X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=alg%2Ftest%2Ftest_seq_span.cpp;h=9e22f3cb3f93fed3425d9a6106c6c12c8660dddb;hp=4989b6cbc8dc37159ed8604da6b71990a8b1e199;hb=97498410e1fc5c39eac0282a6620b8fcb0f02ff3;hpb=75496e2c562d728af983c347527270eba360c6ee

diff --git a/alg/test/test_seq_span.cpp b/alg/test/test_seq_span.cpp
index 4989b6c..9e22f3c 100644
--- a/alg/test/test_seq_span.cpp
+++ b/alg/test/test_seq_span.cpp
@@ -1,5 +1,6 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_seq_span
+#include <boost/test/unit_test.hpp>
 
 #include "seq_span.hpp"
 #include "mussa_exceptions.hpp"
@@ -73,6 +74,23 @@ BOOST_AUTO_TEST_CASE( seqspan_from_seqspan )
   BOOST_CHECK_EQUAL(span3->sequence(), str1);
 }
 
+BOOST_AUTO_TEST_CASE( seqspan_copy )
+{
+  SeqSpanRef span1(new SeqSpan("AAAAGGGG"));
+  SeqSpanRef span2 = span1->subseq(0,4);
+  SeqSpanRef span2ref(span2);  
+  SeqSpanRef span2copy(new SeqSpan(span2));
+  
+  BOOST_CHECK_EQUAL(span2->start(), 0);
+  BOOST_CHECK_EQUAL(span2ref->start(), 0);
+  BOOST_CHECK_EQUAL(span2copy->start(), 0);
+  
+  span2->setStart(2);
+  BOOST_CHECK_EQUAL(span2->start(), 2);
+  BOOST_CHECK_EQUAL(span2ref->start(), 2);
+  BOOST_CHECK_EQUAL(span2copy->start(), 0);  
+}
+
 BOOST_AUTO_TEST_CASE( seqspan_equality )
 {
   std::string str1("AAGGCCTT");
@@ -90,6 +108,25 @@ BOOST_AUTO_TEST_CASE( seqspan_equality )
   BOOST_CHECK_EQUAL(SeqSpan::isFamily(*span2, *span3), false);
 }
 
+BOOST_AUTO_TEST_CASE( seqspan_parents )
+{
+  std::string str1("AAGGCCTT");
+  std::string str2("AACCGGTT");
+  SeqSpanRef s1(new SeqSpan(str1));
+  SeqSpanRef s1_1 = s1->subseq(2,4);
+  SeqSpanRef s2(new SeqSpan(str2));
+  SeqSpanRef s2_1 = s2->subseq(0,2);
+
+  BOOST_CHECK_EQUAL(s1, s1_1->parent());
+  BOOST_CHECK_EQUAL(s2, s2_1->parent());
+  BOOST_CHECK(s1 != s2_1->parent());
+  BOOST_CHECK(s2 != s1_1->parent());
+
+  SeqSpanRef s2_copy = s2;
+
+  BOOST_CHECK_EQUAL(s2_copy, s2_1->parent());
+}
+
 BOOST_AUTO_TEST_CASE( seqspan_find_first_not_of )
 {
   std::string str1("AAAAT");
@@ -288,6 +325,28 @@ BOOST_AUTO_TEST_CASE( seqspan_global_mutable_start_stop )
   BOOST_CHECK_EQUAL( s3->size(), 1);
 }
 
+BOOST_AUTO_TEST_CASE( seqspan_global_mutable_start_stop_minus_strand )
+{
+  std::string seq_string("AAAAGCTA");
+  SeqSpanRef s1(new SeqSpan(seq_string));
+
+  SeqSpanRef s2 = s1->subseq(2,3, SeqSpan::MinusStrand);
+  BOOST_CHECK_EQUAL( s2->start(), 2);
+  BOOST_CHECK_EQUAL( s2->stop(), 2+3);
+  BOOST_CHECK_EQUAL( s2->size(), 3);
+  BOOST_CHECK_EQUAL( s2->sequence(), "CTT");
+  
+  SeqSpanRef s3 = s2->subseq(1,2, SeqSpan::SameStrand);
+  BOOST_CHECK_EQUAL(s3->sequence(), "TT");
+  
+  // Could also argue that it should be CT
+  // if you assume that the locations are all relative to the global sequence
+  // and are then reverse complemented
+  
+  s2->setStart(1);
+  BOOST_CHECK_EQUAL( s2->sequence(), "CTTT");
+}
+
 BOOST_AUTO_TEST_CASE( seqspan_parent_mutable_start_stop )
 {
   std::string seq_string("AAGGCCTT");
@@ -378,4 +437,5 @@ BOOST_AUTO_TEST_CASE( seqspan_strand_plusminus )
   BOOST_CHECK_EQUAL(seq2->sequence(), "AAAA");
   SeqSpanRef seq3 = seq1->subseq(0,4,SeqSpan::MinusStrand); 
   BOOST_CHECK_EQUAL(seq3->sequence(), "TTTT");
-}
\ No newline at end of file
+}
+