rdoc comments preprared

README.rdoc

@@ -35,11 +35,27 @@ Last one is generated from a "Zero-based half-closed[start, end)"  interval
  ref.adjacent = 1
  ref.compare(cmp) # => :right_off
 
+== Overlap metrics
+* When a overlap exist, return a positive integers (>1) for the overlap length.
+* When a overlap does not exist, return a zero or a negative (<= 0) for the space size between the intervals.
+
+ ref = Bio::GenomicInterval.parse("chr1:10-20")
+ cmp = Bio::GenomicInterval.parse("chr1:15-25")
+ ref.overlap(cmp) # => 6
+ cmp2 = Bio::GenomicInterval.parse("chr1:25-35")
+ ref.overlap(cmp) # => -4
+
 == Expansion (or integration)
  ref =   Bio::GenomicInterval.parse("chr1:400-600")
  other = Bio::GenomicInterval.parse("chr1:650-800")
  ref.expand(other).to_s # => "chr1:400-800"
 
+== Center
+ obj1 = Bio::GenomicInterval.parse("chr1:1-3")
+ obj1.center # => "chr1:2-2"
+ obj2 = Bio::GenomicInterval.parse("chr2:1-4")
+ obj2.center # => "chr1:2-2"
+
 == and others
 See RDoc and Rspec specification.
 

lib/bio-genomic-interval.rb

@@ -1,6 +1,10 @@
 module Bio
 
+  #
+  # =a class for manupirate genomic intervals such as "chr1:123-456"
+  #
   class GenomicInterval
+    # a default value to determine the adjacent/very near distance in bp 
     DEFAULT_ADJACENT = 20
 
     def initialize(chrom = "", chr_start = 1, chr_end = 1)
@@ -15,6 +19,10 @@ def initialize(chrom = "", chr_start = 1, chr_end = 1)
 
     attr_accessor :chrom, :chr_start, :chr_end, :adjacent
 
+    #
+    # generate an interval object from a string expressing 
+    # one-based full-closed interval such as "chr1:123-456"
+    # 
     def self.parse(interval)
       chrom, start_end = interval.split(":")
       str_start, str_end = start_end.split("-")[0..1]
@@ -26,24 +34,44 @@ def self.parse(interval)
       end
       self.new(chrom, chr_start, chr_end)
   end
-
+
+    #
+    # generate an interval object from three atguments expressing 
+    # zero-based half-closed interval such as "chr1", 122, 456
+    # 
     def self.zero_based(chrom = "", z_start = 0, z_end = 1)
       z_start += 1
       self.new(chrom, z_start, z_end)
     end
 
+    #
+    # returns one-based full-closed interval such as "chr1:123-456"
+    #
     def to_s
       "#{@chrom}:#{@chr_start}-#{@chr_end}"
     end
 
+    #
+    # returns zero-based half-closed start position
+    # 
     def zero_start
       @chr_start - 1
     end
 
+    #
+    # returns zero-based half-closed end position
+    # 
     def zero_end
       @chr_end
     end
 
+    #
+    # returns one of the followings:
+    #  :different_chrom, :left_adjacent, :right_adjacent
+    #  :left_off, :right_off, :equal
+    #  :contained, :containing, :left_overlapped, :right_overlapped
+    # Imagine that the receiver object is fixed on a number line
+    #
     def compare(other)
       case
       when self.chrom != other.chrom
@@ -107,9 +135,9 @@ def center
       Bio::GenomicInterval.new(self.chrom, center, center)
     end
 
-    # when a overlap exist, return a positive integers (>1) for the overlap length
-    # when a overlap does not exist,
-    #   return a zero or a negative (<= 0) for the space size between the intervals
+    # * When a overlap exist, return a positive integers (>1) for the overlap length.
+    # * When a overlap does not exist, return a zero or a negative (<= 0) for the space size between the intervals.
+    #
     def overlap(other)
       case self.compare(other)
       when :different_chrom