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text:
=head1 LICENSE

Copyright [1999-2013] Wellcome Trust Sanger Institute and the 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.

=cut

package Bio::EnsEMBL::GlyphSet::_alignment_pairwise;

use strict;

use base qw(Bio::EnsEMBL::GlyphSet);

use List::Util qw(min max);

# Useful for debugging. Should all be 0 in checked-in code.
my $debug_force_cigar   = 0; # CIGAR at all resolutions
my $debug_rainbow       = 0; # Joins in rainbow colours to tell them apart
my $debug_force_compact = 0; # render_normal -> render_compact
my $debug_force_text    = 0; # render_normal -> render_text

# Split CIGAR into array, used by cigar_string
sub _parse_cigar {
  my @out;
  while($_[0] =~ s/^(\d*)([A-Z])//) { push @out,[$1||1,$2]; }
  return \@out;
}

# Build CIGAR string from "match/gap" CIGARs in each GenomicAlign.
# (The one good thing we once got automatically from DnaAlignFeatures).
# Based on _convert_GenomicAlignBlocks_into_DnaDnaAlignFeatures, but
# implemented more efficiently.
sub cigar_string {
  my ($self,$gab) = @_;

  my @inputs = map { _parse_cigar($_) } (
    $gab->reference_genomic_align->cigar_line,
    $gab->get_all_non_reference_genomic_aligns->[0]->cigar_line
  );
  if($gab->reference_slice_strand < 0) {
    @inputs = map { [ reverse @$_ ] } @inputs;
  }
  my @out;
  while(@{$inputs[0]} and @{$inputs[1]}) {
    my $n = min(map { $_->[0][0] } @inputs);
    my $m = join("",map { ($_->[0][1] eq 'M')?'N':'-' } @inputs);
    $m = { NN => 'M', 'N-' => 'I', '-N' => 'D' }->{$m};
    return undef unless($m);
    push @out,[$n,$m];
    foreach my $in (@inputs) {
      shift @$in unless $in->[0][0] -= $n;
    }
  }
  return join("",map { (($_->[0]==1)?'':$_->[0]).$_->[1] } @out);
}

# Calculates glyphs, -- an array of what needs to be drawn -- from a
# CIGAR string. Can then be passed to draw_cigar_glyphs (or otherwise).
sub calc_cigar_glyphs {
  my ($self,$start,$length,$cigar,$reverse,$flip_tags) = @_;

  my $start_pos = $start - 1;

  my @cigar = @{_parse_cigar($cigar)};
  @cigar = reverse @cigar if($reverse);
  my @positions;
  my $tcount = ($flip_tags?scalar(@cigar)+1:0);
  foreach (@cigar) {
    my ($num,$type) = @$_;
    $tcount += ($flip_tags?-1:1);
    my $end_pos = $start_pos;
    $end_pos += $num unless $type eq 'D';
    if($end_pos<0 or $start_pos>$length) { $start_pos = $end_pos; next; }
    my $num = $end_pos - $start_pos;
    $num += $start_pos if $start_pos<0;               # choped off start
    $num -= $end_pos - $length if $end_pos > $length; # chopped off end
    push @positions,[$type,max($start_pos,0),$num,$tcount];
    $start_pos = $end_pos;
  }
  return \@positions;
}

# Common rectangle-drawing routine
sub draw_rect {
  my ($self,$params,$start,$length,$colour) = @_;

  return $self->Rect({
    x      => $start,
    y      => $params->{'y'} || 0,
    width  => $length,
    height => $params->{'h'},
    colour => $params->{$colour || 'feature_colour'},
  });
}

# Draws CIGAR glyphs as previously calculated by calc_cigar_glyphs.
# Returns a hash of boxes created against their "ID", -- ie position in the
# CIGAR string, -- to allow joins, etc.
sub draw_cigar_glyphs {
  my ($self,$glyphs,$composite,$params) = @_;

  my $index = 0;
  my %boxes;

  # Draw matches
  foreach (@$glyphs) {
    my ($type,$start,$length,$id) = @$_;

    if($type =~ /[MmU=X]/) {
      my $box = $self->draw_rect($params,$start,$length);
      $composite->push($box);
      $boxes{$id} = $box;
    }
  }

  # Reloop to ensure on top of matches
  foreach (@$glyphs) {
    my ($type,$start,$length,$id) = @$_;
    next unless $type eq 'D';
    $composite->push($self->draw_rect($params,$start,0,'delete_colour'));
  }

  return \%boxes;
}

# Combine calc_cigar_glyphs and draw_cigar_glyphs to draw a cigar
sub draw_cigar {
  my ($self,$params,$args,$composite,$gab,$joins) = @_;

  my $glyphs = $self->calc_cigar_glyphs(
    $gab->reference_slice_start,
    $gab->reference_slice->length,
    $self->cigar_string($gab),
    $gab->reference_slice_strand == -1,
    $self->should_draw_cross($gab) && $self->strand==1 # flip tag names
  );
  my $boxes = $self->draw_cigar_glyphs($glyphs,$composite,$params);
  if($params->{'link'}) {
    foreach my $id (keys %$boxes) {
      $joins->{join(":",@{$args->{'tag'}},$id)} = { x => $args->{'drawx'}, box => $boxes->{$id} };
    }
  }
  my $gab_nr = $gab->get_all_non_reference_genomic_aligns->[0];
  my $ori = $gab_nr->dnafrag_strand>0 ? 'Forward' : 'Reverse';
}

# Draw a single, regular, non-CIGAR box
sub draw_non_cigar {
  my ($self,$params,$args,$gab,$joins,$zm) = @_;

  my ($x,$width,$ori,$r,$r1) = $self->calculate_region($gab);
  my $box = $self->draw_rect($params,$x,$width);
  $self->add_zmenu($zm,$box,$ori,$r,$r1);
  $self->push($box);
  if ($params->{'link'}) {
    $joins->{join(":",@{$args->{'tag'}})} = { x => $args->{'drawx'}, box => $box };
  }
  return $box;
}

# Draw green joining crosses and quadrilaterals
my @rainbow = qw(red orange yellow green cyan blue purple);
sub draw_joins {
  my ($self,$joins) = @_;

  my $part = ($self->strand == 1) || 0;
  my @shapes = (
    [[0,0],[0,1],[1,1],[1,0]], # circuit makes quadrilateral,
    [[0,0],[0,1],[1,0],[1,1]], # but zigzag makes cross
  );
  my $feature_key = lc $self->my_config('type');

  foreach my $tag (keys %$joins) {
    foreach my $s (@{$shapes[$joins->{$tag}{'x'}]}) {
      next unless $s->[0] == $part; # only half of it is on each track
      my $colour = $self->my_colour($feature_key, 'join') || 'gold';
      $colour = $rainbow[rand()*7] if($debug_rainbow);
      $self->join_tag($joins->{$tag}{'box'},$tag,{
        x => $s->[1],
        y => !$s->[0], # y start at bottom edge of upper block & vice versa
        z => $self->my_colour($feature_key, 'join_z') || 100,
        col => $colour,
        style => 'fill'
      });
    }
  }
}

# Should we draw a cross rather than a quadrilateral?
sub should_draw_cross {
  my ($self,$gab) = @_;

  my $this_ori  = $gab->reference_slice_strand;
  my $other_ori = $self->my_config('ori');
  my $nonref    = $gab->get_all_non_reference_genomic_aligns->[0];

  # flipdata -- alignment is interstrand
  # flipview -- views are in opposite orientations
  my $flipdata = ($gab->reference_slice_strand != $nonref->dnafrag_strand);
  my $flipview = (($this_ori == -1) xor ($other_ori == -1));
  return ($flipdata xor $flipview);
}

# Features are grouped and rendered together: make those groups
sub build_features_into_sorted_groups {
  my ($self,$gabs) = @_;

  my $container   = $self->{'container'};
  my $strand      = $self->strand;
  my $strand_flag = $self->my_config('strand');
  my $length      = $container->length;
  my $part = ($strand == 1) || 0;
  my %out;
  my $k = 0;
  foreach my $gab (@{$gabs||[]}) {
    my $start = $gab->reference_slice_start;
    my $end = $gab->reference_slice_end;
    my $nonref = $gab->get_all_non_reference_genomic_aligns->[0];
    my $hseqname = $nonref->dnafrag->name;

    my $flip = ( $gab->reference_slice_strand != $nonref->dnafrag_strand );
    next if $end < 1 || $start > $length;
    next if $strand_flag eq 'b' && ($flip xor !$part);
    my $key = $hseqname . ':' . ($gab->group_id || ('00' . $k++));
    push @{$out{$key}{'gabs'}},[$start,$gab];
  }
  # sort contents of groups by start
  foreach my $g (values %out) {
    my @f = map {$_->[1]} sort { $a->[0] <=> $b->[0] } @{$g->{'gabs'}};
    $g->{'len'} = max(map { $_->reference_slice_end   } @f) -
                  min(map { $_->reference_slice_start } @f);
    $g->{'gabs'} = \@f;
  }
  # Sort by length
  return
    map { $_->{'gabs'} } sort { $b->{'len'} <=> $a->{'len'} } values %out;
}

# Sort and exclude irrelevant features for compact display.
# Equivalent to build_features_into_sorted_groups, as used on normal.
sub get_compact_features {
  my ($self,$gabs) = @_;

  my $container   = $self->{'container'};
  my $length      = $container->length;
  my $strand_flag = $self->my_config('strand');
  my $strand      = $self->strand;
  my $part        = ($strand == 1) || 0;
  my @out;
  foreach my $gab (@$gabs) {
    my $start = $gab->reference_slice_start;
    my $end = $gab->reference_slice_end;
    my $nonref = $gab->get_all_non_reference_genomic_aligns->[0];
    my $flip = ( $gab->reference_slice_strand != $nonref->dnafrag_strand );
    next if $end < 1 || $start > $length;
    next if $strand_flag eq 'b' && ($flip xor $part);
    push @out,[$gab->reference_genomic_align->dnafrag_start,$gab];
  }
  return [ map { $_->[1] } sort { $a->[0] <=> $b->[0] } @out ];
}

# Draws out box of nets (hollow box)
sub draw_containing_box {
  my ($self,$gabs,$y_pos) = @_;

  my $ga_first = $gabs->[0];
  my $ga_last = $gabs->[-1];
  my $feature_key    = lc $self->my_config('type');
  my $h              = $self->get_parameter('opt_halfheight') ? 4 : 8;
  my $feature_colour = $self->my_colour($feature_key);
  my $container      = $self->{'container'};
  my $depth          = $self->depth || 6;
  my $length         = $container->length;
  my $ga_first_start = $ga_first->reference_slice_start;
  my $ga_last_end    = $ga_last->reference_slice_end;
  my $width = $ga_last_end;
  if ($width > $length) {
    $width = $length;
  }
  if ($ga_first_start > 0) {
    $width -= $ga_first_start - 1;
  }

  my $seqname = $ga_first->reference_genomic_align->dnafrag->name;
  my $start = $ga_first->reference_slice_start;
  my $end = $ga_first->reference_slice_end;
  my $abs_start = $ga_first->reference_slice->start + $start - 1;
  my $abs_end = $ga_first->reference_slice->start   + $end -1;
  my $n0 = "$seqname:$abs_start-$abs_end";

  my $net_composite = $self->Composite({
    x     => $ga_first_start > 1 ? $ga_first_start - 1 : 0,
    y     => $y_pos,
    width => $width,
    height => $h,
    bordercolour => $feature_colour,
    absolutey => 1,
  });
  return $net_composite;
}

# Makes the tricky n0,n1 parameters for ZMenu URLs
sub make_net_urls {
  my ($self,$gabs) = @_;

  my $ga_first = $gabs->[0];
  my $ga_first_nonref = $ga_first->get_all_non_reference_genomic_aligns->[0];
  # Determine extent of net on target
  my ($hs_net,$he_net);
  foreach my $gab (@$gabs) {
    my $nonref = $gab->get_all_non_reference_genomic_aligns->[0];
    my $hstart = $nonref->dnafrag->start + $nonref->dnafrag_start - 1;
    my $hend = $nonref->dnafrag->start + $nonref->dnafrag_end-1;
    $hs_net = $hstart if (!defined $hs_net) or $hstart < $hs_net;
    $he_net = $hend   if (!defined $he_net) or $hend   > $he_net;
  }
  my $seqname = $ga_first->reference_genomic_align->dnafrag->name;
  my $start = $ga_first->reference_slice_start;
  my $end = $ga_first->reference_slice_end;
  my $abs_start = $ga_first->reference_slice->start + $start - 1;
  my $abs_end = $ga_first->reference_slice->start   + $end -1;
  my $n0 = "$seqname:$abs_start-$abs_end";
  my $n1 = $ga_first_nonref->dnafrag->name. ":$hs_net-$he_net";

  return ($n0,$n1);
}

# Get orientation of GAB
sub get_ori {
  my ($self,$gab) = @_;

  my $nonref = $gab->get_all_non_reference_genomic_aligns->[0];
  return $nonref->dnafrag_strand > 0 ? 'Forward' : 'Reverse';
}

# calculate on-screen region
sub calculate_region {
  my ($self,$gab) = @_;

  my $nonref = $gab->get_all_non_reference_genomic_aligns->[0];
  my $chr = $gab->reference_slice->seq_region_name;
  my $hseqname = $nonref->dnafrag->name;
  my $ori = $self->get_ori($gab);

  # Start and end of image
  my $cstart    = $gab->reference_slice->start;
  my $cend      = $gab->reference_slice->end;

  # Start and end of ref block (inc off-screen)
  my $start2    = $cstart+$gab->reference_slice_start-1;
  my $end2      = $cstart+$gab->reference_slice_end-1;

  # Start and end of nonref block (inc off-screen)
  my $start_nr  = $nonref->dnafrag->start + $nonref->dnafrag_start - 1;
  my $end_nr    = $nonref->dnafrag->start + $nonref->dnafrag_end   - 1;

  # Drawn ref block start/end (ie only on-screen bit)
  my $dstart    = max($start2,$cstart);
  my $dend      = min($end2,$cend);

  # Drawn non-ref block start/end (ie only on-screen bit)
  my $dstart_nr = max($start_nr,$cstart);
  my $dend_nr   = min($end_nr,$cend);

  my $r  = sprintf("%s:%d-%d",$chr,$start2,$end2);
  my $r1 = sprintf("%s:%d-%d",$hseqname,$start_nr,$end_nr);

  return ($dstart-$cstart,$dend-$dstart+1,$ori,$r,$r1);
}

# Calculates y position from bumping considerations
sub calculate_ypos {
  my ($self,$ga_s) = @_;

  my $container      = $self->{'container'};
  my $pix_per_bp     = $self->scalex;
  my $length         = $container->length;
  my $strand      = $self->strand;
  my $depth          = $self->depth || 6;
  my $h              = $self->get_parameter('opt_halfheight') ? 4 : 8;
  my $ga_first = $ga_s->[0];
  my $ga_last = $ga_s->[-1];
  my $ga_first_start = $ga_first->reference_slice_start;
  my $ga_last_end    = $ga_last->reference_slice_end;
  my $bump_start = (($ga_first_start < 1 ? 1 : $ga_first_start) * $pix_per_bp) - 1; # start in pixels
  my $bump_end   = ($ga_last_end > $length ? $length : $ga_last_end) * $pix_per_bp; # end in pixels
  my $row        = $self->bump_row(int $bump_start, int $bump_end);
  my $y_pos = -$row * int(1.5 * $h) * $strand;
  return undef if $row > $depth;
  return $y_pos;
}

# Draws either a CIGAR or non-cigar line of boxes, as appropriate.
sub draw_boxes {
  my ($self,$net_composite,$ga_s,$y_pos,$zm) = @_;

  my $feature_key    = lc $self->my_config('type');
  my $pix_per_bp     = $self->scalex;
  my $draw_cigar     = $pix_per_bp > 0.2 || $debug_force_cigar;
  my $container      = $self->{'container'};
  my $length         = $container->length;

  my $params = {
    feature_colour => $self->my_colour($feature_key),
    delete_colour  => 'black',
    y              => $y_pos,
    h              => $self->get_parameter('opt_halfheight') ? 4 : 8,
    link           => $self->get_parameter('compara') ? $self->my_config('join') : 0,
  };
  my (%joins);

  foreach my $gab (@$ga_s) {
    my @tag = (
      $gab->reference_genomic_align->dbID(),
      $gab->get_all_non_reference_genomic_aligns->[0]->dbID()
    );
    @tag = reverse @tag if $self->strand == 1; # Flip on bottom of link
    my $args = {
      drawx => $self->should_draw_cross($gab),
      tag => \@tag,
    };
    if ($draw_cigar) {
      my $composite = $net_composite;
      unless(defined $composite) {
        my ($x,$width,$ori,$r,$r1) = $self->calculate_region($gab);
        $composite = $self->draw_containing_box([$gab],0);
        $self->add_zmenu($zm,$composite,$ori,$r,$r1);
        $self->push($composite);
      }
      $self->draw_cigar($params,$args,$composite,$gab,\%joins);
    } else {
      $self->draw_non_cigar($params,$args,$gab,\%joins,$zm);
    }
  }
  $self->draw_joins(\%joins);
}

# Things that stay constant for zmenu params (at least within a net)
sub prepare_zmenus {
  my ($self,$gabs,$net) = @_;

  my $url_species =
    ucfirst $gabs->[0]->reference_genomic_align->genome_db->name;
  my ($n0,$n1);
  ($n0,$n1) = $self->make_net_urls($gabs) if $net;
  my $other_species  = $self->my_config('species');
  my $mlss_id        = $self->my_config('method_link_species_set_id');
  return {
    type    => 'Location',
    action  => 'PairwiseAlignment',
    species => $url_species,
    n0      => $n0,
    n1      => $n1,
    s1      => $other_species,
    method  => $self->my_config('type'),
    align   => $mlss_id,
  };
}

# Add ZMenu to box
sub add_zmenu {
  my ($self,$zm,$box,$ori,$r,$r1) = @_;

  $box->href($self->_url({ %$zm, r => $r, r1 => $r1, orient => $ori}));
}

sub empty_track {
  my ($self) = @_;
  unless($self->{'config'}->get_option('opt_empty_tracks')==0) {
    my $name = $self->my_config('name');
    $self->errorTrack("No $name features in this region");
  }
}

# Should we be drawing track at all, maybe this is the wrong strand?
sub this_strand {
  my ($self) = @_;

  my $strand      = $self->strand;
  my $strand_flag = $self->my_config('strand');
  return 0 if $strand_flag eq 'r' && $strand != -1;
  return 0 if $strand_flag eq 'f' && $strand !=  1;
  return 1;
}

sub render_normal {
  my $self = shift;

  return $self->render_compact if $debug_force_compact;
  return $self->render_text if $self->{'text_export'} or $debug_force_text;
  return unless $self->this_strand();

  $self->_init_bump(undef, $self->depth || 6); # initialize bumping

  my $features = $self->features;
  unless(@$features) {
    $self->empty_track();
    return;
  }
  foreach my $ga_s ($self->build_features_into_sorted_groups($features)) {
    next unless @$ga_s;
    my $y_pos = $self->calculate_ypos($ga_s);
    next unless defined $y_pos;
    my $net_composite = $self->draw_containing_box($ga_s,$y_pos);
    my $zm = $self->prepare_zmenus($ga_s,1);
    $self->draw_boxes($net_composite,$ga_s,$y_pos,$zm);
    $self->add_zmenu($zm,$net_composite,$self->get_ori($ga_s->[0]));
    $self->push($net_composite);
  }
}

sub render_compact {
  my $self = shift;

  return $self->render_text if $self->{'text_export'};
  return unless $self->this_strand();
  $self->_init_bump(undef, $self->depth);  # initialize bumping

  my @features = @{$self->get_compact_features($self->features||[])};
  unless(@features) {
    $self->empty_track();
    return;
  }
  $self->draw_boxes(undef,\@features,0,$self->prepare_zmenus(\@features,0));
}

sub features {
  my $self = shift;

  my $compara = $self->dbadaptor('multi',$self->my_config('db'));
  my $mlss_a = $compara->get_MethodLinkSpeciesSetAdaptor;
  my $mlss_id = $self->my_config('method_link_species_set_id');
  my $mlss = $mlss_a->fetch_by_dbID($mlss_id);
  my $gab_a = $compara->get_GenomicAlignBlockAdaptor;
  my $cont = $self->{'container'};
  my $gab_s = $gab_a->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss,$cont);
  # Filter to target non-refs, if specified
  my $target = $self->my_config('target');
  if($target) {
    $gab_s = [
      grep {
        $_->get_all_non_reference_genomic_aligns->[0]->dnafrag->name eq
          $target
      } @{$gab_s || []}
    ];
  }
  return $gab_s;
}

sub render_text {
  my $self = shift;

  return unless $self->this_strand();

  # We don't have "features" so can't use the supertype class. Creating
  # fake features doesn't really help simplify things. May as well do it
  # here. We should probably alter the superclass method to accept gab's.
  my $species = $self->my_config('species');
  my $type    = $self->my_config('type');
  my $db      = $self->my_config('db');

  my @header = qw(seqname source feature start end score stand frame);
  push @header,$species;
  my $out;
  $out = join("\t",@header)."\r\n" unless $type eq 'gff';
  foreach my $gab (@{$self->features}) {
    my $ref = $gab->reference_genomic_align;
    my $nonref = $gab->get_all_non_reference_genomic_aligns->[0];
    my @row = (
      $ref->dnafrag->name,
      $db eq 'vega' ? 'Vega' : 'Ensembl', $type,
      $ref->dnafrag->start + $ref->dnafrag_start - 1,
      $ref->dnafrag->start + $ref->dnafrag_end   - 1,
      $gab->score,'.','.',
      sprintf("%s:%d-%d",$nonref->dnafrag->name,
              $nonref->dnafrag->start + $nonref->dnafrag_start - 1,
              $nonref->dnafrag->start + $nonref->dnafrag_end -1)
      );
      if($type eq 'gff') {
        @row = map { "$header[$_]=$row[$_]" } (0..$#header);
        $out .= join("; ",@row)."\r\n";
      } else {
        $out .= join("\t",@row)."\r\n";
      }
  }
  warn $out;
  return $out;
}

1;

redpajama_set_name: RedPajamaGithub


text:
module FitbitAPI
  class Client

    PERIODS = %w(1d 7d 30d 1w 1m 3m 6m 1y max).freeze

    def format_date(date)
      if [Date, Time, DateTime].include?(date.class)
        date.strftime('%Y-%m-%d')
      elsif date.is_a? String
        if date =~ /\d{4}\-\d{2}\-\d{2}/
          date
        else
          raise FitbitAPI::InvalidArgumentError, "Invalid argument [\"#{date}\"] - string must follow yyyy-MM-dd format."
        end
      else
        raise FitbitAPI::InvalidArgumentError, "Invalid type [#{date.class}] - provide a Date/Time/DateTime or a String(yyyy-MM-dd format)."
      end
    end

    def format_time(time)
      if [Time, DateTime].include?(time.class)
        time.strftime('%H:%M')
      elsif time.is_a? String
        if time =~ /\d{2}\:\d{2}/
          time
        else
          raise FitbitAPI::InvalidArgumentError, "Invalid argument [\"#{time}\"] - string must follow HH:mm format."
        end
      else
        raise FitbitAPI::InvalidArgumentError, "Invalid type [#{time.class}] - provide a Time/DateTime or a String(HH:mm format)."
      end
    end

    def format_scope(scope)
      scope.is_a?(Array) ? scope.join(' ') : scope
    end

    def deep_keys_to_snake_case!(object)
      deep_transform_keys!(object) { |key| to_snake_case(key, replace_dashes: true) }
    end

    def deep_keys_to_camel_case!(object)
      deep_transform_keys!(object) { |key| to_camel_case(key, lower: true) }
    end

    def deep_symbolize_keys!(object)
      deep_transform_keys!(object) { |key| key.to_sym rescue key }
    end

    # Inspired by ActiveSupport's implementation
    def deep_transform_keys!(object, &block)
      case object
      when Hash
        object.keys.each do |key|
          value = object.delete(key)
          object[yield(key)] = deep_transform_keys!(value) { |key| yield(key) }
        end
        object
      when Array
        object.map! { |e| deep_transform_keys!(e) { |key| yield(key) } }
      else
        object
      end
    end

    def to_snake_case(word, opts={})
      string = word.to_s.dup
      return string.downcase if string.match(/\A[A-Z]+\z/)
      string.gsub!(/([A-Z]+)([A-Z][a-z])/, '\1_\2')
      string.gsub!(/([a-z])([A-Z])/, '\1_\2')
      string.gsub!('-', '_') if opts[:replace_dashes]
      string.downcase
    end

    def to_camel_case(word, opts={})
      string = word.to_s
      return string if string.match(/[A-Z]|[a-z]([A-Z0-9]*[a-z][a-z0-9]*[A-Z]|[a-z0-9]*[A-Z][A-Z0-9]*[a-z])[A-Za-z0-9]*/)
      string = word.to_s.split('_').collect(&:capitalize).join
      string.gsub!(/^\w{1}/) { |word| word.downcase } if opts[:lower]
      return string
    end

  end
end


text:
package au.com.mineauz.minigames.commands.set;

import au.com.mineauz.minigames.MinigameUtils;
import au.com.mineauz.minigames.commands.ICommand;
import au.com.mineauz.minigames.minigame.Minigame;
import au.com.mineauz.minigames.minigame.reward.*;
import au.com.mineauz.minigames.minigame.reward.scheme.StandardRewardScheme;
import org.bukkit.ChatColor;
import org.bukkit.Material;
import org.bukkit.command.CommandSender;
import org.bukkit.entity.Player;
import org.bukkit.inventory.ItemStack;

import java.util.ArrayList;
import java.util.List;

public class SetRewardCommand implements ICommand {

    @Override
    public String getName() {
        return "reward";
    }

    @Override
    public String[] getAliases() {
        return null;
    }

    @Override
    public boolean canBeConsole() {
        return true;
    }

    @Override
    public String getDescription() {
        return "Sets the players reward for completing the Minigame for the first time. " +
                "This can be one item or a randomly selected item added to the rewards, depending on its defined rarity. \n" +
                "Possible rarities are: very_common, common, normal, rare and very_rare\n" +
                "NOTE: This can only be used on minigames using the standard reward scheme";
    }

    @Override
    public String[] getParameters() {
        return null;
    }

    @Override
    public String[] getUsage() {
        return new String[]{"/minigame set <Minigame> reward <Item Name> [Quantity] [Rarity]",
                "/minigame set <Minigame> reward $<Money Amount> [Rarity]"
        };
    }

    @Override
    public String getPermissionMessage() {
        return "You do not have permission to set a Minigames reward!";
    }

    @Override
    public String getPermission() {
        return "minigame.set.reward";
    }

    @Override
    public boolean onCommand(CommandSender sender, Minigame minigame,
                             String label, String[] args) {
        if (args != null) {
            RewardsModule module = RewardsModule.getModule(minigame);
            if (!(module.getScheme() instanceof StandardRewardScheme)) {
                sender.sendMessage(ChatColor.RED + "This command can only be used on minigames that use the standard reward scheme");
                return true;
            }

            Rewards rewards = ((StandardRewardScheme) module.getScheme()).getPrimaryReward();

            int quantity = 1;
            double money = -1;
            if (args.length >= 2 && args[1].matches("[0-9]+")) {
                quantity = Integer.parseInt(args[1]);
            }

            ItemStack item = null;
            if (args[0].startsWith("$")) {
                try {
                    money = Double.parseDouble(args[0].replace("$", ""));
                } catch (NumberFormatException ignored) {
                }
            } else {
                item = MinigameUtils.stringToItemStack(args[0], quantity);
            }

            if (item != null && item.getType() != Material.AIR) {
                RewardRarity rarity = RewardRarity.NORMAL;
                if (args.length == 3) {
                    rarity = RewardRarity.valueOf(args[2].toUpperCase());
                }
                ItemReward ir = (ItemReward) RewardTypes.getRewardType("ITEM", rewards);
                ir.setRewardItem(item);
                ir.setRarity(rarity);
                rewards.addReward(ir);

                sender.sendMessage(ChatColor.GRAY + "Added " + item.getAmount() + " of " + MinigameUtils.getItemStackName(item) + " to primary rewards of \"" + minigame.getName(false) + "\" "
                        + "with a rarity of \"" + rarity.toString().toLowerCase().replace("_", " ") + "\"");
                return true;
            } else if (sender instanceof Player && args[0].equals("SLOT")) {
                item = ((Player) sender).getInventory().getItemInMainHand();
                RewardRarity rarity = RewardRarity.NORMAL;
                if (args.length == 2) {
                    rarity = RewardRarity.valueOf(args[1].toUpperCase());
                }
                ItemReward ir = (ItemReward) RewardTypes.getRewardType("ITEM", rewards);
                ir.setRewardItem(item);
                ir.setRarity(rarity);
                rewards.addReward(ir);
                sender.sendMessage(ChatColor.GRAY + "Added " + item.getAmount() + " of " + MinigameUtils.getItemStackName(item) + " to primary rewards of \"" + minigame.getName(false) + "\" "
                        + "with a rarity of " + rarity.toString().toLowerCase().replace("_", " "));
                return true;
            } else if (item != null && item.getType() == Material.AIR) {
                sender.sendMessage(ChatColor.RED + "Primary rewards for \"" + minigame.getName(false) + "\" cannot be Air!");
                return true;
            } else if (money != -1 && plugin.hasEconomy()) {
                RewardRarity rarity = RewardRarity.NORMAL;
                if (args.length == 2) {
                    rarity = RewardRarity.valueOf(args[1].toUpperCase());
                }
                MoneyReward mr = (MoneyReward) RewardTypes.getRewardType("MONEY", rewards);
                mr.setRewardMoney(money);
                mr.setRarity(rarity);
                rewards.addReward(mr);
                sender.sendMessage(ChatColor.GRAY + "Added $" + money + " to primary rewards of \"" + minigame.getName(false) + "\" "
                        + "with a rarity of " + rarity.toString().toLowerCase().replace("_", " "));
                return true;
            } else if (!plugin.hasEconomy()) {
                sender.sendMessage(ChatColor.RED + "Vault required to set a money reward! Download from dev.bukkit.org");
                return true;
            }
        }
        return false;
    }

    @Override
    public List<String> onTabComplete(CommandSender sender, Minigame minigame,
                                      String alias, String[] args) {
        if (args.length == 3 || (args.length == 2 && args[0].startsWith("$"))) {
            List<String> ls = new ArrayList<>();
            for (RewardRarity r : RewardRarity.values()) {
                ls.add(r.toString());
            }
            return MinigameUtils.tabCompleteMatch(ls, args[args.length - 1]);
        }
        return null;
    }

}


text:
<?php

/**
 * @namespace
 */

namespace Solarium\QueryType\Select\Query\Component\Stats;

use Solarium\Core\Configurable;

/**
 * Stats component field class
 */
class Field extends Configurable
{

    /**
     * Field facets (for stats)
     *
     * @var array
     */
    protected $facets = array();

    /**
     * Initialize options
     *
     * Several options need some extra checks or setup work, for these options
     * the setters are called.
     *
     * @return void
     */
    protected function init()
    {
        foreach ($this->options as $name => $value) {
            switch ($name) {
                case 'facet':
                    $this->setFacets($value);
                    break;
            }
        }
    }

    /**
     * Get key value
     *
     * @return string
     */
    public function getKey()
    {
        return $this->getOption('key');
    }

    /**
     * Set key value
     *
     * @param  string $value
     * @return self   Provides fluent interface
     */
    public function setKey($value)
    {
        return $this->setOption('key', $value);
    }

    /**
     * Specify a facet to return in the resultset
     *
     * @param  string $facet
     * @return self   Provides fluent interface
     */
    public function addFacet($facet)
    {
        $this->facets[$facet] = true;

        return $this;
    }

    /**
     * Specify multiple facets to return in the resultset
     *
     * @param string|array $facets can be an array or string with comma
     * separated facetnames
     *
     * @return self Provides fluent interface
     */
    public function addFacets($facets)
    {
        if (is_string($facets)) {
            $facets = explode(',', $facets);
            $facets = array_map('trim', $facets);
        }

        foreach ($facets as $facet) {
            $this->addFacet($facet);
        }

        return $this;
    }

    /**
     * Remove a facet from the facet list
     *
     * @param  string $facet
     * @return self   Provides fluent interface
     */
    public function removeFacet($facet)
    {
        if (isset($this->facets[$facet])) {
            unset($this->facets[$facet]);
        }

        return $this;
    }

    /**
     * Remove all facets from the facet list.
     *
     * @return self Provides fluent interface
     */
    public function clearFacets()
    {
        $this->facets = array();

        return $this;
    }

    /**
     * Get the list of facets
     *
     * @return array
     */
    public function getFacets()
    {
        return array_keys($this->facets);
    }

    /**
     * Set multiple facets
     *
     * This overwrites any existing facets
     *
     * @param  array $facets
     * @return self  Provides fluent interface
     */
    public function setFacets($facets)
    {
        $this->clearFacets();
        $this->addFacets($facets);

        return $this;
    }

}