1 #define BOOST_AUTO_TEST_MAIN
2 #include <boost/test/auto_unit_test.hpp>
3 #include <boost/assign/std/vector.hpp>
4 using namespace boost::assign;
6 #include <boost/shared_ptr.hpp>
12 #include "alg/annotation_colors.hpp"
13 #include "alg/glseqbrowser.hpp"
14 #include "alg/sequence.hpp"
18 BOOST_AUTO_TEST_CASE ( gltracks_connect )
20 string s0("AAGGCCTT");
21 string s1("TTGGCCAA");
22 string s2("GATTACAA");
28 gt.push_sequence(seq0);
29 gt.push_sequence(seq1);
30 gt.push_sequence(seq2);
32 // make up some sample data
34 rc += false, false, false;
36 path += 1,1,1; gt.link(path, rc, 1);
37 path.clear(); path += 1,1,3; gt.link(path, rc, 1);
38 path.clear(); path += 1,2,1; gt.link(path, rc, 1);
39 path.clear(); path += 2,3,3; gt.link(path, rc, 1);
40 path.clear(); path += 3,3,3; gt.link(path, rc, 1);
42 // this represents the "depth" of the path_segment AKA sequences -1
43 BOOST_CHECK_EQUAL( gt.path_segments.size(), 2 );
44 BOOST_CHECK_EQUAL( gt.path_segments[0].size(), 4);
45 BOOST_CHECK_EQUAL( gt.path_segments[1].size(), 4);
46 GlSeqBrowser::segment_key p11(1, 1);
47 GlSeqBrowser::segment_key p23(2, 3);
48 GlSeqBrowser::segment_key p33(3, 3);
49 GlSeqBrowser::segment_key p13(1, 3);
50 GlSeqBrowser::pair_segment_map::iterator psm_i = gt.path_segments[0].find(p11);
51 BOOST_CHECK( psm_i != gt.path_segments[0].end() );
52 BOOST_CHECK_EQUAL( psm_i->second.path_ids.size(), 2 );
53 // exaustively test the other keys in the first row
54 psm_i = gt.path_segments[0].find(p23);
55 BOOST_CHECK( psm_i != gt.path_segments[0].end());
56 psm_i = gt.path_segments[0].find(p33);
57 BOOST_CHECK( psm_i != gt.path_segments[0].end());
59 psm_i = gt.path_segments[0].find(p13);
60 BOOST_CHECK( psm_i == gt.path_segments[0].end());
63 BOOST_CHECK_EQUAL( gt.path_segments.size(), 0 );
66 BOOST_AUTO_TEST_CASE ( gltracks_connect_different_lengths )
68 string s0("AAGGCCTT");
69 string s1("TTGGCCAA");
70 string s2("GATTACAA");
76 gt.push_sequence(seq0);
77 gt.push_sequence(seq1);
78 gt.push_sequence(seq2);
80 // make up some sample data
82 rc += false, false, false;
84 path += 1,1,1; gt.link(path, rc, 5);
85 path.clear(); path += 1,1,3; gt.link(path, rc, 1);
86 path.clear(); path += 2,3,3; gt.link(path, rc, 1);
87 path.clear(); path += 3,3,3; gt.link(path, rc, 3);
88 path.clear(); path += 4,3,3; gt.link(path, rc, 2);
90 // this represents the "depth" of the path_segment AKA sequences -1
91 BOOST_CHECK_EQUAL( gt.path_segments.size(), 2 );
92 BOOST_CHECK_EQUAL( gt.path_segments[0].size(), 4);
93 BOOST_CHECK_EQUAL( gt.path_segments[1].size(), 3);
94 GlSeqBrowser::segment_key p1(1, 1);
95 GlSeqBrowser::pair_segment_map::iterator psm1_i = gt.path_segments[0].find(p1);
96 BOOST_CHECK( psm1_i != gt.path_segments[0].end() );
97 BOOST_CHECK_EQUAL( psm1_i->second.start.x, 1); //start segment x coordinate
98 BOOST_CHECK_EQUAL( psm1_i->second.end.x, 1); //end segment x coordinate
99 BOOST_CHECK_EQUAL( psm1_i->second.length, 5);
100 // there should be two paths, the sizes don't match
101 BOOST_CHECK_EQUAL( psm1_i->second.path_ids.size(), 2 );
103 // look at the second row
104 GlSeqBrowser::segment_key p2(3,3);
105 GlSeqBrowser::pair_segment_map::iterator psm2_i = gt.path_segments[1].find(p2);
106 BOOST_CHECK( psm2_i != gt.path_segments[1].end() );
107 BOOST_CHECK_EQUAL( psm2_i->second.start.x, 3); //start segment x coordinate
108 BOOST_CHECK_EQUAL( psm2_i->second.end.x, 3); //end segment x coordinate
109 BOOST_CHECK_EQUAL( psm2_i->second.length, 3);
112 BOOST_AUTO_TEST_CASE( glseqbrowser_center )
114 string s0("AAGGCCTT");
115 string s1("TTGGCCAA");
116 string s2("GATTACAA");
120 boost::shared_ptr<AnnotationColors> cm(new AnnotationColors);
121 GlSequence glseq0(seq0, cm);
122 GlSequence glseq1(seq1, cm);
123 GlSequence glseq2(seq2, cm);
126 gt.push_sequence(glseq0);
127 gt.push_sequence(glseq1);
128 gt.push_sequence(glseq2);
133 BOOST_CHECK_EQUAL( gt.left(), -gt.border() );
134 BOOST_CHECK_EQUAL( gt.right(), s0.size() + gt.border() );
136 gt.centerOnPath(path);
138 // I didn't bother to compute how the path should shift things
139 // by the magic number 3, i just ran the test and saw how it failed
140 // and hard coded this in.
141 BOOST_CHECK_EQUAL( gt.left(), -18-gt.border() );
142 BOOST_CHECK_EQUAL( gt.right(), s0.size() + gt.border()-11 );
144 // aparently we end up with a different glsequence in the seqbrowser
145 BOOST_CHECK( glseq1.x() != gt.sequences()[1]->x() );
147 BOOST_CHECK_EQUAL( gt.sequences()[0]->x(), (gt.viewportCenter()-15)-path[0] );
148 BOOST_CHECK_EQUAL( gt.sequences()[1]->x(), (gt.viewportCenter()-15)-path[1] );
149 BOOST_CHECK_EQUAL( gt.sequences()[2]->x(), (gt.viewportCenter()-15)-path[2] );
152 BOOST_AUTO_TEST_CASE( setSelectedPaths )
154 string s0("AAGGCCTT");
155 string s1("TTGGCCAA");
156 string s2("GATTACAA");
162 gt.push_sequence(seq0);
163 gt.push_sequence(seq1);
164 gt.push_sequence(seq2);
166 // make up some sample data
168 rc += false, false, false;
170 path += 1,1,1; gt.link(path, rc, 1);
171 path.clear(); path += 1,1,3; gt.link(path, rc, 1);
172 path.clear(); path += 2,3,3; gt.link(path, rc, 1);
173 path.clear(); path += 3,3,3; gt.link(path, rc, 1);
175 vector<int> selected;
177 BOOST_CHECK_EQUAL( gt.selectedPaths().size(), 0 );
178 gt.setSelectedPaths(selected);
179 BOOST_CHECK_EQUAL( gt.selectedPaths().size(), selected.size() );
180 gt.clear_selection();
181 BOOST_CHECK_EQUAL( gt.selectedPaths().size(), 0);
184 BOOST_AUTO_TEST_CASE( setSelectedTracks )
186 string s0("AAGGCCTT");
187 string s1("TTGGCCAA");
188 string s2("GATTACAA");
194 gt.push_sequence(seq0);
195 gt.push_sequence(seq1);
196 gt.push_sequence(seq2);
199 BOOST_CHECK_EQUAL( gt.selectedTracks().size(), 0 );
200 gt.appendSelectedTrack(0, 0, seq0.size());
201 gt.appendSelectedTrack(2, 0, seq2.size());
202 BOOST_CHECK_EQUAL( gt.selectedTracks().size(), 2 );
204 list<Sequence> selected_sequence;
205 BOOST_CHECK_EQUAL(selected_sequence.size(), 0);
206 gt.copySelectedTracksAsSequences(selected_sequence);
207 BOOST_CHECK_EQUAL(selected_sequence.size(), 2);
208 BOOST_CHECK_EQUAL(selected_sequence.front(), seq0);
209 BOOST_CHECK_EQUAL(selected_sequence.back(), seq2);
211 gt.clear_selection();
212 BOOST_CHECK_EQUAL( gt.selectedPaths().size(), 0);
214 gt.appendSelectedTrack(0, 0, 2);
215 list<SequenceLocation> seq_locs;
216 gt.copySelectedTracksAsSeqLocation(seq_locs);
217 BOOST_CHECK_EQUAL(seq_locs.size(), 1);
218 BOOST_CHECK_EQUAL(seq_locs.front().getSequence(), seq0);
219 BOOST_CHECK_EQUAL(seq_locs.front().getLeft(), 0);
220 BOOST_CHECK_EQUAL(seq_locs.front().getRight(), 2);