Test case 1
1: BasePattern basePattern0 = new BasePattern("");
Test case 2
1: BasePattern basePattern0 = new BasePattern("r");
2: boolean boolean0 = basePattern0.matches("uk.ac.sanger.artemis.sequence.BasePattern");
3: assertFalse(boolean0);
Test case 3
1: BasePattern basePattern0 = new BasePattern("N");
2: boolean boolean0 = basePattern0.matches("N");
3: assertTrue(boolean0);
Test case 4
1: BasePattern basePattern0 = new BasePattern("r");
2: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("G~8c[YFB6lQ)E");
3: Bases bases0 = new Bases(fastaStreamSequence0);
4: MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, (-2154), false, false, false);
5: assertNull(markerRange0);
Test case 5
1: BasePattern basePattern0 = new BasePattern("r");
2: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("G~8c[YFB6lQ)E");
3: Bases bases0 = new Bases(fastaStreamSequence0);
4: fastaStreamSequence0.setFromChar(bases0.letter_index);
5: MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, 255, true, true, true);
6: assertTrue(markerRange0.isForwardMarker());
7: assertNotNull(markerRange0);
Test case 6
1: BasePattern basePattern0 = new BasePattern("hr");
2: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("G~8c[YFB6lQ)E");
3: Bases bases0 = new Bases(fastaStreamSequence0);
4: fastaStreamSequence0.setFromChar(bases0.letter_index);
5: MarkerRangeVector markerRangeVector0 = basePattern0.findMatches(bases0, (Marker) null, 968);
6: assertEquals(3, markerRangeVector0.size());
Test case 7
1: BasePattern basePattern0 = new BasePattern("r");
2: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("G~8c[YFB6lQ)E");
3: Bases bases0 = new Bases(fastaStreamSequence0);
4: MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, (-2154), false, true, true);
5: assertNull(markerRange0);
Test case 8
1: BasePattern basePattern0 = new BasePattern("g");
2: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("G~8c[YFB6lQ)E");
3: Bases bases0 = new Bases(fastaStreamSequence0);
4: MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, 255, true, true, true);
5: assertNotNull(markerRange0);
6: assertFalse(markerRange0.isForwardMarker());
Test case 9
1: BasePattern basePattern0 = new BasePattern("g");
2: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("G~8c[YFB6lQ)E");
3: Bases bases0 = new Bases(fastaStreamSequence0);
4: MarkerRangeVector markerRangeVector0 = basePattern0.findMatches(bases0, (Marker) null, 1011);
5: assertEquals(1, markerRangeVector0.size());
Test case 10
1: BasePattern basePattern0 = new BasePattern("NKax7G");
Test case 11
1: BasePattern basePattern0 = new BasePattern("Bl/;]<^UU&N!");
Test case 12
1: int int0 = BasePattern.patternType("c[:");
2: assertEquals((-1), int0);
Test case 13
1: BasePattern basePattern0 = new BasePattern("do^I#_X");
Test case 14
1: int int0 = BasePattern.patternType("enO}");
2: assertEquals((-1), int0);
Test case 15
1: BasePattern basePattern0 = new BasePattern("VI#_-kT/");
Test case 16
1: BasePattern basePattern0 = new BasePattern("j#I.lO_B");
Test case 17
1: BasePattern basePattern0 = new BasePattern("The targetted ontology may not be null");
Test case 18
1: BasePattern basePattern0 = new BasePattern("RwqM4c)_udAnilv");
Test case 19
1: BasePattern basePattern0 = new BasePattern("yFW`j?WCz]g");
Test case 20
1: BasePattern basePattern0 = new BasePattern("K");
2: String string0 = basePattern0.toString();
3: assertEquals("k", string0);
Test case 21
1: BasePattern basePattern0 = new BasePattern("r");
2: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("G~8c[YFB6lQ)E");
3: Bases bases0 = new Bases(fastaStreamSequence0);
4: fastaStreamSequence0.setFromChar(bases0.letter_index);
5: MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, (-2154), false, true, true);
6: assertNull(markerRange0);
Test case 22
1: BasePattern basePattern0 = new BasePattern("r");
2: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("G~8c[YFB6lQ)E");
3: Bases bases0 = new Bases(fastaStreamSequence0);
4: fastaStreamSequence0.setFromChar(bases0.letter_index);
5: MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, 255, false, true, false);
6: assertTrue(markerRange0.isForwardMarker());
Test case 23
1: int int0 = BasePattern.patternType("g");
2: assertEquals(0, int0);
Test case 24
1: int int0 = BasePattern.patternType("hr");
2: assertEquals(1, int0);
Test case 25
1: int int0 = BasePattern.patternType("ixj2UGlP8G0d=Z`8");
2: assertEquals((-1), int0);
Test case 26
1: int int0 = BasePattern.patternType("pattern too short");
2: assertEquals((-1), int0);
Test case 27
1: int int0 = BasePattern.patternType("rna");
2: assertEquals(1, int0);
Test case 28
1: int int0 = BasePattern.patternType("uk.ac.sanger.artemis.sequence.BasePattern");
2: assertEquals((-1), int0);
Test case 29
1: int int0 = BasePattern.patternType("o0_LP,fLk4oO7");
2: assertEquals((-1), int0);
Test case 30
1: int int0 = BasePattern.patternType("s1?");
2: assertEquals((-1), int0);
Test case 31
1: int int0 = BasePattern.patternType("q/GC[E.[{h~bFb,%56");
2: assertEquals((-1), int0);
Test case 32
1: int int0 = BasePattern.patternType("f*lS\"T>bE(UnMlK");
2: assertEquals((-1), int0);
Test case 33
1: int int0 = BasePattern.patternType("mG6h~");
2: assertEquals((-1), int0);
Test case 34
1: int int0 = BasePattern.patternType("k5Km%#+;#fc%zx@#");
2: assertEquals((-1), int0);
Test case 35
1: BasePattern basePattern0 = new BasePattern((String) null);
Test case 36
1: BasePattern basePattern0 = new BasePattern("g");
2: basePattern0.findMatch((Bases) null, (Marker) null, 1063, false, false, false);
Test case 37
1: BasePattern basePattern0 = new BasePattern("R");
2: basePattern0.findMatches((Bases) null, (Marker) null, 3203);
Test case 38
1: BasePattern.patternType((String) null);
Test case 39
1: BasePattern basePattern0 = new BasePattern("r");
2: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("G~8c[YFB6lQ)E");
3: Bases bases0 = new Bases(fastaStreamSequence0);
4: Strand strand0 = bases0.getReverseStrand();
5: Marker marker0 = strand0.makeMarker(7);
6: MarkerRangeVector markerRangeVector0 = basePattern0.findMatches(bases0, marker0, 1);
7: assertEquals(0, markerRangeVector0.size());
Test case 40
1: BasePattern basePattern0 = new BasePattern("hr");
2: boolean boolean0 = basePattern0.matches("&");
3: assertFalse(boolean0);
Test case 41
1: BasePattern basePattern0 = new BasePattern("r");
2: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("&");
3: Bases bases0 = new Bases(fastaStreamSequence0);
4: MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, 862, true, true, false);
5: assertNull(markerRange0);
Test case 42
1: BasePattern basePattern0 = new BasePattern("K");
2: boolean boolean0 = basePattern0.matches("K");
3: assertFalse(boolean0);