bioinform 0.1.12 → 0.1.13

data/spec/support/array_zip_spec.rb

@@ -1,15 +1,15 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/array_zip'
-
-describe Array do
-  context '::zip' do
-    it 'should take any number of arrays and zip them as if #zip was made to first and others' do
-      Array.zip([1,2,3]).should == [1,2,3].zip()
-      Array.zip([1,2,3],[4,5,6]).should == [1,2,3].zip([4,5,6])
-      Array.zip([1,2,3],[4,5,6],[7,8,9]).should == [1,2,3].zip([4,5,6],[7,8,9])
-    end
-    it 'should return empty array if no arrays\'re given' do
-      Array.zip().should == []
-    end
-  end
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/support/array_zip'
+
+describe Array do
+  context '::zip' do
+    it 'should take any number of arrays and zip them as if #zip was made to first and others' do
+      Array.zip([1,2,3]).should == [1,2,3].zip()
+      Array.zip([1,2,3],[4,5,6]).should == [1,2,3].zip([4,5,6])
+      Array.zip([1,2,3],[4,5,6],[7,8,9]).should == [1,2,3].zip([4,5,6],[7,8,9])
+    end
+    it 'should return empty array if no arrays\'re given' do
+      Array.zip().should == []
+    end
+  end
 end

data/spec/support/collect_hash_spec.rb

@@ -1,15 +1,15 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/collect_hash'
-
-describe Enumerable do
-  # %w{A C G T}.collect_hash{|k| [k*2, k*3] }
-  # # ==> {"AA" => "AAA", "CC" => "CCC", "GG" => "GGG", "TT" => "TTT"}
-  context '#collect_hash' do
-    it 'should take a block and create a hash from collected [k,v] pairs' do
-      %w{A C G T}.collect_hash{|k| [k*2, k*3] }.should == {"AA" => "AAA", "CC" => "CCC", "GG" => "GGG", "TT" => "TTT"}
-    end
-    it 'should create a hash from yielded [k,v] pairs if block not given' do
-      %w{A C G T}.each_with_index.collect_hash.should == {"A" => 0, "C" => 1, "G" => 2, "T" => 3}
-    end
-  end
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/support/collect_hash'
+
+describe Enumerable do
+  # %w{A C G T}.collect_hash{|k| [k*2, k*3] }
+  # # ==> {"AA" => "AAA", "CC" => "CCC", "GG" => "GGG", "TT" => "TTT"}
+  context '#collect_hash' do
+    it 'should take a block and create a hash from collected [k,v] pairs' do
+      %w{A C G T}.collect_hash{|k| [k*2, k*3] }.should == {"AA" => "AAA", "CC" => "CCC", "GG" => "GGG", "TT" => "TTT"}
+    end
+    it 'should create a hash from yielded [k,v] pairs if block not given' do
+      %w{A C G T}.each_with_index.collect_hash.should == {"A" => 0, "C" => 1, "G" => 2, "T" => 3}
+    end
+  end
 end

data/spec/support/delete_many_spec.rb

@@ -1,44 +1,44 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/delete_many'
-
-describe Array do
-  before :each do
-    @arr = %w{a b c d e f g h i j b b}
-  end
-  describe '#delete_at_many' do
-    it 'should delete elements at specified indices when indices in ascending order' do
-      @arr.delete_at_many(1,3,7)
-      @arr.should == %w{a c e f g i j b b}
-    end
-    it 'should delete elements at specified indices when indices in descending order' do
-      @arr.delete_at_many(7,3,1)
-      @arr.should == %w{a c e f g i j b b}
-    end
-    it 'should delete elements at specified indices when indices in arbitrary order' do
-      @arr.delete_at_many(3,1,7)
-      @arr.should == %w{a c e f g i j b b}
-    end
-    it 'should delete at each index once' do
-      @arr.delete_at_many(0,0,0,2,0)
-      @arr.should == %w{b d e f g h i j b b}
-    end
-  end
-  describe '#delete_many' do
-    it 'should delete multiple elements with specified values' do
-      @arr.delete_many('b', 'd', 'h', 'b')
-      @arr.should == %w{a c e f g i j}
-    end
-  end
-end
-
-describe Hash do
-  before :each do
-    @arr = {A: 3, T: 6, G: 4, C: 5}
-  end
-  describe '#delete_many' do
-    it 'should delete specified keys' do
-      @arr.delete_many(:T, :C, :F, :T, :T)
-      @arr.should == {A: 3, G: 4}
-    end
-  end
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/support/delete_many'
+
+describe Array do
+  before :each do
+    @arr = %w{a b c d e f g h i j b b}
+  end
+  describe '#delete_at_many' do
+    it 'should delete elements at specified indices when indices in ascending order' do
+      @arr.delete_at_many(1,3,7)
+      @arr.should == %w{a c e f g i j b b}
+    end
+    it 'should delete elements at specified indices when indices in descending order' do
+      @arr.delete_at_many(7,3,1)
+      @arr.should == %w{a c e f g i j b b}
+    end
+    it 'should delete elements at specified indices when indices in arbitrary order' do
+      @arr.delete_at_many(3,1,7)
+      @arr.should == %w{a c e f g i j b b}
+    end
+    it 'should delete at each index once' do
+      @arr.delete_at_many(0,0,0,2,0)
+      @arr.should == %w{b d e f g h i j b b}
+    end
+  end
+  describe '#delete_many' do
+    it 'should delete multiple elements with specified values' do
+      @arr.delete_many('b', 'd', 'h', 'b')
+      @arr.should == %w{a c e f g i j}
+    end
+  end
+end
+
+describe Hash do
+  before :each do
+    @arr = {A: 3, T: 6, G: 4, C: 5}
+  end
+  describe '#delete_many' do
+    it 'should delete specified keys' do
+      @arr.delete_many(:T, :C, :F, :T, :T)
+      @arr.should == {A: 3, G: 4}
+    end
+  end
 end

data/spec/support/inverf_spec.rb

@@ -1,19 +1,19 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/inverf'
-
-describe 'Math#inverf' do
-  it 'should be erf(inverf(x)) == x' do
-    rng = (-0.9..0.9).step(0.1)
-    arr = rng.to_a
-    arr2 = rng.map{|x| Math.inverf(x)}.map{|x| Math.erf(x)}
-    delta = arr.each_index.map{|i| (arr[i] - arr2[i]).abs }
-    delta.each{|el| el.should <= 0.001}
-  end
-  it 'should be erf(inverf(x)) == x' do
-    rng = (-5..5).step(1)
-    arr = rng.to_a
-    arr2 = rng.map{|x| Math.erf(x)}.map{|x| Math.inverf(x)}
-    delta = arr.each_index.map{|i| (arr[i] - arr2[i]).abs }
-    delta.each{|el| el.should <= 0.01}
-  end
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/support/inverf'
+
+describe 'Math#inverf' do
+  it 'should be erf(inverf(x)) == x' do
+    rng = (-0.9..0.9).step(0.1)
+    arr = rng.to_a
+    arr2 = rng.map{|x| Math.inverf(x)}.map{|x| Math.erf(x)}
+    delta = arr.each_index.map{|i| (arr[i] - arr2[i]).abs }
+    delta.each{|el| el.should <= 0.001}
+  end
+  it 'should be erf(inverf(x)) == x' do
+    rng = (-5..5).step(1)
+    arr = rng.to_a
+    arr2 = rng.map{|x| Math.erf(x)}.map{|x| Math.inverf(x)}
+    delta = arr.each_index.map{|i| (arr[i] - arr2[i]).abs }
+    delta.each{|el| el.should <= 0.01}
+  end
 end

data/spec/support/multiline_squish_spec.rb

@@ -1,25 +1,25 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/multiline_squish'
-
-describe String do
-  describe '#multiline_squish' do
-    it 'should replace multiple spaces with one space' do
-      "abc def   ghi\n  jk  lmn".multiline_squish.should == "abc def ghi\njk lmn"
-    end
-    it 'should replace tabs with a space' do
-      "abc\tdef   ghi \t jk".multiline_squish.should == 'abc def ghi jk'
-    end
-    it 'should replace \r\n with \n' do
-      "abc def ghi\r\njk lmn".multiline_squish.should == "abc def ghi\njk lmn"
-    end
-    it 'should preserve rows pagination' do
-      "abc def ghi\njk lmn".multiline_squish.should == "abc def ghi\njk lmn"
-    end
-    it 'should preserve empty lines in the middle of text' do
-      "abc def\n\nghi\n \t  \njk lmn \n\n\n zzz".multiline_squish.should == "abc def\n\nghi\n\njk lmn\n\n\nzzz"
-    end
-    it 'should drop empty lines at begin and at end of string' do
-      "\n  \t\n\nabc def\n\nghi\n \t  \njk lmn \n\n\n zzz\n\n \t  \n".multiline_squish.should == "abc def\n\nghi\n\njk lmn\n\n\nzzz"
-    end
-  end
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/support/multiline_squish'
+
+describe String do
+  describe '#multiline_squish' do
+    it 'should replace multiple spaces with one space' do
+      "abc def   ghi\n  jk  lmn".multiline_squish.should == "abc def ghi\njk lmn"
+    end
+    it 'should replace tabs with a space' do
+      "abc\tdef   ghi \t jk".multiline_squish.should == 'abc def ghi jk'
+    end
+    it 'should replace \r\n with \n' do
+      "abc def ghi\r\njk lmn".multiline_squish.should == "abc def ghi\njk lmn"
+    end
+    it 'should preserve rows pagination' do
+      "abc def ghi\njk lmn".multiline_squish.should == "abc def ghi\njk lmn"
+    end
+    it 'should preserve empty lines in the middle of text' do
+      "abc def\n\nghi\n \t  \njk lmn \n\n\n zzz".multiline_squish.should == "abc def\n\nghi\n\njk lmn\n\n\nzzz"
+    end
+    it 'should drop empty lines at begin and at end of string' do
+      "\n  \t\n\nabc def\n\nghi\n \t  \njk lmn \n\n\n zzz\n\n \t  \n".multiline_squish.should == "abc def\n\nghi\n\njk lmn\n\n\nzzz"
+    end
+  end
 end

data/spec/support/partial_sums_spec.rb

@@ -1,30 +1,30 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/partial_sums'
-
-describe 'Array#partial_sums' do
-  context 'when no initial value given' do
-    it 'should return an array of the same size with partial sums of elements 0..ind inclusive with float elements' do
-      [2,3,4,5].partial_sums.should == [2, 5, 9, 14]
-      [2,3,4,5].partial_sums.last.should be_kind_of(Float)
-    end
-  end
-  it 'should start counting from argument when it\'s given. Type of values depends on type of initial value' do
-    [2,3,4,5].partial_sums(100).should == [102,105,109,114]
-    [2,3,4,5].partial_sums(100).last.should be_kind_of(Integer)
-  end
-end
-
-{1 => 5, 4 => 3, 3 => 2}.partial_sums == {1=>5, 3=>7, 4=>10}
-
-describe 'Hash#partial_sums' do
-  context 'when no initial value given' do
-    it 'should return a hash with float values of the same size with partial sums of elements that has keys <= than argument' do
-      {1 => 5, 4 => 3, 3 => 2}.partial_sums.should == {1=>5, 3=>7, 4=>10}
-      {1 => 5, 4 => 3, 3 => 2}.partial_sums.values.last.should be_kind_of(Float)
-    end
-  end
-  it 'should start counting from argument when it\'s given. Type of values depends on type of initial value' do
-    {1 => 5, 4 => 3, 3 => 2}.partial_sums(100).should == {1=>105, 3=>107, 4=>110}
-    {1 => 5, 4 => 3, 3 => 2}.partial_sums(100).values.last.should be_kind_of(Integer)
-  end
-end
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/support/partial_sums'
+
+describe 'Array#partial_sums' do
+  context 'when no initial value given' do
+    it 'should return an array of the same size with partial sums of elements 0..ind inclusive with float elements' do
+      [2,3,4,5].partial_sums.should == [2, 5, 9, 14]
+      [2,3,4,5].partial_sums.last.should be_kind_of(Float)
+    end
+  end
+  it 'should start counting from argument when it\'s given. Type of values depends on type of initial value' do
+    [2,3,4,5].partial_sums(100).should == [102,105,109,114]
+    [2,3,4,5].partial_sums(100).last.should be_kind_of(Integer)
+  end
+end
+
+{1 => 5, 4 => 3, 3 => 2}.partial_sums == {1=>5, 3=>7, 4=>10}
+
+describe 'Hash#partial_sums' do
+  context 'when no initial value given' do
+    it 'should return a hash with float values of the same size with partial sums of elements that has keys <= than argument' do
+      {1 => 5, 4 => 3, 3 => 2}.partial_sums.should == {1=>5, 3=>7, 4=>10}
+      {1 => 5, 4 => 3, 3 => 2}.partial_sums.values.last.should be_kind_of(Float)
+    end
+  end
+  it 'should start counting from argument when it\'s given. Type of values depends on type of initial value' do
+    {1 => 5, 4 => 3, 3 => 2}.partial_sums(100).should == {1=>105, 3=>107, 4=>110}
+    {1 => 5, 4 => 3, 3 => 2}.partial_sums(100).values.last.should be_kind_of(Integer)
+  end
+end

data/spec/support/same_by_spec.rb

@@ -1,36 +1,36 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/same_by'
-
-describe Enumerable do
-  describe '#same_by?' do
-    it 'should be work with both hashes and arrays' do
-      ['a','b','c'].same_by?{|k| k.length}
-      {'a'=>13,'b'=>12,'c'=>14}.same_by?{|k,v| v < 20}
-    end
-    it 'should be true for empty collections' do
-      [].same_by?(&:length).should be_true
-      [].same_by?.should be_true
-    end
-    context 'without block' do
-      it 'should compare if all elements of collection are the same' do
-        %w{cat cat cat}.same_by?.should be_true
-        %w{cat dog rat}.same_by?.should be_false
-      end
-    end
-    context 'with a block' do
-      it 'should compare enumerables by a value of block' do
-        %w{cat dog rat}.same_by?(&:length).should be_true
-        %w{cat dog rabbit}.same_by?(&:length).should be_false
-      end
-      it 'should be true if all elements are true' do
-        [4,8,2,2].same_by?(&:even?).should be_true
-      end
-      it 'should be true if all elements are false' do
-        [1,3,9,7].same_by?(&:even?).should be_true
-      end
-      it 'should be false if some elements are true and some are false' do
-        [1,8,3,2].same_by?(&:even?).should be_false
-      end
-    end
-  end
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/support/same_by'
+
+describe Enumerable do
+  describe '#same_by?' do
+    it 'should be work with both hashes and arrays' do
+      ['a','b','c'].same_by?{|k| k.length}
+      {'a'=>13,'b'=>12,'c'=>14}.same_by?{|k,v| v < 20}
+    end
+    it 'should be true for empty collections' do
+      [].same_by?(&:length).should be_true
+      [].same_by?.should be_true
+    end
+    context 'without block' do
+      it 'should compare if all elements of collection are the same' do
+        %w{cat cat cat}.same_by?.should be_true
+        %w{cat dog rat}.same_by?.should be_false
+      end
+    end
+    context 'with a block' do
+      it 'should compare enumerables by a value of block' do
+        %w{cat dog rat}.same_by?(&:length).should be_true
+        %w{cat dog rabbit}.same_by?(&:length).should be_false
+      end
+      it 'should be true if all elements are true' do
+        [4,8,2,2].same_by?(&:even?).should be_true
+      end
+      it 'should be true if all elements are false' do
+        [1,3,9,7].same_by?(&:even?).should be_true
+      end
+      it 'should be false if some elements are true and some are false' do
+        [1,8,3,2].same_by?(&:even?).should be_false
+      end
+    end
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bioinform
 version: !ruby/object:Gem::Version
-  version: 0.1.12
+  version: 0.1.13
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-22 00:00:00.000000000 Z
+date: 2013-12-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: docopt
@@ -180,7 +180,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.4
+rubygems_version: 2.1.11
 signing_key: 
 specification_version: 4
 summary: Classes for work with different input formats of positional matrices and