### Home Classes Methods

### In Files

- lib/bio/db/gff.rb

### Parent

Bio::GFF::Record

### Namespace

- CLASS Bio::GFF::GFF2::Record::Value

### Methods

- ::new
- ::parse
- #==
- #add_attribute
- #attribute
- #attributes_to_hash
- #comment_only?
- #comments
- #comments=
- #delete_attribute
- #delete_attributes
- #get_attribute
- #get_attributes
- #parse
- #replace_attributes
- #set_attribute
- #sort_attributes_by_tag!
- #to_s

### Included Modules

- Bio::GFF::GFF2::Escape

### Files

- KNOWN_ISSUES.rdoc
- README.rdoc
- README_DEV.rdoc
- RELEASE_NOTES.rdoc
- Changes-1.3.rdoc
- RELEASE_NOTES-1.4.0.rdoc
- RELEASE_NOTES-1.4.1.rdoc
- RELEASE_NOTES-1.4.2.rdoc

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No matching classes.

# Bio::GFF::GFF2::Record

Stores GFF2 record.

### Attributes

comment[RW]

Comment for the GFF record

### Public Class Methods

new(*arg) click to toggle source

Creates a Bio::GFF::GFF2::Record object. Is typically not called directly, but is called automatically when creating a Bio::GFF::GFF2 object.

Arguments:

- str: a tab-delimited line in GFF2 format

Arguments:

- seqname: seqname (String or nil)

- source: source (String or nil)

- feature: feature type (String)

- start_position: start (Integer)

- end_position: end (Integer)

- score: score (Float or nil)

- strand: strand (String or nil)

- frame: frame (Integer or nil)

- attributes: attributes (Array or nil)

    # File lib/bio/db/gff.rb, line 382
    def initialize(*arg)
      if arg.size == 1 then
        parse(arg[0])
      else
        @seqname, @source, @feature,
        start, endp, @score, @strand, frame,
        @attributes = arg
        @start = start ? start.to_i : nil
        @end   = endp  ? endp.to_i : nil
        @score = score ? score.to_f : nil
        @frame = frame ? frame.to_i : nil
      end
      @attributes ||= []
    end

parse(str) click to toggle source

Parses a GFF2-formatted line and returns a new Bio::GFF::GFF2::Record object.

    # File lib/bio/db/gff.rb, line 361
    def self.parse(str)
      self.new.parse(str)
    end

### Public Instance Methods

==(other) click to toggle source

Returns true if self == other. Otherwise, returns false.

    # File lib/bio/db/gff.rb, line 479
    def ==(other)
      super ||
        ((self.class == other.class and
          self.seqname == other.seqname and
          self.source  == other.source and
          self.feature == other.feature and
          self.start   == other.start and
          self.end     == other.end and
          self.score   == other.score and
          self.strand  == other.strand and
          self.frame   == other.frame and
          self.attributes == other.attributes) ? true : false)
    end

add_attribute(tag, value) click to toggle source

Adds a new tag-value pair.

Arguments:

- (required) tag: String

- (required) value: String or Bio::GFF::GFF2::Record::Value object.

Returns | value

    # File lib/bio/db/gff.rb, line 583
    def add_attribute(tag, value)
      @attributes.push([ String.new(tag), value ])
    end

attribute(tag) click to toggle source
Alias for: get_attribute
attributes_to_hash() click to toggle source

Returns hash representation of attributes.

Note: If two or more tag-value pairs with same tag names exist, only the first tag-value pair is used for each tag.

Returns | Hash object

    # File lib/bio/db/gff.rb, line 661
    def attributes_to_hash
      h = {}
      @attributes.each do |x|
        key, val = x
        h[key] = val unless h[key]
      end
      h
    end

comment_only?() click to toggle source

Returns true if the entry is empty except for comment. Otherwise, returns false.

    # File lib/bio/db/gff.rb, line 439
    def comment_only?
      if !@seqname and
          !@source and
          !@feature and
          !@start and
          !@end and
          !@score and
          !@strand and
          !@frame and
          @attributes.empty? then
        true
      else
        false
      end
    end

comments() click to toggle source

"comments" is deprecated. Instead, use "comment".

    # File lib/bio/db/gff.rb, line 401
    def comments
      warn "#{self.class.to_s}#comments is deprecated. Instead, use \"comment\"."
      self.comment
    end

comments=(str) click to toggle source

"comments=" is deprecated. Instead, use "comment=".

    # File lib/bio/db/gff.rb, line 407
    def comments=(str)
      warn "#{self.class.to_s}#comments= is deprecated. Instead, use \"comment=\"."
      self.comment = str
    end

delete_attribute(tag, value) click to toggle source

Removes a specific tag-value pair.

Note that if two or more tag-value pairs found, only the first tag-value pair is removed.

Arguments:

- (required) tag: String

- (required) value: String or Bio::GFF::GFF2::Record::Value object.

Returns | if removed, value. Otherwise, nil.

    # File lib/bio/db/gff.rb, line 597
    def delete_attribute(tag, value)
      removed = nil
      if i = @attributes.index([ tag, value ]) then
        ary = @attributes.delete_at(i)
        removed = ary[1]
      end
      removed
    end

delete_attributes(tag) click to toggle source

Removes all attributes with the specified tag.

Arguments:

- (required) tag: String

Returns | if removed, self. Otherwise, nil.

    # File lib/bio/db/gff.rb, line 612
    def delete_attributes(tag)
      @attributes.reject! do |x|
        x[0] == tag
      end ? self : nil
    end

get_attribute(tag) click to toggle source

Gets the attribute value for the given tag.

Note that if two or more tag-value pairs with the same name found, only the first value is returned.

Arguments:

- (required) tag: String

Returns | String, Bio::GFF::GFF2::Record::Value object, or nil.

    # File lib/bio/db/gff.rb, line 501
    def get_attribute(tag)
      ary = @attributes.assoc(tag)
      ary ? ary[1] : nil
    end

Also aliased as: attribute
get_attributes(tag) click to toggle source

Gets the attribute values for the given tag. This method always returns an array.

Arguments:

- (required) tag: String

Returns | Array containing String or \

Bio::GFF::GFF2::Record::Value objects.

    # File lib/bio/db/gff.rb, line 514
    def get_attributes(tag)
      ary = @attributes.find_all do |x|
        x[0] == tag
      end
      ary.collect! { |x| x[1] }
      ary
    end

parse(string) click to toggle source

Parses a GFF2-formatted line and stores data from the string. Note that all existing data is wiped out.

    # File lib/bio/db/gff.rb, line 414
    def parse(string)
      if /^\s*\#/ =~ string then
        @comment = string[/\#(.*)/, 1].chomp
        columns = []
      else
        columns = string.chomp.split("\t", 10)
        @comment = columns[9][/\#(.*)/, 1].chomp if columns[9]
      end

      @seqname, @source, @feature,
      start, endp, score, @strand, frame =
        columns[0, 8].collect { |x|
        str = unescape(x)
        str == '.' ? nil : str
      }
      @start = start ? start.to_i : nil
      @end   = endp  ? endp.to_i : nil
      @score = score ? score.to_f : nil
      @frame = frame ? frame.to_i : nil

      @attributes = parse_attributes(columns[8])
    end

replace_attributes(tag, *values) click to toggle source

Replaces values for the given tags with new values. Existing values for the tag are completely wiped out and replaced by new tag-value pairs. If the tag does not exist, the tag-value pairs are newly added.

Arguments:

- (required) tag: String

- (required) values: String or Bio::GFF::GFF2::Record::Value objects.

Returns | self

    # File lib/bio/db/gff.rb, line 556
    def replace_attributes(tag, *values)
      i = 0
      @attributes.reject! do |x|
        if x[0] == tag then
          if i >= values.size then
            true
          else
            x[1] = values[i]
            i += 1
            false
          end
        else
          false
        end
      end
      (i...(values.size)).each do |j|
        @attributes.push [ String.new(tag), values[j] ]
      end
      self
    end

set_attribute(tag, value) click to toggle source

Sets value for the given tag. If the tag exists, the value of the tag is replaced with value. Note that if two or more tag-value pairs with the same name found, only the first tag-value pair is replaced.

If the tag does not exist, the tag-value pair is newly added.

Arguments:

- (required) tag: String

- (required) value: String or Bio::GFF::GFF2::Record::Value object.

Returns | value

    # File lib/bio/db/gff.rb, line 533
    def set_attribute(tag, value)
      ary = @attributes.find do |x|
        x[0] == tag
      end
      if ary then
        ary[1] = value
      else
        ary = [ String.new(tag), value ]
        @attributes.push ary
      end
      value
    end

sort_attributes_by_tag!(tags = nil) click to toggle source

Sorts attributes order by given tag name's order. If a block is given, the argument tags is ignored, and yields two tag names like Array#sort!.

Arguments:

- (required or optional) tags: Array containing String objects

Returns | self

    # File lib/bio/db/gff.rb, line 626
    def sort_attributes_by_tag!(tags = nil)
      h = {}
      s = @attributes.size
      @attributes.each_with_index { |x, i|  h[x] = i }
      if block_given? then
        @attributes.sort! do |x, y|
          r = yield x[0], y[0]
          if r == 0 then
            r = (h[x] || s) <=> (h[y] || s)
          end
          r
        end
      else
        unless tags then
          raise ArgumentError, 'wrong number of arguments (0 for 1) or wrong argument value'
        end
        @attributes.sort! do |x, y|
          r = (tags.index(x[0]) || tags.size) <=>
            (tags.index(y[0]) || tags.size)
          if r == 0 then
            r = (h[x] || s) <=> (h[y] || s)
          end
          r
        end
      end
      self
    end

to_s() click to toggle source

Return the record as a GFF2 compatible string

    # File lib/bio/db/gff.rb, line 456
    def to_s
      cmnt = if defined?(@comment) and @comment and
                 !@comment.to_s.strip.empty? then
               @comment.gsub(/[\r\n]+/, ' ')
             else
               false
             end
      return "\##{cmnt}\n" if self.comment_only? and cmnt
      [
       gff2_column_to_s(@seqname),
       gff2_column_to_s(@source),
       gff2_column_to_s(@feature),
       gff2_column_to_s(@start),
       gff2_column_to_s(@end),
       gff2_column_to_s(@score),
       gff2_column_to_s(@strand),
       gff2_column_to_s(@frame),
       attributes_to_s(@attributes)
      ].join("\t") +
        (cmnt ? "\t\##{cmnt}\n" : "\n")
    end

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