-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_mussa
+#include <boost/test/unit_test.hpp>
+
+#include <boost/filesystem/path.hpp>
+#include <boost/filesystem/operations.hpp>
+namespace fs = boost::filesystem;
+#include <boost/assign/list_of.hpp>
+#include <boost/assign/list_inserter.hpp>
+#include <boost/assign.hpp>
+namespace assign = boost::assign;
#include <string>
+#include <sstream>
+#include <vector>
#include "alg/mussa.hpp"
+#include "mussa_exceptions.hpp"
+
+using namespace std;
//! can we initialize a mussa object?
BOOST_AUTO_TEST_CASE( mussa_simple )
{
Mussa m;
+ BOOST_CHECK_EQUAL(m.empty(), true);
BOOST_CHECK_EQUAL(m.get_name(), "" );
BOOST_CHECK_EQUAL(m.get_window(), 0);
BOOST_CHECK_EQUAL(m.get_threshold(), 0);
BOOST_CHECK_EQUAL(m.get_window(), 30);
m.set_threshold(21);
BOOST_CHECK_EQUAL(m.get_threshold(), 21);
+ BOOST_CHECK_EQUAL(m.get_soft_threshold(), 21);
+ m.set_soft_threshold(19);
+ BOOST_CHECK_EQUAL(m.get_soft_threshold(), 21);
+ m.set_soft_threshold(35);
+ BOOST_CHECK_EQUAL(m.get_soft_threshold(), 30);
+ m.set_soft_threshold(25);
+ BOOST_CHECK_EQUAL(m.get_soft_threshold(), 25);
m.set_analysis_mode(Mussa::RadialNway);
BOOST_CHECK_EQUAL(m.get_analysis_mode(), Mussa::RadialNway);
+ // make sure our path is empty
+ BOOST_CHECK_EQUAL(m.get_analysis_path().string(), fs::path().string() );
m.clear();
BOOST_CHECK_EQUAL(m.get_name(), "" );
BOOST_CHECK_EQUAL(m.get_analysis_mode(), Mussa::TransitiveNway);
}
+BOOST_AUTO_TEST_CASE ( mussa_title )
+{
+ Mussa m;
+
+ BOOST_CHECK_EQUAL( m.get_title(), "Unnamed");
+ string foo("foo");
+ m.set_name(foo);
+ BOOST_CHECK_EQUAL( m.get_title(), foo);
+ string foopath_name("/my/silly/path");
+ fs::path foopath(foopath_name);
+ m.set_analysis_path(foopath);
+ BOOST_CHECK_EQUAL( m.get_title().size(), 14);
+}
+
BOOST_AUTO_TEST_CASE( mussa_analysis_name )
{
Mussa m;
std::string s2("TTTTNNNN");
Mussa analysis;
- analysis.add_a_seq(s0);
- analysis.add_a_seq(s1);
- analysis.add_a_seq(s2);
+ BOOST_CHECK_EQUAL(analysis.empty(), true);
+ analysis.append_sequence(s0);
+ analysis.append_sequence(s1);
+ analysis.append_sequence(s2);
+ BOOST_CHECK_EQUAL( analysis.empty(), false);
BOOST_CHECK_EQUAL( analysis.sequences().size(), 3 );
- BOOST_CHECK_EQUAL( analysis.sequences()[0].get_seq(), s0);
- BOOST_CHECK_EQUAL( analysis.sequences()[1].get_seq(), s1);
- BOOST_CHECK_EQUAL( analysis.sequences()[2].get_seq(), s2);
+ BOOST_CHECK_EQUAL( *(analysis.sequences()[0]), s0);
+ BOOST_CHECK_EQUAL( *(analysis.sequences()[1]), s1);
+ BOOST_CHECK_EQUAL( *(analysis.sequences()[2]), s2);
}
// for some reason we can call nway once safely but it
BOOST_AUTO_TEST_CASE ( empty_mussa_set_threshold )
{
Mussa m;
- m.set_soft_thres(15);
+ m.set_soft_threshold(15);
m.nway();
- m.set_soft_thres(25);
+ m.set_soft_threshold(25);
m.nway();
}
-#include <unistd.h>
+BOOST_AUTO_TEST_CASE( mussa_load_mupa_crlf )
+{
+ fs::path example_path(EXAMPLE_DIR, fs::native);
+ fs::path seq_path(example_path / "seq" / "mouse_mck_pro.fa");
+ fs::path annot_path(example_path / "mm_mck3test.annot");
+
+ std::string mupa(
+ "# hello\015\012"
+ "ANA_NAME load_mupa_crlf\015\012");
+ mupa += "SEQUENCE " + seq_path.native_file_string() + "\015\012";
+ mupa += "ANNOTATION " + annot_path.native_file_string() + "\015\012";
+
+ istringstream mupa_stream(mupa);
+ Mussa m;
+ fs::path base;
+ m.load_mupa_stream( mupa_stream, base );
+ // Should run with no exceptions
+}
+
+BOOST_AUTO_TEST_CASE( mussa_load_mupa_comment_character )
+{
+ fs::path mupa_path(EXAMPLE_DIR, fs::native);
+ fs::path seq_path = fs::initial_path() / "seq" / "mouse_mck_pro.fa";
+ fs::path annot_path = fs::initial_path() / "mm_mck3test.annot";
+
+ std::string mupa(
+ "# hello\015\012"
+ "ANA_NAME load_mupa_crlf\015\012");
+ mupa += "#SEQUENCE " + seq_path.native_file_string() + "\015\012";
+ mupa += "#ANNOTATION " + annot_path.native_file_string() + "\015\012";
+
+ istringstream mupa_stream(mupa);
+ Mussa m;
+ fs::path base;
+ m.load_mupa_stream( mupa_stream, base );
+ // Should run with no exceptions
+}
+
+BOOST_AUTO_TEST_CASE( mussa_load_mupa_exception )
+{
+ std::string mupa(
+ "# hello\015\012"
+ "ANA_NAME load_mupa_crlf\015\012"
+ "mwahhaha I broke you!\n"
+ );
+
+ istringstream mupa_stream(mupa);
+ Mussa m;
+ fs::path base;
+ BOOST_CHECK_THROW(m.load_mupa_stream( mupa_stream, base ), mussa_load_error);
+}
+
BOOST_AUTO_TEST_CASE( mussa_load_mupa )
{
+ fs::path mupa_path(EXAMPLE_DIR, fs::native);
+ fs::path result_path = fs::initial_path() / "mck3test_w30_t20";
+ mupa_path /= "mck3test.mupa";
+
Mussa m1;
- chdir( "examples" );
- m1.load_mupa_file( "mck3test.mupa" );
- m1.analyze(0, 0);
+ m1.load_mupa_file( mupa_path );
+ m1.analyze();
+ m1.save( result_path );
+ BOOST_CHECK_EQUAL( m1.empty(), false);
BOOST_CHECK_EQUAL( m1.get_name(), std::string("mck3test") );
BOOST_CHECK( m1.size() > 0 );
+ BOOST_CHECK_EQUAL( m1.get_analysis_path().string(), result_path.string());
Mussa m2;
- std::string saved_analysis_path("mck3test_w30_t20");
- m2.load( saved_analysis_path );
- chdir( ".." );
-
- BOOST_CHECK_EQUAL( m2.get_name(), saved_analysis_path );
+ m2.load( result_path );
+ BOOST_CHECK_EQUAL( m2.empty(), false);
+ BOOST_CHECK_EQUAL( m2.get_name(), result_path.leaf() );
BOOST_CHECK_EQUAL( m1.size(), m2.size() );
+ BOOST_CHECK_EQUAL( result_path.string(), m2.get_analysis_path().string() );
+ // check clear a bit
+ m2.clear();
+ BOOST_CHECK_EQUAL( m2.empty(), true);
+ BOOST_CHECK_EQUAL( m2.is_dirty(), false );
+ BOOST_CHECK_EQUAL( m2.get_analysis_path().string(), fs::path().string());
}
BOOST_AUTO_TEST_CASE( mussa_load_full_path )
{
Mussa m1;
- chdir( "examples" );
- const int bufsize = 1024;
- char path_buf[bufsize];
- getcwd(path_buf, bufsize);
- std::string path(path_buf);
- chdir( ".." );
- path += "/mck3test.mupa";
- m1.load_mupa_file( path );
- m1.analyze(0, 0);
+ fs::path full_path(fs::path(EXAMPLE_DIR, fs::native) / "mck3test.mupa");
+ m1.load_mupa_file( full_path );
+ m1.analyze();
BOOST_CHECK( m1.size() > 0);
+ BOOST_CHECK_EQUAL( m1.get_window(), 30 );
+ BOOST_CHECK_EQUAL( m1.get_threshold(), 20);
+ BOOST_CHECK_EQUAL( m1.is_dirty(), true);
+ BOOST_CHECK_EQUAL( m1.get_analysis_path().string(), "");
+}
+
+BOOST_AUTO_TEST_CASE( mussa_valid_motifs_in_new_analysis )
+{
+ Mussa m1;
+ fs::path full_path(fs::path(EXAMPLE_DIR, fs::native) / "mck3test.mupa");
+ m1.load_mupa_file( full_path );
+ m1.analyze();
+ // check motifs
+ BOOST_CHECK( m1.sequences().size() > 0 );
+ BOOST_CHECK_EQUAL( m1.sequences()[0]->motifs().size(), 0 );
+}
+
+// make sure we know that mupa files cannot be directories
+BOOST_AUTO_TEST_CASE( mussa_mupa_is_file_not_directory )
+{
+ fs::path curdir(".");
+ Mussa m1;
+ BOOST_CHECK_THROW(m1.load_mupa_file( curdir ), mussa_load_error );
+}
+
+// catch error if annotation isn't a file
+BOOST_AUTO_TEST_CASE( mussa_annotation_is_not_file )
+{
+ Mussa m1;
+ fs::path full_path(fs::path(EXAMPLE_DIR, fs::native) / "directory.mupa");
+ BOOST_CHECK_THROW( m1.load_mupa_file( full_path ), mussa_load_error );
+}
+
+BOOST_AUTO_TEST_CASE( mussa_load_analysis )
+{
+ fs::path example_dir(EXAMPLE_DIR, fs::native);
+ Mussa m1;
+ m1.load_mupa_file( example_dir / "mck3test.mupa" );
+ m1.analyze();
+
+ Mussa m2;
+ fs::path analysis_path = fs::initial_path() / "mck3test_w30_t20";
+ m2.load( analysis_path );
+
+ BOOST_CHECK_EQUAL( m1.size(), m2.size() );
+ BOOST_CHECK_EQUAL( m1.get_window(), m2.get_window() );
+ BOOST_CHECK_EQUAL( m1.get_threshold(), m2.get_threshold() );
+ BOOST_CHECK_EQUAL( m2.get_analysis_path().string(), analysis_path.string());
+}
+
+BOOST_AUTO_TEST_CASE( mussa_load_motif )
+{
+ string data = "AAGG 1.0 1.0 0.0\n"
+ "GGTT 0.0 0.1 1.0 1.0\n";
+
+ istringstream test_istream(data);
+
+ Mussa m1;
+ m1.append_sequence("AAAAGGGGTTTT");
+ m1.append_sequence("GGGCCCCTTCCAATT");
+ m1.load_motifs(test_istream);
+
+ BOOST_CHECK_EQUAL( m1.motifs().size(), 2);
+ for (Mussa::vector_sequence_type::const_iterator seq_i = m1.sequences().begin();
+ seq_i != m1.sequences().end();
+ ++seq_i)
+ {
+ BOOST_CHECK( (*seq_i)->motifs().size() > 0 );
+ }
+}
+
+BOOST_AUTO_TEST_CASE( mussa_load_broken_motif )
+{
+ string data = "AAGG 1.0 1.0 0.0\n"
+ "GGTT 0.0 0.1 1.0 1.0\n"
+ "ZZCTA 0.1 0.0 1.0\n";
+
+ istringstream test_istream(data);
+
+ Mussa m1;
+ m1.append_sequence("AAAAGGGGTTTT");
+ m1.append_sequence("GGGCCCCTTCCAATT");
+ BOOST_CHECK_THROW(m1.load_motifs(test_istream), motif_load_error);
+
+ BOOST_CHECK_EQUAL( m1.motifs().size(), 0);
+}
+
+BOOST_AUTO_TEST_CASE( mussa_named_motif )
+{
+ string data = "CCAATT cat 0.1 0.2 0.3\n";
+ istringstream test_istream(data);
+
+ Mussa m1;
+ m1.append_sequence("AAAAGGGGTTTT");
+ m1.append_sequence("GGGCCCCTTCCAATT");
+ m1.load_motifs(test_istream);
+
+ std::set<Sequence> motifs = m1.motifs();
+ BOOST_REQUIRE_EQUAL(motifs.size(), 1);
+ BOOST_CHECK_EQUAL(motifs.begin()->get_name(), "cat");
+}
+
+BOOST_AUTO_TEST_CASE( mussa_weirdly_spaced_named_motif )
+{
+ string data = "CCAATT cat_meow123 0.1 0.2 0.3\n";
+ istringstream test_istream(data);
+
+ Mussa m1;
+ m1.append_sequence("AAAAGGGGTTTT");
+ m1.append_sequence("GGGCCCCTTCCAATT");
+ m1.load_motifs(test_istream);
+
+ std::set<Sequence> motifs = m1.motifs();
+ BOOST_REQUIRE_EQUAL(motifs.size(), 1);
+ BOOST_CHECK_EQUAL(motifs.begin()->get_name(), "cat_meow123");
+}
+
+BOOST_AUTO_TEST_CASE( mussa_name_quoted_motif )
+{
+ string data = "CCAATT \"cat meow 123\" 0.1 0.2 0.3\n";
+ istringstream test_istream(data);
+
+ Mussa m1;
+ m1.append_sequence("AAAAGGGGTTTT");
+ m1.append_sequence("GGGCCCCTTCCAATT");
+ m1.load_motifs(test_istream);
+
+ std::set<Sequence> motifs = m1.motifs();
+ BOOST_REQUIRE_EQUAL(motifs.size(), 1);
+ BOOST_CHECK_EQUAL(motifs.begin()->get_name(), "cat meow 123");
+}
+
+BOOST_AUTO_TEST_CASE( mussa_name_embedded_quote_motif )
+{
+ // pretty obviously this shouldn't work as " are our delimiter
+ // and i'm too lazy to add support for \ in the parser
+ string data = "ATA 0.5 0.5 0.5\n"
+ "CCAATT \"cat \"meow 123\" 0.1 0.2 0.3\n";
+ istringstream test_istream(data);
+
+ Mussa m1;
+ m1.append_sequence("AAAAGGGGTTTT");
+ m1.append_sequence("GGGCCCCTTCCAATT");
+ BOOST_CHECK_THROW( m1.load_motifs(test_istream), motif_load_error);
+
+ std::set<Sequence> motifs = m1.motifs();
+ BOOST_REQUIRE_EQUAL(motifs.size(), 0);
+}
+
+BOOST_AUTO_TEST_CASE( mussa_save_motif )
+{
+ string data = "ATA 1 1 1 1\n"
+ "CAT \"my name\" 1 0 0.5 0.5\n";
+ istringstream data_istream(data);
+
+ Mussa m1;
+ m1.append_sequence("AAAAGGGGTTTT");
+ m1.append_sequence("GGGCCCCTTCCAATT");
+ m1.load_motifs(data_istream);
+
+ string save;
+ ostringstream save_ostream(save);
+ m1.save_motifs(save_ostream);
+
+ istringstream reloaded_istream(save_ostream.str());
+ Mussa m2;
+ m2.append_sequence("AAAAGGGGTTTT");
+ m2.append_sequence("GGGCCCCTTCCAATT");
+ m2.load_motifs(reloaded_istream);
+
+ BOOST_REQUIRE_EQUAL(m1.motifs().size(), m2.motifs().size());
+ Mussa::motif_set::const_iterator m1motif = m1.motifs().begin();
+ Mussa::motif_set::const_iterator m2motif = m2.motifs().begin();
+ for (;
+ m1motif != m1.motifs().end() and m2motif != m2.motifs().end();
+ ++m1motif, ++m2motif)
+ {
+ BOOST_CHECK_EQUAL(m1motif->get_sequence(), m2motif->get_sequence());
+ BOOST_CHECK_EQUAL(m1motif->get_name(), m2motif->get_name());
+ BOOST_CHECK_EQUAL(m1.colorMapper()->lookup("motif", m1motif->get_sequence()),
+ m2.colorMapper()->lookup("motif", m2motif->get_sequence()));
+ }
+}
+
+BOOST_AUTO_TEST_CASE( mussa_add_motif )
+{
+ vector<Sequence> motifs;
+ motifs.push_back("AAGG");
+ vector<Color> colors;
+ colors.push_back(Color(1.0, 0.0, 0.0));
+
+ Mussa m1;
+ m1.append_sequence("AAAAGGGGTTTT");
+ m1.append_sequence("GGGCCCCTTGGTT");
+ m1.set_motifs(motifs, colors);
+ int first_size = m1.motifs().size();
+ BOOST_CHECK_EQUAL( first_size, 1 );
+ BOOST_REQUIRE(first_size > 0);
+ BOOST_CHECK_EQUAL(*(m1.motifs().begin()), motifs.front());
+ // make sure that our sequences have the right number of motifs
+ BOOST_CHECK_EQUAL(m1.sequences()[0]->motifs().size(), 1);
+ BOOST_CHECK_EQUAL(m1.sequences()[1]->motifs().size(), 1); // because of rc
+
+ // verify that setting the motif clears the arrays
+ m1.set_motifs(motifs, colors);
+ BOOST_CHECK_EQUAL( first_size, m1.motifs().size() );
+ // make sure that our sequences have the right number of motifs
+ BOOST_CHECK_EQUAL(m1.sequences()[0]->motifs().size(), 1);
+ BOOST_CHECK_EQUAL(m1.sequences()[1]->motifs().size(), 1);
+
+ // add a different motif
+ motifs.clear();
+ motifs.push_back("CCTTGG");
+ BOOST_CHECK_EQUAL(motifs.size(), 1);
+ m1.set_motifs(motifs, colors);
+ BOOST_CHECK_EQUAL(m1.motifs().size(), 1);
+ BOOST_REQUIRE(m1.motifs().size() > 0);
+ BOOST_CHECK_EQUAL(*(m1.motifs().begin()), motifs.front());
+ BOOST_CHECK_EQUAL(m1.sequences()[0]->motifs().size(), 0);
+ BOOST_CHECK_EQUAL(m1.sequences()[1]->motifs().size(), 1);
+
+ // try a motif that doesn't exist
+ motifs.clear();
+ motifs.push_back("CCTTGG");
+ BOOST_CHECK_EQUAL(motifs.size(), 1);
+ m1.set_motifs(motifs, colors);
+ BOOST_CHECK_EQUAL(m1.motifs().size(), 1);
+ BOOST_CHECK_EQUAL(m1.sequences()[0]->motifs().size(), 0);
+ BOOST_CHECK_EQUAL(m1.sequences()[1]->motifs().size(), 1);
+
+}
+
+static void
+two_way_local_align_test(const Mussa::vector_sequence_type &seqs,
+ const list<ConservedPath::path_type>& result,
+ const list<vector<bool> >& reversed)
+{
+ map<char, vector <char> > m;
+ assign::insert(m)('A', assign::list_of('A')('T') )
+ ('T', assign::list_of('T')('A') )
+ ('G', assign::list_of('G')('C') )
+ ('C', assign::list_of('C')('G') );
+ list<vector<bool> >::const_iterator rc_i = reversed.begin();
+
+ for(list<ConservedPath::path_type>::const_iterator base_i = result.begin();
+ base_i != result.end();
+ ++base_i, ++rc_i)
+ {
+ // since the reverse compliment flag is relative to the first sequence
+ // the first one should always be false
+ BOOST_CHECK_EQUAL( (*rc_i)[0], false );
+ const int first_path_basepair_index = (*base_i)[0];
+ const int second_path_basepair_index = (*base_i)[1];
+ const char first_basepair = (*seqs[0])[first_path_basepair_index];
+ const char second_basepair = (*seqs[1])[second_path_basepair_index];
+ // get our index into our reverse compliment map m
+ const int second_compliment_index = (*rc_i)[1];
+ // lookup the forward or reverse compliment depending on our rc flag
+ const char complimented_second = m[second_basepair][second_compliment_index];
+
+ BOOST_CHECK_EQUAL( first_basepair, complimented_second) ;
+ }
}
+
+BOOST_AUTO_TEST_CASE( two_way_local_alignment )
+{
+ string s0("GCGCATAT");
+ string s1("AAAAAAAT");
+ Sequence seq1(s1);
+
+ Mussa analysis;
+ analysis.append_sequence(s0);
+ analysis.append_sequence(s1);
+ analysis.set_threshold(3);
+ analysis.set_window(4);
+ analysis.analyze();
+ NwayPaths npath = analysis.paths();
+ BOOST_REQUIRE_EQUAL( npath.pathz.size(), 2 );
+
+ list<ConservedPath::path_type> result;
+ list<vector<bool> > reversed;
+ list<ConservedPath>::iterator pathz_i = npath.pathz.begin();
+
+ list<ConservedPath> selected_paths;
+ selected_paths.push_back(*pathz_i);
+ analysis.createLocalAlignment(selected_paths.begin(),
+ selected_paths.end(),
+ result,
+ reversed);
+
+ two_way_local_align_test(analysis.sequences(), result, reversed);
+
+ ++pathz_i;
+ result.clear();
+ reversed.clear();
+ selected_paths.clear();
+ selected_paths.push_back(*pathz_i);
+ analysis.createLocalAlignment(selected_paths.begin(),
+ selected_paths.end(),
+ result,
+ reversed);
+ two_way_local_align_test(analysis.sequences(), result, reversed);
+}
+
+BOOST_AUTO_TEST_CASE( three_way_local_alignment )
+{
+ string s0("AGCAGGGAGGGTTTAAATGGCACCCAGCAGTTGGTGTGAGG");
+ string s1("AGCGGGAAGGGTTTAAATGGCACCGGGCAGTTGGCGTGAGG");
+ string s2("CAGCGCCGGGGTTTAAATGGCACCGAGCAGTTGGCGCAGGG");
+
+ Mussa analysis;
+ analysis.append_sequence(s0);
+ analysis.append_sequence(s1);
+ analysis.append_sequence(s2);
+ analysis.set_threshold(23);
+ analysis.set_window(30);
+ analysis.analyze();
+ NwayPaths npath = analysis.paths();
+ BOOST_CHECK_EQUAL( npath.refined_pathz.size(), 1 );
+
+ list<ConservedPath::path_type> result;
+ list<vector<bool> > reversed;
+ // grab 1 path (since there's only one)
+ list<ConservedPath>::iterator pathz_i = npath.pathz.begin();
+ list<ConservedPath> selected_paths;
+ selected_paths.push_back(*pathz_i);
+ analysis.createLocalAlignment(selected_paths.begin(),
+ selected_paths.end(),
+ result,
+ reversed);
+
+ for(std::list<ConservedPath::path_type>::iterator result_i = result.begin();
+ result_i != result.end();
+ ++result_i)
+ {
+ ConservedPath::path_element first_element = *(result_i->begin());
+ for (ConservedPath::path_type::iterator element_i = result_i->begin();
+ element_i != result_i->end();
+ ++element_i)
+ {
+ BOOST_CHECK_EQUAL( *element_i, first_element );
+ BOOST_CHECK_EQUAL( s0[*element_i], s1[*element_i] );
+ BOOST_CHECK_EQUAL( s1[*element_i], s2[*element_i] );
+ BOOST_CHECK_EQUAL( s0[*element_i], s2[*element_i] );
+ }
+ }
+}
+
+BOOST_AUTO_TEST_CASE( mussa_window_larger_than_sequence )
+{
+ string s0("AGCAGGG");
+ string s1("CAGCGGG");
+
+ Mussa analysis;
+ analysis.append_sequence(s0);
+ analysis.append_sequence(s1);
+ analysis.set_threshold(23);
+ analysis.set_window(30);
+ BOOST_CHECK_THROW(analysis.analyze(), seqcomp_error);
+}
+
+BOOST_AUTO_TEST_CASE( subanalysis )
+{
+ Sequence s1("AATGAAGATTTTAATGCTTTAATTTTGTTTTGTAAACTTCGAATTTCCAAAATTTGAAA");
+ Sequence s2("AGGAGCAAGTTCGCTTCATCGAGAATTTTTAATTTTTAGTCAAATTTTCCAATGTCTGA");
+
+ Mussa analysis;
+ analysis.append_sequence(s1);
+ analysis.append_sequence(s2);
+ analysis.set_threshold(8);
+ analysis.set_window(8);
+ analysis.analyze();
+
+ NwayPaths perfect_path = analysis.paths();
+ int perfect_match_count = perfect_path.pathz.size();
+
+ Sequence sub1 = s1.subseq(2, s1.size()-4);
+ Sequence sub2 = s2.subseq(2, s2.size()-4);
+ Mussa subanalysis;
+ subanalysis.append_sequence(sub1);
+ subanalysis.append_sequence(sub2);
+ subanalysis.set_threshold(7);
+ subanalysis.set_window(8);
+ subanalysis.analyze();
+ NwayPaths one_mismatch_path = subanalysis.paths();
+ int one_mismatch_count = one_mismatch_path.pathz.size();
+
+ BOOST_CHECK( perfect_match_count < one_mismatch_count );
+}
+
+BOOST_AUTO_TEST_CASE( dirty_flag )
+{
+ Mussa m;
+ BOOST_CHECK_EQUAL(m.is_dirty(), false);
+ m.set_name("foo");
+ BOOST_CHECK_EQUAL(m.is_dirty(), true);
+ m.clear();
+ m.set_window(30);
+ BOOST_CHECK_EQUAL(m.is_dirty(), true);
+ m.clear();
+ m.set_threshold(1);
+ BOOST_CHECK_EQUAL(m.is_dirty(), true);
+ m.clear();
+ m.set_soft_threshold(1);
+ BOOST_CHECK_EQUAL(m.is_dirty(), false);
+ m.clear();
+ m.append_sequence("AAGGCCTT");
+ BOOST_CHECK_EQUAL(m.is_dirty(), true);
+}
+
projects / mussa.git / blobdiff