my $strand1 = $self->{'strand'} || 1;
  my $strand2 = $self->{'hstrand'}|| 1;

  my ( $start1, $start2 );

  if( $strand1 == 1 ) {
    $start1 = $self->{'start'};
  } else {
    $start1 = $self->{'end'};
  }

  if( $strand2 == 1 ) {
    $start2 = $self->{'hstart'};
  } else {
    $start2 = $self->{'hend'};
  }

  #
  # Construct ungapped blocks as FeaturePairs objects for each MATCH
  #
  foreach my $piece (@pieces) {

    my ($length) = ( $piece =~ /^(\d*)/ );
    if( $length eq "" ) { $length = 1 }
    my $mapped_length;

    # explicit if statements to avoid rounding problems
    # and make sure we have sane coordinate systems
    if( $query_unit == 1 && $hit_unit == 3 ) {
      $mapped_length = $length*3;
    } elsif( $query_unit == 3 && $hit_unit == 1 ) {
      $mapped_length = $length / 3;
    } elsif ( $query_unit == 1 && $hit_unit == 1 ) {
      $mapped_length = $length;
    } else {
      throw("Internal error $query_unit $hit_unit, currently only " .
            "allowing 1 or 3 ");
    }

    if( int($mapped_length) != $mapped_length and
        ($piece =~ /M$/ or $piece =~ /D$/)) {
      throw("Internal error with mismapped length of hit, query " .
            "$query_unit, hit $hit_unit, length $length");
    }

    if( $piece =~ /M$/ ) {
      #
      # MATCH
      #
      my ( $qstart, $qend);
      if( $strand1 == 1 ) {
        $qstart = $start1;
        $qend = $start1 + $length - 1;
        $start1 = $qend + 1;
      } else {
        $qend = $start1;
        $qstart = $start1 - $length + 1;
        $start1 = $qstart - 1;
      }

      my ($hstart, $hend);
      if( $strand2 == 1 ) {
        $hstart = $start2;
        $hend = $start2 + $mapped_length - 1;
        $start2 = $hend + 1;
      } else {
        $hend = $start2;
        $hstart = $start2 - $mapped_length + 1;
        $start2 = $hstart - 1;
      }


      push @features, Bio::EnsEMBL::FeaturePair->new
        (-SLICE      => $self->{'slice'},
         -SEQNAME   => $self->{'seqname'},
         -START      => $qstart,
         -END        => $qend,
         -STRAND     => $strand1,
         -HSLICE      => $self->{'hslice'},
         -HSEQNAME   => $self->{'hseqname'},
         -HSTART     => $hstart,
         -HEND       => $hend,
         -HSTRAND    => $strand2,
         -SCORE      => $self->{'score'},
         -PERCENT_ID => $self->{'percent_id'},
         -ANALYSIS   => $self->{'analysis'},
         -P_VALUE    => $self->{'p_value'},
         -EXTERNAL_DB_ID => $self->{'external_db_id'}, 
         -HCOVERAGE   => $self->{'hcoverage'},
         -GROUP_ID    => $self->{'group_id'},
         -LEVEL_ID    => $self->{'level_id'});
      

      # end M cigar bits 
    } elsif( $piece =~ /I$/ ) {
      #
      # INSERT
      #
      if( $strand1 == 1 ) {
        $start1 += $length;
      } else {
        $start1 -= $length;
      }
    } elsif( $piece =~ /D$/ ) {
      #
      # DELETION
      #
      if( $strand2 == 1 ) {
        $start2 += $mapped_length;
      } else {
        $start2 -= $mapped_length;
      }
    } else {
      throw( "Illegal cigar line $string!" );
    }
  }

  return \@features;
}

protected void Bio::EnsEMBL::BaseAlignFeature::_parse_features ( ) [inherited]

  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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sub _parse_features {
  my ($self,$features ) = @_;

  my $query_unit = $self->_query_unit();
  my $hit_unit = $self->_hit_unit();

  if (ref($features) ne "ARRAY") {
    throw("features must be an array reference not a [".ref($features)."]");
  }

  my $strand  = $features->[0]->strand;

  throw ('FeaturePair needs to have strand == 1 or strand == -1') if(!$strand);

  my @f;

  #
  # Sort the features on their start position
  # Ascending order on positive strand, descending on negative strand
  #
  if( $strand == 1 ) {
    @f = sort {$a->start <=> $b->start} @$features;
  } else {
    @f = sort { $b->start <=> $a->start} @$features;
  }

  my $hstrand     = $f[0]->hstrand;
  my $slice       = $f[0]->slice();
  my $hslice       = $f[0]->hslice();
  my $name        = $slice->name() if($slice);
  my $hname       = $f[0]->hseqname;
  my $score       = $f[0]->score;
  my $percent     = $f[0]->percent_id;
  my $analysis    = $f[0]->analysis;
  my $pvalue      = $f[0]->p_value();
  my $external_db_id = $f[0]->external_db_id;
  my $hcoverage   = $f[0]->hcoverage;
  my $group_id    = $f[0]->group_id;
  my $level_id    = $f[0]->level_id;

  my $seqname = $f[0]->seqname;
  # implicit strand 1 for peptide sequences
  $strand  ||= 1;
  $hstrand ||= 1;
  my $ori = $strand * $hstrand;

  throw("No features in the array to parse") if(scalar(@f) == 0);

  my $prev1; # where last feature q part ended
  my $prev2; # where last feature s part ended

  my $string;

  # Use strandedness info of query and hit to make sure both sets of 
  # start and end  coordinates are oriented the right way around.
  my $f1start;
  my $f1end;
  my $f2end;
  my $f2start;

  if ($strand == 1) {
    $f1start = $f[0]->start;
    $f1end = $f[-1]->end;
  } else {
    $f1start = $f[-1]->start;
    $f1end = $f[0]->end;
  }

  if ($hstrand == 1) {
    $f2start = $f[0]->hstart;
    $f2end = $f[-1]->hend;
  } else {
    $f2start = $f[-1]->hstart;
    $f2end = $f[0]->hend;
  }

  #
  # Loop through each portion of alignment and construct cigar string
  #

  foreach my $f (@f) {
    #
    # Sanity checks
    #

    if (!$f->isa("Bio::EnsEMBL::FeaturePair")) {
      throw("Array element [$f] is not a Bio::EnsEMBL::FeaturePair");
    }
    if( defined($f->hstrand()) && $f->hstrand() != $hstrand ) {
      throw("Inconsistent hstrands in feature array");
    }
    if( defined($f->strand()) && ($f->strand != $strand)) {
      throw("Inconsistent strands in feature array");
    }
    if ( defined($name) && $name ne $f->slice->name()) {
      throw("Inconsistent names in feature array [$name - ".
            $f->slice->name()."]");
    }
    if ( defined($hname) && $hname ne $f->hseqname) {
      throw("Inconsistent hit names in feature array [$hname - ".
            $f->hseqname . "]");
    }
    if ( defined($score) && $score ne $f->score) {
      throw("Inconsisent scores in feature array [$score - " .
            $f->score . "]");
    }
    if (defined($f->percent_id) && $percent ne $f->percent_id) {
      throw("Inconsistent pids in feature array [$percent - " .
            $f->percent_id . "]");
    }
    if(defined($pvalue) && $pvalue != $f->p_value()) {
      throw("Inconsistant p_values in feature arraw [$pvalue " .
            $f->p_value() . "]");
    }
    if($seqname && $seqname ne $f->seqname){
      throw("Inconsistent seqname in feature array [$seqname - ".
            $f->seqname . "]");
    }
    my $start1 = $f->start;      #source sequence alignment start
    my $start2 = $f->hstart();   #hit sequence alignment start

    #
    # More sanity checking
    #
    if (defined($prev1)) {
      if ( $strand == 1 ) {
        if ($f->start < $prev1) {
          throw("Inconsistent coords in feature array (forward strand).\n" .
               "Start [".$f->start()."] in current feature should be greater " .
           "than previous feature end [$prev1].");
        }
      } else {
        if ($f->end > $prev1) {
          throw("Inconsistent coords in feature array (reverse strand).\n" .
                "End [".$f->end() ."] should be less than previous feature " .
                "start [$prev1].");
        }
      }
    }

    my $length = ($f->end - $f->start + 1);    #length of source seq alignment
    my $hlength = ($f->hend - $f->hstart + 1); #length of hit seq alignment

    # using multiplication to avoid rounding errors, hence the
    # switch from query to hit for the ratios

    #
    # Yet more sanity checking
    #
    if($query_unit > $hit_unit){
      # I am going to make the assumption here that this situation will 
      # only occur with DnaPepAlignFeatures, this may not be true
      my $query_p_length = sprintf "%.0f", ($length/$query_unit);
      my $hit_p_length = sprintf "%.0f", ($hlength * $hit_unit);
      if( $query_p_length != $hit_p_length) {
        throw( "Feature lengths not comparable Lengths:" .$length .
               " " . $hlength . " Ratios:" . $query_unit . " " .
               $hit_unit );
      }
    } else{
      my $query_d_length = sprintf "%.0f", ($length*$hit_unit);
      my $hit_d_length = sprintf "%.0f", ($hlength * $query_unit);
      if( $length * $hit_unit != $hlength * $query_unit ) {
        throw( "Feature lengths not comparable Lengths:" . $length .
               " " . $hlength . " Ratios:" . $query_unit . " " .
               $hit_unit );
      }
    }

    my $hlengthfactor = ($query_unit/$hit_unit);

    #
    # Check to see if there is an I type (insertion) gap:
    #   If there is a space between the end of the last source sequence 
    #   alignment and the start of this one, then this is an insertion
    #

    my $insertion_flag = 0;
    if( $strand == 1 ) {
      if( ( defined $prev1 ) && ( $f->start > $prev1 + 1  )) {

        #there is an insertion
        $insertion_flag = 1;
        my $gap = $f->start - $prev1 - 1;
        if( $gap == 1 ) {
          $gap = ""; # no need for a number if gap length is 1
        }
        $string .= "$gap"."I";

      }

      #shift our position in the source seq alignment
      $prev1 = $f->end();
    } else {

      if(( defined $prev1 ) && ($f->end + 1 < $prev1 )) {

        #there is an insertion
        $insertion_flag = 1;
        my $gap = $prev1 - $f->end() - 1;
        if( $gap == 1 ) {
          $gap = ""; # no need for a number if gap length is 1
        }
        $string .= "$gap"."I";
      }

      #shift our position in the source seq alignment
      $prev1 = $f->start();
    }

    #
    # Check to see if there is a D type (deletion) gap
    #   There is a deletion gap if there is a space between the end of the
    #   last portion of the hit sequence alignment and this one
    #
    if( $hstrand == 1 ) {
      if((  defined $prev2 ) && ( $f->hstart() > $prev2 + 1 )) {

        #there is a deletion
        my $gap = $f->hstart - $prev2 - 1;
        my $gap2 = int( $gap * $hlengthfactor + 0.5 );
    
        if( $gap2 == 1 ) {
          $gap2 = "";  # no need for a number if gap length is 1
        }
        $string .= "$gap2"."D";

        #sanity check,  Should not be an insertion and deletion
        if($insertion_flag) {
          if ($message_only_once) {
            warning("Should not be an deletion and insertion on the " .
                    "same alignment region. cigar_line=$string\n");
            $message_only_once = 0;
          }
        }
      }
      #shift our position in the hit seq alignment
      $prev2 = $f->hend();

     } else {
      if( ( defined $prev2 ) && ( $f->hend() + 1 < $prev2 )) {

        #there is a deletion
        my $gap = $prev2 - $f->hend - 1;
        my $gap2 = int( $gap * $hlengthfactor + 0.5 );
    
        if( $gap2 == 1 ) {
          $gap2 = "";  # no need for a number if gap length is 1
        }
        $string .= "$gap2"."D";

        #sanity check,  Should not be an insertion and deletion
        if($insertion_flag) {
          if ($message_only_once) {
            warning("Should not be an deletion and insertion on the " .
                    "same alignment region. prev2 = $prev2; f->hend() = " .
                    $f->hend() . "; cigar_line = $string;\n");
            $message_only_once = 0;
          }
        }
      }
      #shift our position in the hit seq alignment
      $prev2 = $f->hstart();
    }

    my $matchlength = $f->end() - $f->start() + 1;
    if( $matchlength == 1 ) {
      $matchlength = "";
    }
    $string .= $matchlength."M";
  }

  $self->{'start'}      = $f1start;
  $self->{'end'}        = $f1end;
  $self->{'seqname'}    = $seqname;
  $self->{'strand'}     = $strand;
  $self->{'score'}      = $score;
  $self->{'percent_id'} = $percent;
  $self->{'analysis'}   = $analysis;
  $self->{'slice'}      = $slice;
  $self->{'hslice'}     = $hslice;
  $self->{'hstart'}     = $f2start;
  $self->{'hend'}       = $f2end;
  $self->{'hstrand'}    = $hstrand;
  $self->{'hseqname'}   = $hname;
  $self->{'cigar_string'} = $string;
  $self->{'p_value'}      = $pvalue;
  $self->{'external_db_id'} = $external_db_id; 
  $self->{'hcoverage'}    = $hcoverage; 
  $self->{'group_id'}     = $group_id;
  $self->{'level_id'}     = $level_id;
}

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

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

Code:

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Reimplemented from Bio::EnsEMBL::BaseAlignFeature.

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

Code:

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

Undocumented method

Code:

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public Int Bio::EnsEMBL::BaseAlignFeature::alignment_length ( ) [inherited]

  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 ( ) [inherited]

  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

Code:

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

Undocumented method

Code:

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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

Code:

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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

Code:

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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

Code:

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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

Code:

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

  Description:
Deprecated:
use start(), end(), strand(), slice(), etc.
               methods instead

Code:

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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

Code:

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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

Code:

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sub get_all_alt_locations {
  my $self = shift;
  my $return_all = shift || 0;

  my $slice = $self->{'slice'} or return [];
  my $sa = $slice->adaptor() or return [];

  # get slice of entire region
  $slice = $sa->fetch_by_seq_region_id($slice->get_seq_region_id);

  my $axfa = $sa->db->get_AssemblyExceptionFeatureAdaptor();
  my $axfs = $axfa->fetch_all_by_Slice($slice);

  my (@haps, @alt);

  foreach my $axf (@$axfs) {
    if(uc($axf->type()) eq 'HAP') {
      push @haps, $axf;
    } elsif(uc($axf->type()) =~ 'PAR') {
      push @alt, $axf;
    } elsif( $axf->type() eq "PATCH_FIX"){
      push @haps, $axf;
    } elsif( $axf->type() eq "PATCH_FIX REF"){
      push @haps, $axf  if $return_all > 0 ;
    } elsif( $axf->type() eq "HAP REF" ) {
      push @haps, $axf if $return_all > 0 ;
      # do nothing when you are on REF
    } elsif( $axf->type() eq "PATCH_NOVEL"){
      push @haps, $axf;
    }elsif( $axf->type() eq "PATCH_NOVEL REF"){
      push @haps, $axf  if $return_all > 0 ;
    } else {
      warning("Unknown exception feature type ". $axf->type()."- ignoring.");
    }
  }

  # regions surrounding hap are those of interest, not hap itself
  # convert hap alt. exc. features to regions around haps instead
  foreach my $h (@haps) {
    my $haslice = $h->alternate_slice();
    my $hacs    = $haslice->coord_system();

    if($h->start() > 1 && $haslice->start() > 1) {
      my $aslice = $sa->fetch_by_region($hacs->name(),
                                        $haslice->seq_region_name(),
                                        1,
                                        $haslice->start()-1,
                                        $haslice->strand(),
                                        $hacs->version());

      push @alt, Bio::EnsEMBL::AssemblyExceptionFeature->new
        (-start  => 1,
         -end    => $h->start()-1,
         -alternate_slice => $aslice);
    }

    if($h->end() < $slice->seq_region_length() &&
       $haslice->end < $haslice->seq_region_length()) {
      my $aslice = $sa->fetch_by_region($hacs->name(),
                                        $haslice->seq_region_name(),
                                        $haslice->end()+1,
                                        $haslice->seq_region_length(),
                                        $haslice->strand(),
                                        $hacs->version());

      push @alt, Bio::EnsEMBL::AssemblyExceptionFeature->new
        (-start  => $h->end() + 1,
         -end    => $slice->seq_region_length(),
         -alternate_slice => $aslice);
    }
  }


  # check if exception regions contain our feature

  my @features;

  foreach my $axf (@alt) {
    # ignore other region if feature is not entirely on it
    next if($self->seq_region_start() < $axf->start() ||
            $self->seq_region_end()   > $axf->end());

    # quick shallow copy of the feature
    my $f;
    %$f = %$self;
    bless $f, ref($self);

    my $aslice = $axf->alternate_slice();

    # position feature on entire slice of other region
    $f->{'start'}  = $f->seq_region_start() - $axf->start() + $aslice->start();
    $f->{'end'}    = $f->seq_region_end()   - $axf->start() + $aslice->start();
    $f->{'strand'} *= $aslice->strand();

    $f->{'slice'} = $sa->fetch_by_seq_region_id($aslice->get_seq_region_id());

    push @features, $f;
  }

  return \@features;
}

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

Code:

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

Description:

Deprecated:: do not use

Code:

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

Description:

Deprecated:: do not use

Code:

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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

Code:

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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

Code:

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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

Code:

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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

Code:

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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

Code:

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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

Code:

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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

Code:

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

Undocumented method

Code:

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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

Code:

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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)

Code:

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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

Code:

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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

Code:

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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 ( ) [inherited]

  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 ( ) [inherited]

  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 ( ) [inherited]

  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 ( ) [inherited]

 
  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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sub transfer {
  my $self = shift;
  my $slice = shift;

  if(!$slice || !ref($slice) || (!$slice->isa('Bio::EnsEMBL::Slice') && !$slice->isa('Bio::EnsEMBL::LRGSlice'))) {
    throw('Slice argument is required');
  }

  #make a shallow copy of the feature to be transfered
  my $feature;
  %{$feature} = %{$self};
  bless $feature, ref($self);

  my $current_slice = $self->{'slice'};

  if(!$current_slice) {
    warning("Feature cannot be transfered without attached slice.");
    return undef;
  }

  my $cur_cs = $current_slice->coord_system();
  my $dest_cs = $slice->coord_system();

  #if we are not in the same coord system a transformation step is needed first
  if(!$dest_cs->equals($cur_cs)) {
    $feature = $feature->transform($dest_cs->name, $dest_cs->version, $slice);
    return undef if(!defined($feature));
    $current_slice = $feature->{'slice'};
  }

  # feature went to entirely different seq_region
  if($current_slice->seq_region_name() ne $slice->seq_region_name()) {
    return undef;
  }

  #if the current feature positions are not relative to the start of the
  #seq region, convert them so they are
  my $cur_slice_start  = $current_slice->start();
  my $cur_slice_strand = $current_slice->strand();
  if($cur_slice_start != 1 || $cur_slice_strand != 1) {
    my $fstart = $feature->{'start'};
    my $fend   = $feature->{'end'};

    if($cur_slice_strand == 1) {
      $feature->{'start'} = $fstart + $cur_slice_start - 1;
      $feature->{'end'}   = $fend   + $cur_slice_start - 1;
    } else {
      my $cur_slice_end = $current_slice->end();
      $feature->{'start'}  = $cur_slice_end - $fend   + 1;
      $feature->{'end'}    = $cur_slice_end - $fstart + 1;
      $feature->{'strand'} *= -1;
    }
  }

  my $fstart = $feature->{'start'};
  my $fend   = $feature->{'end'};

  #convert to destination slice coords
  if($slice->strand == 1) {
    $feature->{'start'} = $fstart - $slice->start() + 1;
    $feature->{'end'}   = $fend   - $slice->start() + 1;
  } else {
    $feature->{'start'} = $slice->end() - $fend   + 1;
    $feature->{'end'}   = $slice->end() - $fstart + 1;
    $feature->{'strand'} *= -1;
  }

  $feature->{'slice'} = $slice;

  return $feature;
}

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

public Bio::EnsEMBL::PepDnaAlignFeature::transform ( )

  Arg [1]    : none
  Example    : none
  Description: Overwrites Bio:EnsEMBL:Feature->transform as
               to give error message
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::BaseAlignFeature.

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

Undocumented method

Code:

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public List Bio::EnsEMBL::BaseAlignFeature::ungapped_features ( ) [inherited]

  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:

Bio/EnsEMBL/PepDnaAlignFeature.pm

Class Summary

Synopsis

Available Methods

Method Documentation