refactored backtrack methods to use options hash in method invocations

[biopieces.git] / code_ruby / test / maasha / seq / test_backtrack.rb

diff --git a/code_ruby/test/maasha/seq/test_backtrack.rb b/code_ruby/test/maasha/seq/test_backtrack.rb
index 6000dc025cdc5ab3af7309ed6b66a7be94d4c451..79d530045cfb03bbbafff686d5aca210d9d023dd 100644 (file)
--- a/code_ruby/test/maasha/seq/test_backtrack.rb
+++ b/code_ruby/test/maasha/seq/test_backtrack.rb
@@ -51,66 +51,66 @@ class BackTrackTest < Test::Unit::TestCase
 
   test "#patscan with bad start raises" do
     [-1, 20].each { |start| 
-      assert_raise(BackTrackError) { @seq.patscan("N", start) }
+      assert_raise(BackTrackError) { @seq.patscan("N", start: start) }
     }
   end
 
   test "#patscan with OK start dont raise" do
     [0, 19].each { |start| 
-      assert_nothing_raised { @seq.patscan("N", start) }
+      assert_nothing_raised { @seq.patscan("N", start: start) }
     }
   end
 
   test "#patscan with bad stop raises" do
     [-1, 20].each { |stop|
-      assert_raise(BackTrackError) { @seq.patscan("N", [0, stop]) }
+      assert_raise(BackTrackError) { @seq.patscan("N", stop: stop) }
     }
   end
 
   test "#patscan with OK stop dont raise" do
     [0, 19].each { |stop|
-      assert_nothing_raised { @seq.patscan("N", [0, stop]) }
+      assert_nothing_raised { @seq.patscan("N", stop: stop) }
     }
   end
 
   test "#patscan with stop returns correctly" do
-    assert_nil(@seq.patmatch("G", [0, 2]))
-    assert_equal("3:1:g", @seq.patmatch("G", [0, 3]).to_s)
+    assert_nil(@seq.patmatch("G", start: 0, stop: 2))
+    assert_equal("3:1:g", @seq.patmatch("G", start: 0, stop: 3).to_s)
   end
 
   test "#patscan with bad mis raises" do
     [-1, 6].each { |mis| 
-      assert_raise(BackTrackError) { @seq.patscan("N", 0, mis) }
+      assert_raise(BackTrackError) { @seq.patscan("N", max_mismatches: mis) }
     }
   end
 
   test "#patscan with OK mis dont raise" do
     [0, 5].each { |mis| 
-      assert_nothing_raised { @seq.patscan("N", 0, mis) }
+      assert_nothing_raised { @seq.patscan("N", max_mismatches: mis) }
     }
   end
 
   test "#patscan with bad ins raises" do
     [-1, 6].each { |ins| 
-      assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, ins) }
+      assert_raise(BackTrackError) { @seq.patscan("N", max_insertions: ins) }
     }
   end
 
   test "#patscan with OK ins dont raise" do
     [0, 5].each { |ins| 
-      assert_nothing_raised { @seq.patscan("N", 0, 0, ins) }
+      assert_nothing_raised { @seq.patscan("N", max_insertions: ins) }
     }
   end
 
   test "#patscan with bad del raises" do
     [-1, 6].each { |del| 
-      assert_raise(BackTrackError) { @seq.patscan("N", 0, 0, 0, del) }
+      assert_raise(BackTrackError) { @seq.patscan("N", max_deletions: del) }
     }
   end
 
   test "#patscan with OK del dont raise" do
     [0, 5].each { |del| 
-      assert_nothing_raised { @seq.patscan("N", 0, 0, 0, del) }
+      assert_nothing_raised { @seq.patscan("N", max_deletions: del) }
     }
   end
 
@@ -127,36 +127,39 @@ class BackTrackTest < Test::Unit::TestCase
   end
 
   test "#patscan start is ok" do
-    assert_equal("10:1:g", @seq.patscan("N", 10).first.to_s)
-    assert_equal("19:1:g", @seq.patscan("N", 10).last.to_s)
+    assert_equal("10:1:g", @seq.patscan("N", start: 10).first.to_s)
+    assert_equal("19:1:g", @seq.patscan("N", start: 10).last.to_s)
   end
 
   test "#patscan mis left is ok" do
-    assert_equal("0:7:tacgatg", @seq.patscan("Aacgatg", 0, 1).first.to_s)
+    assert_equal("0:7:tacgatg", @seq.patscan("Aacgatg", max_mismatches: 1).first.to_s)
   end
 
   test "#patscan mis right is ok" do
-    assert_equal("13:7:tgcacgg", @seq.patscan("tgcacgA", 0, 1).first.to_s)
+    assert_equal("13:7:tgcacgg", @seq.patscan("tgcacgA", max_mismatches: 1).first.to_s)
   end
 
   test "#patscan ins left is ok" do
-    assert_equal("0:7:tacgatg", @seq.patscan("Atacgatg", 0, 0, 1).first.to_s)
+    assert_equal("0:7:tacgatg", @seq.patscan("Atacgatg", max_insertions: 1).first.to_s)
   end
 
   test "#patscan ins right is ok" do
-    assert_equal("13:7:tgcacgg", @seq.patscan("tgcacggA", 0, 0, 1).first.to_s)
+    assert_equal("13:7:tgcacgg", @seq.patscan("tgcacggA", max_insertions: 1).first.to_s)
   end
 
   test "#patscan del left is ok" do
-    assert_equal("0:7:tacgatg", @seq.patscan("acgatg", 0, 0, 0, 1).first.to_s)
+    assert_equal("0:7:tacgatg", @seq.patscan("acgatg", max_deletions: 1).first.to_s)
   end
 
   test "#patscan del right is ok" do
-    assert_equal("12:8:atgcacgg", @seq.patscan("tgcacgg", 0, 0, 0, 1).first.to_s)
+    assert_equal("12:8:atgcacgg", @seq.patscan("tgcacgg", max_deletions: 1).first.to_s)
   end
 
   test "#patscan ambiguity mis ins del all ok" do
-    assert_equal("0:20:tacgatgctagcatgcacgg", @seq.patscan("tacatgcNagGatgcCacgg", 0, 1, 1, 1).first.to_s)
+    assert_equal("0:20:tacgatgctagcatgcacgg", @seq.patscan("tacatgcNagGatgcCacgg",
+                                                           max_mismatches: 1,
+                                                           max_insertions: 1,
+                                                           max_deletions: 1).first.to_s)
   end
 end