corrects tests and DB comparisons

.rspec

@@ -1,2 +1 @@
 --color
---require spec_helper

rakefile.rb

@@ -1,9 +1,17 @@
+require 'byebug'
+
 require 'rake/testtask'
 require 'rake/clean'
 require 'rspec/core/rake_task'
 
 RSpec::Core::RakeTask.new(:spec) do |t|
-  t.pattern = Dir.glob('test/**/test_*.rb')
+  t.pattern = Dir.glob('test/test_*.rb')
+  t.rspec_opts = '--format documentation'
+  # t.rspec_opts << ' more options'
+end
+
+RSpec::Core::RakeTask.new(:'spec:db') do |t|
+  t.pattern = Dir.glob('test/test_results_db.rb')
   t.rspec_opts = '--format documentation'
   # t.rspec_opts << ' more options'
 end

src/results_db.rb

@@ -31,9 +31,10 @@ def row
   end
 
   def <=>(other)
-    (identity <=> other.identity &&
-     coverage <=> other.coverage &&
-     evalue <=> other.evalue)
+    (identity <=> other.identity).nonzero? ||
+      (coverage <=> other.coverage).nonzero? ||
+      (evalue <=> other.evalue).nonzero? ||
+      0
   end
 
   def [](key)
@@ -80,6 +81,10 @@ def initialize(identity_min, identity_max, output_dir, logger = nil)
     @logger.progname = 'ResultDB'
   end
 
+  def [](key)
+    db[key]
+  end
+
   def values
     @db.values.sort_by do |line|
       [line['file'], line['pident'], line['qcovs'], line['sseqid']]
@@ -125,13 +130,18 @@ def add(db_id, new_row)
       write_deleted new_row
       return false
     end
+    if db_id.nil?
+      db_id = size + 1
+    end
     # set current row as existing one
     cur_row = db[db_id]
     # initialize best row as nil, to be assigned in the
     #  next if clause
     best_row = nil
     # check if there is a element in @db with the 'db_id'
     if cur_row
+      #require 'byebug'
+      #byebug
       # add to redundant array the worst element
       old_row = if new_row > cur_row
                   best_row = new_row

test/test_blastn.rb

@@ -1,4 +1,4 @@
-require_relative 'spec_helper'
+require_relative 'test_helper'
 require_relative 'blast_helpers'
 
 RSpec.configure do |c|

test/test_results_db.rb

@@ -1,4 +1,4 @@
-require_relative 'spec_helper'
+require_relative 'test_helper'
 require_relative '../src/results_db'
 require 'logger'
 
@@ -15,25 +15,29 @@
     }
   end
 
+  create_db = proc do |min = 40, max = 100|
+    ResultsDB.new min, max, './'
+  end
+
   #
   #
   it 'should add all elements' do
-    results = ResultsDB.new 40
+    results = create_db.call(40)
     #
-    results.add(1, create_el.call('50', '40', '10E-20', 'aaa', 'blackberry'))
-    results.add(2, create_el.call('50', '40', '10E-20', 'aab', 'blackberry'))
-    results.add(3, create_el.call('50', '40', '10E-20', 'aaa', 'blackberry'))
+    results.add(nil, create_el.call('50', '40', '10E-20', 'aaa', 'blackberry'))
+    results.add(nil, create_el.call('50', '40', '10E-20', 'aab', 'blackberry'))
+    results.add(nil, create_el.call('50', '40', '10E-20', 'aaa', 'blackberry'))
 
     expect(results.size).to eq(3)
   end
 
   it 'should prune duplicate qseq elements' do
-    results = ResultsDB.new 40
+    results = create_db.call(40)
     #
-    results.add(1, create_el.call('30', '40', '10E-20', 'aaa', 'blackberry'))
-    results.add(2, create_el.call('50', '40', '10E-20', 'aab', 'blackberry'))
-    results.add(3, create_el.call('50', '40', '10E-20', 'aaa', 'blackberry'))
-    results.add(4, create_el.call('70', '40', '10E-20', 'aaa', 'blackberry'))
+    results.add(nil, create_el.call('30', '40', '10E-20', 'aaa', 'blackberry'))
+    results.add(nil, create_el.call('50', '40', '10E-20', 'aab', 'blackberry'))
+    results.add(nil, create_el.call('50', '40', '10E-20', 'aaa', 'blackberry'))
+    results.add(nil, create_el.call('70', '40', '10E-20', 'aaa', 'blackberry'))
 
     results.remove_identical('qseq')
 
@@ -42,23 +46,68 @@
 
   #
   it 'should prune duplicate qseq elements and use the database' do
-    results = ResultsDB.new 40
+    results = create_db.call(40)
     #
-    results.add(1, create_el.call('30', '40', '10E-20', 'aaa', 'blackberry'))
-    results.add(2, create_el.call('50', '40', '10E-20', 'aab', 'blackberry'))
-    results.add(3, create_el.call('50', '40', '10E-20', 'aaa', 'blackberry'))
-    results.add(4, create_el.call('70', '40', '10E-20', 'aaa', 'blackberry'))
-    results.add(5, create_el.call('70', '40', '10E-20', 'aaa', 'bilberry'))
+    results.add(nil, create_el.call('30', '40', '10E-20', 'aaa', 'blackberry'))
+    results.add(nil, create_el.call('50', '40', '10E-20', 'aab', 'blackberry'))
+    results.add(nil, create_el.call('50', '40', '10E-20', 'aaa', 'blackberry'))
+    results.add(nil, create_el.call('70', '40', '10E-20', 'aaa', 'blackberry'))
+    results.add(nil, create_el.call('70', '40', '10E-20', 'aaa', 'bilberry'))
 
     results.remove_identical('qseq')
 
     expect(results.size).to eq(3)
   end
 
+  it 'should compare well between DB items' do
+    db1 = DB.new \
+      create_el.call('30', '40', '10E-20', 'aaa', 'blackberry')
+    db2 = DB.new \
+      create_el.call('40', '40', '10E-20', 'aaa', 'blackberry')
+
+    expect(db1).to be < db2
+
+    db1 = DB.new \
+      create_el.call('30', '50', '10E-20', 'aaa', 'blackberry')
+    db2 = DB.new \
+      create_el.call('30', '40', '10E-20', 'aaa', 'blackberry')
+
+    expect(db1).to be > db2
+
+    db1 = DB.new \
+      create_el.call('30', '40', '0', 'aaa', 'blackberry')
+    db2 = DB.new \
+      create_el.call('30', '40', '10E-20', 'aaa', 'blackberry')
+
+    expect(db1).to be < db2
+
+    db1 = DB.new \
+      create_el.call('30', '40', '10E-20', 'aaa', 'blackberry')
+    db2 = DB.new \
+      create_el.call('30', '40', '10E-20', 'aaa', 'blackberry')
+
+    expect(db1).to eq(db2)
+  end
+
+  #
+  #
+  it 'should only take the best one' do
+    results = create_db.call(40)
+    #
+    results.add('i', create_el.call('30', '40', '10E-20', 'aaa', 'blackberry'))
+    results.add('i', create_el.call('50', '40', '10E-20', 'aab', 'blackberry'))
+    results.add('i', create_el.call('50', '40', '10E-20', 'aaa', 'blackberry'))
+    results.add('i', create_el.call('70', '40', '10E-20', 'aaa', 'blackberry'))
+    #
+    expect(results.size).to eq(1)
+    expect(results['i'].identity).to eq(70)
+    #
+  end
+
   #
   #
   it 'should add only elements with different id' do
-    results = ResultsDB.new 40
+    results = create_db.call(40)
     #
     results.add('1', create_el.call('50', '40', '10E-20', 'aaa', 'blackberry'))
     #

test/test_tblastx.rb

@@ -1,4 +1,4 @@
-require_relative 'spec_helper'
+require_relative 'test_helper'
 require_relative 'blast_helpers'
 
 RSpec.configure do |c|