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Sequence_test.hpp
1 /*
2  * SequenceTest.hpp
3  *
4  * Created on: 27 Sep 2013
5  * Author: ck
6  */
7 
8 #ifndef SEQUENCETEST_HPP_
9 #define SEQUENCETEST_HPP_
10 
11 #include "../lib/Sequence/SequenceSet.hpp"
12 #include "../lib/Sequence/Seq_functs.hpp"
13 
14 
15 class Sequence_Test : public CxxTest::TestSuite
16 {
17 public:
18 
19  void test_normal_seq()
20  {
21  MDAT::Sequence seq("NAME1", "ACGCTSLDJPSIOFEWJSLWE", "AHA", 2);
22  TS_ASSERT_EQUALS(seq.name(), "NAME1");
23  TS_ASSERT_EQUALS(seq.sequence(), "ACGCTSLDJPSIOFEWJSLWE");
24  TS_ASSERT_EQUALS(seq.comment(), "AHA");
25  TS_ASSERT_EQUALS(seq.id(), 2);
26  seq.name("NEW_NAME");
27  TS_ASSERT_EQUALS(seq.name(), "NEW_NAME");
28  seq.sequence("PPPPEPEKEKSD");
29  TS_ASSERT_EQUALS(seq.sequence(), "PPPPEPEKEKSD");
30  seq.comment("THIS IS A TEST");
31  TS_ASSERT_EQUALS(seq.comment(), "THIS IS A TEST");
32  seq.id(0);
33  TS_ASSERT_EQUALS(seq.id(), 0);
34  seq.append("AAAA");
35  TS_ASSERT_EQUALS(seq.sequence(), "PPPPEPEKEKSDAAAA")
36  seq.to_lower();
37  TS_ASSERT_EQUALS(seq.sequence(), "ppppepekeksdaaaa")
38  seq.to_upper();
39  TS_ASSERT_EQUALS(seq.sequence(), "PPPPEPEKEKSDAAAA")
40  seq.insert_gaps("mmmm-----mmmmmm--mmmmmm");
41  TS_ASSERT_EQUALS(seq.sequence(), "PPPPEP--EKEKSD-----AAAA");
42  MDAT::Sequence sub_seq = substr(seq, 1,4);
43  TS_ASSERT_EQUALS(sub_seq.sequence(), "PPPE");
44 
45 
46  }
47 
48  void test_protein_seq()
49  {
50  MDAT::ProteinSequence seq("NAME1", "ACGCTSLDJPSIOFEWJSLWE", "AHA", 2);
51  TS_ASSERT_EQUALS(seq.name(), "NAME1");
52  TS_ASSERT_EQUALS(seq.sequence(), "ACGCTSLDJPSIOFEWJSLWE");
53  TS_ASSERT_EQUALS(seq.comment(), "AHA");
54  TS_ASSERT_EQUALS(seq.id(), 2);
55  }
56 
57 
58 
59 };
60 
61 
62 #endif /* SEQUENCETEST_HPP_ */