rbbt-util 5.44.0 → 6.0.3

data/lib/rbbt/tsv/manipulate.rb

@@ -1,747 +1,750 @@
-module TSV
-  
-  attr_accessor :monitor
-
-  class Traverser
-    attr_accessor :new_key_field, :new_fields, :new_key_field_name, :new_field_names, :type, :uniq
-
-    def process_null(key, values)
-      [[key], values]
-    end
-
-    def process_subset_list(key, values)
-      [key, @new_fields.collect{|field| field == :key ?  key : values[field] }]
-    end
-
-    def process_subset_all_but_list(key, values)
-      new = values.dup
-      new.delete_at(0 - @new_fields)
-      [key, new]
-    end
-
-    def process_reorder_single(key, values)
-      new_key = @new_key_field == :key ? key : values
-      new_value = @new_fields.collect{|field| field == :key ?  key : values }.first
-      return [new_key, new_value]
-      [ [values[@new_key_field]], 
-        @new_fields.collect{|field| field == :key ?  key : values[field] }]
-    end
-
-    def process_reorder_list(key, values)
-      [ [values[@new_key_field]], 
-        @new_fields.collect{|field| field == :key ?  key : values[field] }]
-    end
-
-    def process_reorder_double_uniq(key, values)
-      [ values[@new_key_field].uniq, 
-        @new_fields.collect{|field| field == :key ?  
-          [key] : values[field] }
-      ]
-    end
-
-    def process_subset_double(key, values)
-      [[key], @new_fields.collect{|field| field == :key ?  [key] : values[field] }]
-    end
-
-    def process_subset_all_but_double(key, values)
-      new = values.dup
-      new.delete_at(0 - @new_fields)
-      [[key], new]
-    end
-
-    def process_reorder_double(key, values)
-      [ values[@new_key_field], 
-        @new_fields.collect{|field| field == :key ?  
-          [key] : values[field] }
-      ]
-    end
-
-    def process_reorder_flat(key, values)
-      [ values,
-        @new_fields.collect{|field| field == :key ?  
-          [key] : values[field] }.flatten
-      ]
-    end
-
-    def initialize(key_field, fields, new_key_field, new_fields, type, uniq)
-      @new_key_field = TSV.identify_field(key_field, fields, new_key_field)
-
-      raise "Key field #{ new_key_field } not found" if @new_key_field.nil?
-      @new_fields = case new_fields
-                    when nil
-                      case 
-                      when @new_key_field == :key
-                        :all
-                      when fields.nil?
-                        - @new_key_field
-                      else 
-                        new = (0..fields.length - 1).to_a
-                        new.delete_at(@new_key_field)
-                        new.unshift :key
-                        new
-                      end
-                    when Array
-                      new_fields.collect do |field|
-                        TSV.identify_field(key_field, fields, field)
-                      end
-                    when String, Symbol
-                      [TSV.identify_field(key_field, fields, new_fields)]
-                    else
-                      raise "Unknown format for new_fields (should be nil, Array or String): #{new_fields.inspect}"
-                    end
-
-      @new_key_field_name = case 
-                            when @new_key_field == :key
-                              key_field
-                            else
-                              fields[@new_key_field] if Array === fields
-                            end
-
-      if Array === fields
-        @new_field_names = case
-                           when fields.nil?
-                             nil
-                           when Array === @new_fields
-                             @new_field_names = @new_fields.collect do |field|
-                               case 
-                               when field == :key
-                                 key_field
-                               else
-                                 fields[field]
-                               end
-                             end
-                           when @new_fields == :all
-                             fields
-                           when (Numeric === @new_fields and @new_fields <= 0)
-                             new = fields.dup
-                             new.delete_at(- @new_fields)
-                             new.unshift key_field
-                             new
-                           end
-      end
-
-      case
-      when (@new_key_field == :key and (@new_fields == :all or fields.nil? or @new_fields == (0..fields.length - 1).to_a))
-        self.instance_eval do alias process process_null end
-      when @new_key_field == :key 
-        if type == :double
-          if Numeric === @new_fields and @new_fields <= 0
-            self.instance_eval do alias process process_subset_all_but_double end
-          else
-            self.instance_eval do alias process process_subset_double end
-          end
-        else
-          if Numeric === @new_fields and @new_fields <= 0
-            self.instance_eval do alias process process_subset_all_but_list end
-          else
-            self.instance_eval do alias process process_subset_list end
-          end
-        end
-      else
-        case type 
-        when :double
-          if uniq
-            self.instance_eval do alias process process_reorder_double_uniq end
-          else
-            self.instance_eval do alias process process_reorder_double end
-          end
-        when :flat
-          self.instance_eval do alias process process_reorder_flat end
-        when :single
-          self.instance_eval do alias process process_reorder_single end
-        else
-          self.instance_eval do alias process process_reorder_list end
-        end
-      end
-    end
-  end
-
-  #{{{ Methods
-
-  def through(new_key_field = nil, new_fields = nil, uniq = false, zipped = false)
-
-    traverser = Traverser.new key_field, fields, new_key_field, new_fields, type, uniq
-
-    if @monitor
-      if Log::ProgressBar === @monitor
-        @monitor.max = size
-        progress_monitor = @monitor
-      else
-        desc = "Iterating TSV"
-        step = 100
-        if Hash === @monitor
-          desc = @monitor[:desc] if @monitor.include? :desc 
-          step = @monitor[:step] if @monitor.include? :step 
-        elsif String === @monitor
-          desc = @monitor
-        end
-        progress_monitor = Log::ProgressBar.new_bar(size, :desc => desc)
-      end
-    else
-      progress_monitor = nil
-    end
-
-    each do |key, value|
-      progress_monitor.tick if progress_monitor
-
-      keys, value = traverser.process(key, value)
-
-      next if keys.nil?
-      
-      keys = [keys].compact unless Array === keys
-
-      # Annotated with Entity and NamedArray
-      if not @unnamed and not traverser.new_field_names.nil? 
-
-        case type
-        when :double, :list
-          #Log.warn "Value frozen: #{ value }" if value.frozen?
-
-          value.nil? ?
-            nil :
-            NamedArray.setup(value, traverser.new_field_names, key, entity_options, entity_templates)
-
-        when :flat, :single
-          prepare_entity(value, traverser.new_field_names.first, entity_options)
-        end
-      end
-
-
-
-      if zipped
-
-        keys.each_with_index do |k,i|
-          v = value.collect{|v|
-            r = v[i]
-            r = v[0] if r.nil?
-            r
-          }
-
-          if not @unnamed 
-            k = Misc.prepare_entity(k, traverser.new_key_field_name, entity_options)
-          end
-
-          v.key = k if NamedArray === v
-
-          yield k, v
- 
-        end
-
-      else
-
-        keys.each do |key|
-          if not @unnamed
-            k = Misc.prepare_entity(k, traverser.new_key_field_name, entity_options)
-          end
-          value.key = key if NamedArray === value
-          yield key, value
-        end
-
-      end
-
-    end
-
-    Log::ProgressBar.remove_bar progress_monitor if progress_monitor
-
-    [traverser.new_key_field_name, traverser.new_field_names]
-  end
-
-  def reorder(new_key_field = nil, new_fields = nil, options = {}) 
-    zipped, uniq, merge = Misc.process_options options, :zipped, :uniq, :merge
-
-    persist_options = Misc.pull_keys options, :persist
-    persist_options[:prefix] = "Reorder"
-
-    Persist.persist_tsv self, self.filename, self.options.merge({:key_field => new_key_field, :fields => new_fields}), persist_options do |data|
-      data.serializer = type if data.respond_to? :serializer and data.serializer == :type
-
-      new_key_field_name, new_field_names = nil, nil
-      with_unnamed do
-        if zipped or (type != :double and type != :flat)
-          new_key_field_name, new_field_names = through new_key_field, new_fields, uniq, zipped do |key, value|
-            if merge 
-              if data[key]
-                new_values = data[key].dup
-                value.each_with_index do |v,i|
-                  new_values[i] += [v]
-                end
-                data[key] = new_values if Array === value
-              else
-                data[key] = value.collect{|v| [v]} if Array === value
-              end
-            else
-              data[key] = value.clone if Array === value
-            end
-          end
-        else
-          case type 
-          when :double
-            new_key_field_name, new_field_names = through new_key_field, new_fields, uniq, zipped do |keys, value|
-              keys = [keys] unless Array === keys
-              keys.each do |key|
-                if data[key] 
-                  current = data[key].dup
-                  value.each_with_index do |v, i|
-                    if current[i]
-                      current[i] += v if v
-                    else
-                      current[i] = v || []
-                    end
-                  end
-                  data[key] = current 
-                else
-                  data[key] = value.collect{|v| v.nil? ? nil : v.dup}
-                end
-              end
-            end
-          when :flat
-            new_key_field_name, new_field_names = through new_key_field, new_fields, uniq, zipped do |key, value|
-              data[key] ||= []
-              data[key] += value
-            end
-          else
-            raise "Unkown type #{type}"
-          end
-        end
-      end
-
-      #if real_data and real_data.respond_to? :persistence_path
-      #  real_data.serializer = type if real_data.respond_to? :serializer
-      #  real_data.merge!(data)
-      #  data = real_data
-      #end
-
-      data.extend TSV unless TSV === data
-      self.annotate(data)
-      data.entity_options = self.entity_options
-      data.entity_templates = self.entity_templates
-
-      data.key_field = new_key_field_name
-      data.fields = new_field_names
-      data.fields.each do |field|
-        data.entity_templates[field] = entity_templates[field] if entity_templates.include? field
-      end
-      data.type = zipped ? (merge ? :double : :list) : type
-
-      data
-    end
-  end
-
-  def slice(fields)
-    reorder :key, fields
-  end
-
-  def sort(*fields)
-    fields = nil if fields.empty?
-
-    elems = []
-    through :key, fields do |key, value|
-      elems << case
-      when block_given?
-        [key, yield(*value)]
-      else
-        case
-        when type == :single
-          [key, value]
-        when type == :double
-          [key, value.first.first]
-        else
-          [key, value.first]
-        end
-      end
-    end
-
-    elems.sort_by{|k,v| v}.collect{|k,v| k}
-  end
-
-  def subset(keys)
-    new = TSV.setup({}, :key_field => key_field, :fields => fields, :type => type, :filename => filename, :identifiers => identifiers)
-    self.with_unnamed do
-      keys.each do |k|
-        new[k] = self[k] if self.include?(k)
-      end
-    end
-    new
-  end
-
-  def select(method = nil, invert = false, &block)
-    new = TSV.setup({}, :key_field => key_field, :fields => fields, :type => type, :filename => filename, :identifiers => identifiers)
-
-    self.annotate(new)
-    #new.key_field = key_field
-    #new.fields    = fields.dup unless fields.nil?
-    #new.type      = type
-    #new.filename  = filename
-    #new.namespace = namespace
-    #new.entity_options = entity_options
-    #new.entity_templates = entity_templates
-    
-    case
-    when (method.nil? and block_given?)
-      through do |key, values|
-        new[key] = values if invert ^ (yield key, values)
-      end
-    when Array === method
-      method = Set.new method
-      with_unnamed do
-        case type
-        when :single
-          through do |key, value|
-            new[key] = value if invert ^ (method.include? key or method.include? value)
-          end
-        when :list, :flat
-          through do |key, values|
-            new[key] = values if invert ^ (method.include? key or (method & values).length > 0)
-          end
-        else
-          through do |key, values|
-            new[key] = values if invert ^ (method.include? key or (method & values.flatten).length > 0)
-          end
-        end
-      end
-    when Regexp === method
-      with_unnamed do
-        through do |key, values|
-          new[key] = values if invert ^ ([key,values].flatten.select{|v| v =~ method}.any?)
-        end
-      end
-    when (String === method || Symbol === method)
-      if block_given?
-        case 
-        when block.arity == 1
-          with_unnamed do
-            case
-            when (method == key_field or method == :key)
-              through do |key, values|
-                new[key] = values if invert ^ (yield(key))
-              end
-            when (type == :single or type == :flat)
-              through do |key, value|
-                new[key] = value if invert ^ (yield(value))
-              end
-            else
-              pos = identify_field method
-              raise "Field #{ method } not identified. Available: #{ fields * ", " }" if pos.nil?
-
-              through do |key, values|
-                new[key] = values if invert ^ (yield(values[pos]))
-              end
-            end
-          end
-        when block.arity == 2
-          with_unnamed do
-            case
-            when (method == key_field or method == :key)
-              through do |key, values|
-                new[key] = values if invert ^ (yield(key, key))
-              end
-            when (type == :single or type == :flat)
-              through do |key, value|
-                new[key] = value if invert ^ (yield(key, value))
-              end
-            else
-              pos = identify_field method
-              through do |key, values|
-                new[key] = values if invert ^ (yield(key, values[pos]))
-              end
-            end
-
-          end
-        end
-
-      else
-        with_unnamed do
-          through do |key, values|
-            new[key] = values if invert ^ ([key,values].flatten.select{|v| v == method}.any?)
-          end
-        end
-      end
-    when Hash === method
-      key  = method.keys.first
-      method = method.values.first
-      case
-      when (Array === method and (key == :key or key_field == key))
-        with_unnamed do
-          Annotated.purge(method).each{|key| 
-            new[key] = self[key] if invert ^ (self.include? key)
-          }
-        end
-      when Array === method
-        with_unnamed do
-          method = Set.new method unless Set === method
-          case type
-          when :single
-            through :key, key do |key, value|
-              new[key] = self[key] if invert ^ (method.include? value)
-            end
-          when :list
-            through :key, key do |key, values|
-              new[key] = self[key] if invert ^ (method.include? values.first)
-            end
-          when :flat #untested
-            through :key, key do |key, values|
-              new[key] = self[key] if invert ^ ((method & values.flatten).any?)
-            end
-          else
-            through :key, key do |key, values|
-              new[key] = self[key] if invert ^ ((method & values.flatten).any?)
-            end
-          end
-        end
-
-      when Regexp === method
-        with_unnamed do
-          through :key, key do |key, values|
-            values = [values] if type == :single
-            new[key] = self[key] if invert ^ (values.flatten.select{|v| v =~ method}.any?)
-          end
-        end
-
-      when (String === method and method =~ /name:(.*)/)
-        name = $1
-        old_unnamed = self.unnamed
-        self.unnamed = false
-        if name.strip =~ /^\/(.*)\/$/
-          regexp = Regexp.new $1
-          through :key, key do |key, values|
-            case type
-            when :single
-              values = values.annotate([values])
-            when :double
-              values = values[0]
-            end
-            new[key] = self[key] if invert ^ (values.select{|v| v.name =~ regexp}.any?)
-          end
-        else
-          through :key, key do |key, values|
-            case type
-            when :single
-              values = values.annotate([values])
-            when :double
-              values = values[0]
-            end
-            new[key] = self[key] if invert ^ (values.select{|v| v.name == name}.any?)
-          end
-        end
-        self.unnamed = old_unnamed
-
-      when String === method
-        if method =~ /^([<>]=?)(.*)/
-          with_unnamed do
-            through :key, key do |key, values|
-              value = Array === values ? values.flatten.first : values
-              new[key] = self[key] if value.to_f.send($1, $2.to_f)
-            end
-          end
-        else
-          with_unnamed do
-            through :key, key do |key, values|
-              values = [values] if type == :single
-              new[key] = self[key] if invert ^ (values.flatten.select{|v| v == method}.length > 0)
-            end
-          end
-        end
-      when Numeric === method
-        with_unnamed do
-          through :key, key do |key, values|
-            new[key] = self[key] if invert ^ (values.flatten.length >= method)
-          end
-        end
-      when Proc === method
-        with_unnamed do
-          through :key, key do |key, values|
-            values = [values] if type == :single
-            new[key] = self[key] if invert ^ (values.flatten.select{|v| method.call(v)}.length > 0)
-          end
-        end
-      end
-    end
-
-    new
-  end
-
-  def column(field, cast = nil)
-    new = slice(field)
-
-    new.with_unnamed do
-      new.each do |k,v|
-        nv = v.first 
-        nv = nv.send(cast) unless cast.nil?
-        new[k] = nv
-      end
-    end
-
-    case type
-    when :double, :flat
-      new.type = :flat
-    else
-      new.type = :single
-    end
-
-    new
-  end
-
-  def column_values(field, options = {})
-    all = []
-    through :key, field do |k,values|
-      values = Array === values ? values.flatten : [values]
-      all.concat values
-    end
-    prepare_entity(all, field, options = {})
-  end
-
-
-  def process_key(&block)
-    new = annotate({})
-    through do |key, values|
-      key = case 
-            when block.arity == 1
-              yield(key)
-            when block.arity == 2
-              yield(key, values)
-            else
-              raise "Unexpected arity in block, must be 1, 2 or 3: #{block.arity}"
-            end
-      new[key] = values
-    end
-    new
-  end
-
-  def process(field, &block)
-    field_pos = identify_field field
-
-    through do |key, values|
-      case
-      when type == :single
-        field_values = values
-      when type == :flat
-        field_values = values
-      else
-        next if values.nil?
-        field_values = values[field_pos]
-      end
-
-      new_values = case 
-                   when block.arity == 1
-                     yield(field_values)
-                   when block.arity == 2
-                     yield(field_values, key)
-                   when block.arity == 3
-                     yield(field_values, key, values)
-                   else
-                     raise "Unexpected arity in block, must be 1, 2 or 3: #{block.arity}"
-                   end
-
-      case
-      when type == :single
-        self[key] = new_values
-      when type == :flat
-        self[key] = new_values
-      else
-        if ! values[field_pos].frozen? && ((String === values[field_pos] && String === new_values) ||
-          (Array === values[field_pos] && Array === new_values))
-           values[field_pos].replace new_values
-        else
-          values[field_pos] = new_values
-        end
-        self[key] = values
-      end
-    end
-
-    self
-  end
-
-  def add_field(name = nil)
-    old_monitor = @monitor
-    @monitor = {:desc => "Adding field #{ name }"} if TrueClass === monitor
-
-    through do |key, values|
-      new_values = yield(key, values)
-      new_values = [new_values] if type == :double and not Array === new_values
-
-      case
-      when (values.nil? and (fields.nil? or fields.empty?))
-        values = [new_values]
-      when values.nil?  
-        values = [nil] * fields.length + [new_values]
-      when Array === values
-        values += [new_values]
-      else
-        values << new_values
-      end
-
-      self[key] = values
-    end
-    @monitor = old_monitor
-
-    if not fields.nil? and not name.nil?
-      new_fields = self.fields + [name]
-      self.fields = new_fields
-    end
-
-    self
-  end
-
-  def add_fields(names = [])
-    old_monitor = @monitor
-    @monitor = {:desc => "Adding field #{ names * ", " }"} if TrueClass === monitor
-
-    through do |key, values|
-      values ||= fields ? [nil] * fields : []
-      new_values = yield(key, values)
-
-      case type
-      when :double
-        new_values = new_values.collect{|v| [v] } if Array === new_values and new_values.first and not Array === new_values.first
-        values += new_values || [nil] * names.length
-      when :list
-        values += new_values || [nil] * names.length
-      end
-
-      self[key] = values
-    end
-    @monitor = old_monitor
-
-    if not fields.nil? and not (names.nil? or names.empty?)
-      new_fields = self.fields + names
-      self.fields = new_fields
-    end
-
-    self
-  end
-
-  def transpose_list(key_field="Unkown ID")
-    new_fields = keys.dup
-    new = self.annotate({})
-    TSV.setup(new, :key_field => key_field, :fields => new_fields, :type => type, :filename => filename, :identifiers => identifiers)
-
-    require 'matrix'
-    m = Matrix.rows values 
-    new_rows = m.transpose.to_a
-
-    fields.zip(new_rows) do |key,row|
-      new[key] = row
-    end
-
-    new
-  end
-
-  def transpose_double(key_field = "Unkown ID")
-    sep = "-!SEP--#{rand 10000}!-"
-    tmp = self.to_list{|v| v * sep}
-    new = tmp.transpose_list(key_field)
-    new.to_double{|v| v.split(sep)}
-  end
-
-  def transpose(key_field = "Unkown ID")
-    case type
-    when :single, :flat
-      self.to_list.transpose_list key_field
-    when :list
-      transpose_list key_field
-    when :double
-      transpose_double key_field
-    end
-  end
-
-end
+#module TSV
+#  
+#  def self.identify_field(key_field, fields, name)
+#    return 0 if name == :key || key_field.start_with?(name.to_s)
+#    pos = NamedArray.identify_name(fields, name)
+#    pos.nil? ? nil : pos + 1
+#  end
+#
+#  def identify_field(name)
+#    TSV.identify_field(@key_field, @fields, name)
+#  end
+#
+#  attr_accessor :monitor
+#
+#  class Traverser
+#    attr_accessor :new_key_field, :new_fields, :new_key_field_name, :new_field_names, :type, :uniq
+#
+#    def process_null(key, values)
+#      [[key], values]
+#    end
+#
+#    def process_subset_list(key, values)
+#      [key, @new_fields.collect{|field| field == :key ?  key : values[field] }]
+#    end
+#
+#    def process_subset_all_but_list(key, values)
+#      new = values.dup
+#      new.delete_at(0 - @new_fields)
+#      [key, new]
+#    end
+#
+#    def process_reorder_single(key, values)
+#      new_key = @new_key_field == :key ? key : values
+#      new_value = @new_fields.collect{|field| field == :key ?  key : values }.first
+#      return [new_key, new_value]
+#      [ [values[@new_key_field]], 
+#        @new_fields.collect{|field| field == :key ?  key : values[field] }]
+#    end
+#
+#    def process_reorder_list(key, values)
+#      [ [values[@new_key_field]], 
+#        @new_fields.collect{|field| field == :key ?  key : values[field] }]
+#    end
+#
+#    def process_reorder_double_uniq(key, values)
+#      [ values[@new_key_field].uniq, 
+#        @new_fields.collect{|field| field == :key ?  
+#          [key] : values[field] }
+#      ]
+#    end
+#
+#    def process_subset_double(key, values)
+#      [[key], @new_fields.collect{|field| field == :key ?  [key] : values[field] }]
+#    end
+#
+#    def process_subset_all_but_double(key, values)
+#      new = values.dup
+#      new.delete_at(0 - @new_fields)
+#      [[key], new]
+#    end
+#
+#    def process_reorder_double(key, values)
+#      [ values[@new_key_field], 
+#        @new_fields.collect{|field| field == :key ?  
+#          [key] : values[field] }
+#      ]
+#    end
+#
+#    def process_reorder_flat(key, values)
+#      [ values,
+#        @new_fields.collect{|field| field == :key ?  
+#          [key] : values[field] }.flatten
+#      ]
+#    end
+#
+#    def initialize(key_field, fields, new_key_field, new_fields, type, uniq)
+#      @new_key_field = TSV.identify_field(key_field, fields, new_key_field)
+#
+#      raise "Key field #{ new_key_field } not found" if @new_key_field.nil?
+#      @new_fields = case new_fields
+#                    when nil
+#                      case 
+#                      when @new_key_field == :key
+#                        :all
+#                      when fields.nil?
+#                        - @new_key_field
+#                      else 
+#                        new = (0..fields.length - 1).to_a
+#                        new.delete_at(@new_key_field)
+#                        new.unshift :key
+#                        new
+#                      end
+#                    when Array
+#                      new_fields.collect do |field|
+#                        TSV.identify_field(key_field, fields, field)
+#                      end
+#                    when String, Symbol
+#                      [TSV.identify_field(key_field, fields, new_fields)]
+#                    else
+#                      raise "Unknown format for new_fields (should be nil, Array or String): #{new_fields.inspect}"
+#                    end
+#
+#      @new_key_field_name = case 
+#                            when @new_key_field == :key
+#                              key_field
+#                            else
+#                              fields[@new_key_field] if Array === fields
+#                            end
+#
+#      if Array === fields
+#        @new_field_names = case
+#                           when fields.nil?
+#                             nil
+#                           when Array === @new_fields
+#                             @new_field_names = @new_fields.collect do |field|
+#                               case 
+#                               when field == :key
+#                                 key_field
+#                               else
+#                                 fields[field]
+#                               end
+#                             end
+#                           when @new_fields == :all
+#                             fields
+#                           when (Numeric === @new_fields and @new_fields <= 0)
+#                             new = fields.dup
+#                             new.delete_at(- @new_fields)
+#                             new.unshift key_field
+#                             new
+#                           end
+#      end
+#
+#      case
+#      when (@new_key_field == :key and (@new_fields == :all or fields.nil? or @new_fields == (0..fields.length - 1).to_a))
+#        self.instance_eval do alias process process_null end
+#      when @new_key_field == :key 
+#        if type == :double
+#          if Numeric === @new_fields and @new_fields <= 0
+#            self.instance_eval do alias process process_subset_all_but_double end
+#          else
+#            self.instance_eval do alias process process_subset_double end
+#          end
+#        else
+#          if Numeric === @new_fields and @new_fields <= 0
+#            self.instance_eval do alias process process_subset_all_but_list end
+#          else
+#            self.instance_eval do alias process process_subset_list end
+#          end
+#        end
+#      else
+#        case type 
+#        when :double
+#          if uniq
+#            self.instance_eval do alias process process_reorder_double_uniq end
+#          else
+#            self.instance_eval do alias process process_reorder_double end
+#          end
+#        when :flat
+#          self.instance_eval do alias process process_reorder_flat end
+#        when :single
+#          self.instance_eval do alias process process_reorder_single end
+#        else
+#          self.instance_eval do alias process process_reorder_list end
+#        end
+#      end
+#    end
+#  end
+#
+#  #{{{ Methods
+#
+#  def through(new_key_field = nil, new_fields = nil, uniq = false, zipped = false)
+#
+#    traverser = Traverser.new key_field, fields, new_key_field, new_fields, type, uniq
+#
+#    if @monitor
+#      if Log::ProgressBar === @monitor
+#        @monitor.max = size
+#        progress_monitor = @monitor
+#      else
+#        desc = "Iterating TSV"
+#        step = 100
+#        if Hash === @monitor
+#          desc = @monitor[:desc] if @monitor.include? :desc 
+#          step = @monitor[:step] if @monitor.include? :step 
+#        elsif String === @monitor
+#          desc = @monitor
+#        end
+#        progress_monitor = Log::ProgressBar.new_bar(size, :desc => desc)
+#      end
+#    else
+#      progress_monitor = nil
+#    end
+#
+#    each do |key, value|
+#      progress_monitor.tick if progress_monitor
+#
+#      keys, value = traverser.process(key, value)
+#
+#      next if keys.nil?
+#      
+#      keys = [keys].compact unless Array === keys
+#
+#      # Annotated with Entity and NamedArray
+#      if not @unnamed and not traverser.new_field_names.nil? 
+#
+#        case type
+#        when :double, :list
+#          #Log.warn "Value frozen: #{ value }" if value.frozen?
+#
+#          value.nil? ?
+#            nil :
+#            NamedArray.setup(value, traverser.new_field_names, key, entity_options, entity_templates)
+#
+#        when :flat, :single
+#          prepare_entity(value, traverser.new_field_names.first, entity_options)
+#        end
+#      end
+#
+#
+#
+#      if zipped
+#
+#        keys.each_with_index do |k,i|
+#          v = value.collect{|v|
+#            r = v[i]
+#            r = v[0] if r.nil?
+#            r
+#          }
+#
+#          if not @unnamed 
+#            k = Misc.prepare_entity(k, traverser.new_key_field_name, entity_options)
+#          end
+#
+#          v.key = k if NamedArray === v
+#
+#          yield k, v
+# 
+#        end
+#
+#      else
+#
+#        keys.each do |key|
+#          if not @unnamed
+#            k = Misc.prepare_entity(k, traverser.new_key_field_name, entity_options)
+#          end
+#          value.key = key if NamedArray === value
+#          yield key, value
+#        end
+#
+#      end
+#
+#    end
+#
+#    Log::ProgressBar.remove_bar progress_monitor if progress_monitor
+#
+#    [traverser.new_key_field_name, traverser.new_field_names]
+#  end
+#
+#  def reorder(new_key_field = nil, new_fields = nil, options = {}) 
+#    zipped, uniq, merge = Misc.process_options options, :zipped, :uniq, :merge
+#
+#    persist_options = Misc.pull_keys options, :persist
+#    persist_options[:prefix] = "Reorder"
+#
+#    Persist.persist_tsv self, self.filename, self.options.merge({:key_field => new_key_field, :fields => new_fields}), persist_options do |data|
+#      data.serializer = type if data.respond_to? :serializer and data.serializer == :type
+#
+#      new_key_field_name, new_field_names = nil, nil
+#      with_unnamed do
+#        if zipped or (type != :double and type != :flat)
+#          new_key_field_name, new_field_names = through new_key_field, new_fields, uniq, zipped do |key, value|
+#            if merge 
+#              if data[key]
+#                new_values = data[key].dup
+#                value.each_with_index do |v,i|
+#                  new_values[i] += [v]
+#                end
+#                data[key] = new_values if Array === value
+#              else
+#                data[key] = value.collect{|v| [v]} if Array === value
+#              end
+#            else
+#              data[key] = value.clone if Array === value
+#            end
+#          end
+#        else
+#          case type 
+#          when :double
+#            new_key_field_name, new_field_names = through new_key_field, new_fields, uniq, zipped do |keys, value|
+#              keys = [keys] unless Array === keys
+#              keys.each do |key|
+#                if data[key] 
+#                  current = data[key].dup
+#                  value.each_with_index do |v, i|
+#                    if current[i]
+#                      current[i] += v if v
+#                    else
+#                      current[i] = v || []
+#                    end
+#                  end
+#                  data[key] = current 
+#                else
+#                  data[key] = value.collect{|v| v.nil? ? nil : v.dup}
+#                end
+#              end
+#            end
+#          when :flat
+#            new_key_field_name, new_field_names = through new_key_field, new_fields, uniq, zipped do |key, value|
+#              data[key] ||= []
+#              data[key] += value
+#            end
+#          else
+#            raise "Unkown type #{type}"
+#          end
+#        end
+#      end
+#
+#      #if real_data and real_data.respond_to? :persistence_path
+#      #  real_data.serializer = type if real_data.respond_to? :serializer
+#      #  real_data.merge!(data)
+#      #  data = real_data
+#      #end
+#
+#      data.extend TSV unless TSV === data
+#      self.annotate(data)
+#      data.entity_options = self.entity_options
+#      data.entity_templates = self.entity_templates
+#
+#      data.key_field = new_key_field_name
+#      data.fields = new_field_names
+#      data.fields.each do |field|
+#        data.entity_templates[field] = entity_templates[field] if entity_templates.include? field
+#      end
+#      data.type = zipped ? (merge ? :double : :list) : type
+#
+#      data
+#    end
+#  end
+#
+#  def slice(fields)
+#    reorder :key, fields
+#  end
+#
+#  def sort(*fields)
+#    fields = nil if fields.empty?
+#
+#    elems = []
+#    through :key, fields do |key, value|
+#      elems << case
+#      when block_given?
+#        [key, yield(*value)]
+#      else
+#        case
+#        when type == :single
+#          [key, value]
+#        when type == :double
+#          [key, value.first.first]
+#        else
+#          [key, value.first]
+#        end
+#      end
+#    end
+#
+#    elems.sort_by{|k,v| v}.collect{|k,v| k}
+#  end
+#
+#  def subset(keys)
+#    new = TSV.setup({}, :key_field => key_field, :fields => fields, :type => type, :filename => filename, :identifiers => identifiers)
+#    self.with_unnamed do
+#      keys.each do |k|
+#        new[k] = self[k] if self.include?(k)
+#      end
+#    end
+#    new
+#  end
+#
+#  def select(method = nil, invert = false, &block)
+#    new = TSV.setup({}, :key_field => key_field, :fields => fields, :type => type, :filename => filename, :identifiers => identifiers)
+#
+#    self.annotate(new)
+#    
+#    case
+#    when (method.nil? and block_given?)
+#      through do |key, values|
+#        new[key] = values if invert ^ (yield key, values)
+#      end
+#    when Array === method
+#      method = Set.new method
+#      with_unnamed do
+#        case type
+#        when :single
+#          through do |key, value|
+#            new[key] = value if invert ^ (method.include? key or method.include? value)
+#          end
+#        when :list, :flat
+#          through do |key, values|
+#            new[key] = values if invert ^ (method.include? key or (method & values).length > 0)
+#          end
+#        else
+#          through do |key, values|
+#            new[key] = values if invert ^ (method.include? key or (method & values.flatten).length > 0)
+#          end
+#        end
+#      end
+#    when Regexp === method
+#      with_unnamed do
+#        through do |key, values|
+#          new[key] = values if invert ^ ([key,values].flatten.select{|v| v =~ method}.any?)
+#        end
+#      end
+#    when (String === method || Symbol === method)
+#      if block_given?
+#        case 
+#        when block.arity == 1
+#          with_unnamed do
+#            case
+#            when (method == key_field or method == :key)
+#              through do |key, values|
+#                new[key] = values if invert ^ (yield(key))
+#              end
+#            when (type == :single or type == :flat)
+#              through do |key, value|
+#                new[key] = value if invert ^ (yield(value))
+#              end
+#            else
+#              pos = identify_field method
+#              raise "Field #{ method } not identified. Available: #{ fields * ", " }" if pos.nil?
+#
+#              through do |key, values|
+#                new[key] = values if invert ^ (yield(values[pos]))
+#              end
+#            end
+#          end
+#        when block.arity == 2
+#          with_unnamed do
+#            case
+#            when (method == key_field or method == :key)
+#              through do |key, values|
+#                new[key] = values if invert ^ (yield(key, key))
+#              end
+#            when (type == :single or type == :flat)
+#              through do |key, value|
+#                new[key] = value if invert ^ (yield(key, value))
+#              end
+#            else
+#              pos = identify_field method
+#              through do |key, values|
+#                new[key] = values if invert ^ (yield(key, values[pos]))
+#              end
+#            end
+#
+#          end
+#        end
+#
+#      else
+#        with_unnamed do
+#          through do |key, values|
+#            new[key] = values if invert ^ ([key,values].flatten.select{|v| v == method}.any?)
+#          end
+#        end
+#      end
+#    when Hash === method
+#      key  = method.keys.first
+#      method = method.values.first
+#      case
+#      when (Array === method and (key == :key or key_field == key))
+#        with_unnamed do
+#          Annotated.purge(method).each{|key| 
+#            new[key] = self[key] if invert ^ (self.include? key)
+#          }
+#        end
+#      when Array === method
+#        with_unnamed do
+#          method = Set.new method unless Set === method
+#          case type
+#          when :single
+#            through :key, key do |key, value|
+#              new[key] = self[key] if invert ^ (method.include? value)
+#            end
+#          when :list
+#            through :key, key do |key, values|
+#              new[key] = self[key] if invert ^ (method.include? values.first)
+#            end
+#          when :flat #untested
+#            through :key, key do |key, values|
+#              new[key] = self[key] if invert ^ ((method & values.flatten).any?)
+#            end
+#          else
+#            through :key, key do |key, values|
+#              new[key] = self[key] if invert ^ ((method & values.flatten).any?)
+#            end
+#          end
+#        end
+#
+#      when Regexp === method
+#        with_unnamed do
+#          through :key, key do |key, values|
+#            values = [values] if type == :single
+#            new[key] = self[key] if invert ^ (values.flatten.select{|v| v =~ method}.any?)
+#          end
+#        end
+#
+#      when (String === method and method =~ /name:(.*)/)
+#        name = $1
+#        old_unnamed = self.unnamed
+#        self.unnamed = false
+#        if name.strip =~ /^\/(.*)\/$/
+#          regexp = Regexp.new $1
+#          through :key, key do |key, values|
+#            case type
+#            when :single
+#              values = values.annotate([values])
+#            when :double
+#              values = values[0]
+#            end
+#            new[key] = self[key] if invert ^ (values.select{|v| v.name =~ regexp}.any?)
+#          end
+#        else
+#          through :key, key do |key, values|
+#            case type
+#            when :single
+#              values = values.annotate([values])
+#            when :double
+#              values = values[0]
+#            end
+#            new[key] = self[key] if invert ^ (values.select{|v| v.name == name}.any?)
+#          end
+#        end
+#        self.unnamed = old_unnamed
+#
+#      when String === method
+#        if method =~ /^([<>]=?)(.*)/
+#          with_unnamed do
+#            through :key, key do |key, values|
+#              value = Array === values ? values.flatten.first : values
+#              new[key] = self[key] if value.to_f.send($1, $2.to_f)
+#            end
+#          end
+#        else
+#          with_unnamed do
+#            through :key, key do |key, values|
+#              values = [values] if type == :single
+#              new[key] = self[key] if invert ^ (values.flatten.select{|v| v == method}.length > 0)
+#            end
+#          end
+#        end
+#      when Numeric === method
+#        with_unnamed do
+#          through :key, key do |key, values|
+#            new[key] = self[key] if invert ^ (values.flatten.length >= method)
+#          end
+#        end
+#      when Proc === method
+#        with_unnamed do
+#          through :key, key do |key, values|
+#            values = [values] if type == :single
+#            new[key] = self[key] if invert ^ (values.flatten.select{|v| method.call(v)}.length > 0)
+#          end
+#        end
+#      end
+#    end
+#
+#    new
+#  end
+#
+#  def column(field, cast = nil)
+#    new = slice(field)
+#
+#    new.with_unnamed do
+#      new.each do |k,v|
+#        nv = v.first 
+#        nv = nv.send(cast) unless cast.nil?
+#        new[k] = nv
+#      end
+#    end
+#
+#    case type
+#    when :double, :flat
+#      new.type = :flat
+#    else
+#      new.type = :single
+#    end
+#
+#    new
+#  end
+#
+#  def column_values(field, options = {})
+#    all = []
+#    through :key, field do |k,values|
+#      values = Array === values ? values.flatten : [values]
+#      all.concat values
+#    end
+#    prepare_entity(all, field, options = {})
+#  end
+#
+#
+#  def process_key(&block)
+#    new = annotate({})
+#    through do |key, values|
+#      key = case 
+#            when block.arity == 1
+#              yield(key)
+#            when block.arity == 2
+#              yield(key, values)
+#            else
+#              raise "Unexpected arity in block, must be 1, 2 or 3: #{block.arity}"
+#            end
+#      new[key] = values
+#    end
+#    new
+#  end
+#
+#  def process(field, &block)
+#    field_pos = identify_field field
+#
+#    through do |key, values|
+#      case
+#      when type == :single
+#        field_values = values
+#      when type == :flat
+#        field_values = values
+#      else
+#        next if values.nil?
+#        field_values = values[field_pos]
+#      end
+#
+#      new_values = case 
+#                   when block.arity == 1
+#                     yield(field_values)
+#                   when block.arity == 2
+#                     yield(field_values, key)
+#                   when block.arity == 3
+#                     yield(field_values, key, values)
+#                   else
+#                     raise "Unexpected arity in block, must be 1, 2 or 3: #{block.arity}"
+#                   end
+#
+#      case
+#      when type == :single
+#        self[key] = new_values
+#      when type == :flat
+#        self[key] = new_values
+#      else
+#        if ! values[field_pos].frozen? && ((String === values[field_pos] && String === new_values) ||
+#          (Array === values[field_pos] && Array === new_values))
+#           values[field_pos].replace new_values
+#        else
+#          values[field_pos] = new_values
+#        end
+#        self[key] = values
+#      end
+#    end
+#
+#    self
+#  end
+#
+#  def add_field(name = nil)
+#    old_monitor = @monitor
+#    @monitor = {:desc => "Adding field #{ name }"} if TrueClass === monitor
+#
+#    through do |key, values|
+#      new_values = yield(key, values)
+#      new_values = [new_values] if type == :double and not Array === new_values
+#
+#      case
+#      when (values.nil? and (fields.nil? or fields.empty?))
+#        values = [new_values]
+#      when values.nil?  
+#        values = [nil] * fields.length + [new_values]
+#      when Array === values
+#        values += [new_values]
+#      else
+#        values << new_values
+#      end
+#
+#      self[key] = values
+#    end
+#    @monitor = old_monitor
+#
+#    if not fields.nil? and not name.nil?
+#      new_fields = self.fields + [name]
+#      self.fields = new_fields
+#    end
+#
+#    self
+#  end
+#
+#  def add_fields(names = [])
+#    old_monitor = @monitor
+#    @monitor = {:desc => "Adding field #{ names * ", " }"} if TrueClass === monitor
+#
+#    through do |key, values|
+#      values ||= fields ? [nil] * fields : []
+#      new_values = yield(key, values)
+#
+#      case type
+#      when :double
+#        new_values = new_values.collect{|v| [v] } if Array === new_values and new_values.first and not Array === new_values.first
+#        values += new_values || [nil] * names.length
+#      when :list
+#        values += new_values || [nil] * names.length
+#      end
+#
+#      self[key] = values
+#    end
+#    @monitor = old_monitor
+#
+#    if not fields.nil? and not (names.nil? or names.empty?)
+#      new_fields = self.fields + names
+#      self.fields = new_fields
+#    end
+#
+#    self
+#  end
+#
+#  def transpose_list(key_field="Unkown ID")
+#    new_fields = keys.dup
+#    new = self.annotate({})
+#    TSV.setup(new, :key_field => key_field, :fields => new_fields, :type => type, :filename => filename, :identifiers => identifiers)
+#
+#    require 'matrix'
+#    m = Matrix.rows values 
+#    new_rows = m.transpose.to_a
+#
+#    fields.zip(new_rows) do |key,row|
+#      new[key] = row
+#    end
+#
+#    new
+#  end
+#
+#  def transpose_double(key_field = "Unkown ID")
+#    sep = "-!SEP--#{rand 10000}!-"
+#    tmp = self.to_list{|v| v * sep}
+#    new = tmp.transpose_list(key_field)
+#    new.to_double{|v| v.split(sep)}
+#  end
+#
+#  def transpose(key_field = "Unkown ID")
+#    case type
+#    when :single, :flat
+#      self.to_list.transpose_list key_field
+#    when :list
+#      transpose_list key_field
+#    when :double
+#      transpose_double key_field
+#    end
+#  end
+#
+#end