Test case 1
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("NOW TRYING TO CONTINUE TO COMMIT");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = new Strand(bases0, 0);
4: Range range0 = new Range(2, 2);
5: strand0.getTranslation(range0, false);
6: assertEquals(2, strand0.getDirection());
Test case 2
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("NOW TRYING TO CONTINUE TO COMMIT", "NOW TRYING TO CONTINUE TO COMMIT");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = bases0.getReverseStrand();
4: Range range0 = new Range(2, 2);
5: strand0.getSpacedTranslation(range0, false);
6: assertEquals(2, strand0.getDirection());
Test case 3
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = bases0.getReverseStrand();
4: Range range0 = new Range(0);
5: String string0 = strand0.getRawSubSequence(range0);
6: assertEquals("@", string0);
Test case 4
1: Strand.markerRangeBases((MarkerRange) null);
Test case 5
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("vi.-mWH3Q");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = new Strand(bases0, 1);
4: Marker marker0 = strand0.makeMarker(1);
5: MarkerRange markerRange0 = Strand.getORFAroundMarker(marker0, false);
6: Strand.deleteRange(markerRange0);
7: assertEquals(6, genbankStreamSequence0.length());
8: assertEquals(6, genbankStreamSequence0.getOtherCount());
Test case 6
1: Strand.getCodonAtMarker((Marker) null);
Test case 7
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("vi.-mWH3Q");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = new Strand(bases0, 1);
4: Range range0 = new Range(0);
5: String[] stringArray0 = new String[5];
6: StringVector stringVector0 = new StringVector(stringArray0);
7: strand0.getMatchingCodons(range0, stringVector0);
8: assertEquals(2, strand0.getDirection());
Test case 8
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("d");
2: Bases bases0 = new Bases(emblStreamSequence0);
3: Strand strand0 = bases0.getForwardStrand();
4: strand0.makeMarkerRangeFromPositions(0, 0);
Test case 9
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
4: bases0.addBases(1, 1, "vTgt!f:6B&i!%@?LS");
5: SimpleGotoEventSource simpleGotoEventSource0 = new SimpleGotoEventSource(simpleEntryGroup0);
6: MarkerRange markerRange0 = simpleGotoEventSource0.gotoBase(1);
7: MarkerRange[] markerRangeArray0 = Strand.getOpenReadingFrameRanges(markerRange0, 2, 2, 0);
8: assertNotNull(markerRangeArray0);
Test case 10
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("org.biojava.bio.seq.impl.SimpleHomologyFeature", "org.biojava.bio.seq.impl.SimpleHomologyFeature");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = bases0.getReverseStrand();
4: Range range0 = new Range((-5), 1);
5: strand0.getStopOrStartCodons(range0, (StringVector) null);
6: assertEquals(2, strand0.getDirection());
Test case 11
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence(";PUDTxscLL,?8TIo");
2: Bases bases0 = new Bases(emblStreamSequence0);
3: Strand strand0 = new Strand(bases0, 5);
4: strand0.getRawSubSequenceC((Range) null);
Test case 12
1: Bases bases0 = new Bases((Sequence) null);
2: Strand strand0 = bases0.getReverseStrand();
3: strand0.getStrandBases();
Test case 13
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("d");
2: Bases bases0 = new Bases(emblStreamSequence0);
3: Strand strand0 = bases0.getForwardStrand();
4: String string0 = strand0.getStrandBases();
5: assertEquals("d", string0);
Test case 14
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("vi.-mWH3Q");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = new Strand(bases0, 1);
4: Marker marker0 = strand0.makeMarkerFromRawPosition(5);
5: MarkerRange markerRange0 = Strand.getORFAroundMarker(marker0, false);
6: Range range0 = markerRange0.getRange();
7: char[] charArray0 = strand0.getRawSubSequenceC(range0);
8: assertArrayEquals(new char[] {'m', 'n', 'n'}, charArray0);
9: assertEquals(2, strand0.getDirection());
Test case 15
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
4: bases0.addBases(1, 1, "vTgt!f:6B&i!%@?LS");
5: SimpleGotoEventSource simpleGotoEventSource0 = new SimpleGotoEventSource(simpleEntryGroup0);
6: MarkerRange markerRange0 = simpleGotoEventSource0.gotoBase(1);
7: Strand.getOpenReadingFrameRanges(markerRange0, 2, 2003, 0);
Test case 16
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("jMQ/n?Z-5GP<}b3F0U");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = bases0.getForwardStrand();
4: Marker marker0 = strand0.makeMarkerFromRawPosition(1);
5: assertEquals(1, marker0.getPosition());
Test case 17
1: Bases bases0 = new Bases((Sequence) null);
2: Strand strand0 = new Strand(bases0, (-2618));
3: strand0.makeMarkerRangeFromRawPositions(0, (-5));
Test case 18
1: Bases bases0 = new Bases((Sequence) null);
2: Strand strand0 = bases0.getForwardStrand();
3: strand0.makeMarkerRangeFromRawPositions(5, (-5));
Test case 19
1: char[] charArray0 = new char[4];
2: CharArrayReader charArrayReader0 = new CharArrayReader(charArray0);
3: LineNumberReader lineNumberReader0 = new LineNumberReader(charArrayReader0);
4: LinePushBackReader linePushBackReader0 = new LinePushBackReader(lineNumberReader0);
5: RawStreamSequence rawStreamSequence0 = new RawStreamSequence(linePushBackReader0);
6: Bases bases0 = new Bases(rawStreamSequence0);
7: Strand strand0 = bases0.getReverseStrand();
8: strand0.getACount();
9: assertEquals(2, strand0.getDirection());
Test case 20
1: RawStreamSequence rawStreamSequence0 = new RawStreamSequence("");
2: Bases bases0 = new Bases(rawStreamSequence0);
3: Strand strand0 = bases0.getForwardStrand();
4: strand0.getACount();
5: assertTrue(strand0.isForwardStrand());
Test case 21
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("NOW TRYING TO CONTINUE TO COMMIT");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = new Strand(bases0, 0);
4: strand0.getTCount();
5: assertEquals(2, strand0.getDirection());
Test case 22
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("vi.-mWH3Q");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = bases0.getForwardStrand();
4: strand0.getGCount();
5: assertTrue(strand0.isForwardStrand());
Test case 23
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("vi.-mWH3Q");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = new Strand(bases0, 1);
4: strand0.getCCount();
5: assertEquals(2, strand0.getDirection());
Test case 24
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("uk.ac.sanger.artemis.sequence.Strand", "{$!0e!M|");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
4: Entry entry0 = simpleEntryGroup0.createEntry("");
5: Feature feature0 = entry0.createFeature();
6: Strand strand0 = feature0.getStrand();
7: strand0.getCCount();
Test case 25
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("vi.-mWH3Q");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = new Strand(bases0, 1);
4: int int0 = strand0.getRawPosition(0);
5: assertEquals(10, int0);
6: assertEquals(2, strand0.getDirection());
Test case 26
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence(" sessions");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = new Strand(bases0, 0);
4: Bases bases1 = strand0.getBases();
5: assertSame(bases1, bases0);
Test case 27
1: Bases bases0 = new Bases((Sequence) null);
2: Strand strand0 = bases0.getForwardStrand();
3: strand0.getSequenceLength();
Test case 28
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("NOW TRYING TO CONTINUE TO COMMIT", "NOW TRYING TO CONTINUE TO COMMIT");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = bases0.getReverseStrand();
4: Range range0 = new Range(2, 2);
5: strand0.getSubSequence(range0);
6: assertEquals(2, strand0.getDirection());
Test case 29
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("@3s>u1<|PZI@42");
2: Bases bases0 = new Bases(emblStreamSequence0);
3: Strand strand0 = new Strand(bases0, 120);
4: int int0 = strand0.getDirection();
5: assertEquals(2, int0);
Test case 30
1: RawStreamSequence rawStreamSequence0 = new RawStreamSequence("uk.ac.sanger.artemis.sequence.Strand");
2: Bases bases0 = new Bases(rawStreamSequence0);
3: Strand strand0 = bases0.getForwardStrand();
4: int int0 = strand0.getDirection();
5: assertEquals(1, int0);
Test case 31
1: Bases bases0 = new Bases((Sequence) null);
2: Strand strand0 = new Strand(bases0, (-5));
3: boolean boolean0 = strand0.isForwardStrand();
4: assertEquals(2, strand0.getDirection());
5: assertFalse(boolean0);
Test case 32
1: Strand.addBases((Marker) null, "gDd/IkgoY");
Test case 33
1: Strand.deleteRange((MarkerRange) null);
Test case 34
1: Strand strand0 = new Strand((Bases) null, 3);
2: strand0.getACount();
Test case 35
1: Strand strand0 = new Strand((Bases) null, 191);
2: strand0.getDirection();
Test case 36
1: Bases bases0 = new Bases((Sequence) null);
2: Strand strand0 = new Strand(bases0, 1);
3: strand0.getGCount();
Test case 37
1: StringVector stringVector0 = new StringVector();
2: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("j'VPj8P{HvYL@^@CrmG");
3: Bases bases0 = new Bases(genbankStreamSequence0);
4: Strand strand0 = bases0.getForwardStrand();
5: strand0.getMatchingCodons((Range) null, stringVector0);
Test case 38
1: Strand.getORFAroundMarker((Marker) null, true);
Test case 39
1: Strand.getOpenReadingFrameRanges((MarkerRange) null, (-2575), (-2010), 75);
Test case 40
1: Strand strand0 = new Strand((Bases) null, 4414);
2: strand0.getRawPosition(8000);
Test case 41
1: Strand strand0 = new Strand((Bases) null, 0);
2: strand0.getRawSubSequence((Range) null);
Test case 42
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("uk.ac.sanger.artemis.sequence.Strand");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Range range0 = new Range(74);
4: Strand strand0 = bases0.getReverseStrand();
5: strand0.getSpacedTranslation(range0, false);
Test case 43
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = new Strand(bases0, (-1660));
4: strand0.getSpacedTranslation((Range) null, false);
Test case 44
1: Strand strand0 = new Strand((Bases) null, 0);
2: Range range0 = new Range((-5), 1);
3: StringVector stringVector0 = SelectionViewer.getBaseSummary("S,Cn");
4: strand0.getStopOrStartCodons(range0, stringVector0);
Test case 45
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("vi.-mWH3Q");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = new Strand(bases0, 1);
4: strand0.getSubSequence((Range) null);
Test case 46
1: Strand strand0 = new Strand((Bases) null, 3);
2: strand0.getTCount();
Test case 47
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("vi.-mWH3Q");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = new Strand(bases0, 1);
4: Range range0 = new Range((-1));
5: strand0.getTranslation(range0, false);
Test case 48
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("uk.ac.sanger.artemis.sequence.Strand", "{$!0e!M|");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
4: Entry entry0 = simpleEntryGroup0.createEntry("");
5: Feature feature0 = entry0.createFeature();
6: Strand strand0 = feature0.getStrand();
7: strand0.getTranslation((Range) null, false);
Test case 49
1: Strand strand0 = new Strand((Bases) null, (-1));
2: strand0.makeMarker((-1));
Test case 50
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("C");
2: Bases bases0 = new Bases(emblStreamSequence0);
3: Strand strand0 = bases0.getReverseStrand();
4: strand0.makeMarker((-2338));
Test case 51
1: Strand strand0 = new Strand((Bases) null, (-736));
2: strand0.makeMarkerFromRawPosition((-736));
Test case 52
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("@3s>u1<|PZI@42");
2: Bases bases0 = new Bases(emblStreamSequence0);
3: Strand strand0 = new Strand(bases0, 120);
4: strand0.makeMarkerFromRawPosition(0);
Test case 53
1: Strand strand0 = new Strand((Bases) null, (-38));
2: strand0.makeMarkerRangeFromPositions((-2950), 676);
Test case 54
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("vi.-mWH3Q");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = new Strand(bases0, 1);
4: Marker marker0 = strand0.makeMarkerFromRawPosition(5);
5: String string0 = Strand.getCodonAtMarker(marker0);
6: assertEquals(2, strand0.getDirection());
7: assertEquals("knn", string0);
Test case 55
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("internal error - unexpected exception: ");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = new Strand(bases0, 3);
4: int int0 = strand0.getGCount();
5: assertEquals(2, strand0.getDirection());
6: assertEquals(2, int0);
Test case 56
1: Bases bases0 = new Bases((Sequence) null);
2: Strand strand0 = bases0.getForwardStrand();
3: assertTrue(strand0.isForwardStrand());
4:
5: int int0 = strand0.getRawPosition((-5));
6: assertEquals((-5), int0);
Test case 57
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("vi.-mWH3Q");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = bases0.getForwardStrand();
4: int int0 = strand0.getRawPosition(0);
5: assertEquals(0, int0);
Test case 58
1: EmblStreamSequence emblStreamSequence0 = new EmblStreamSequence("@3s>u1<|PZI@42");
2: Bases bases0 = new Bases(emblStreamSequence0);
3: Strand strand0 = new Strand(bases0, 120);
4: int int0 = strand0.getSequenceLength();
5: assertEquals(14, int0);
Test case 59
1: char[] charArray0 = new char[4];
2: CharArrayReader charArrayReader0 = new CharArrayReader(charArray0);
3: LineNumberReader lineNumberReader0 = new LineNumberReader(charArrayReader0);
4: LinePushBackReader linePushBackReader0 = new LinePushBackReader(lineNumberReader0);
5: RawStreamSequence rawStreamSequence0 = new RawStreamSequence(linePushBackReader0);
6: Bases bases0 = new Bases(rawStreamSequence0);
7: Strand strand0 = bases0.getReverseStrand();
8: int int0 = strand0.getSequenceLength();
9: assertEquals(0, int0);
Test case 60
1: RawStreamSequence rawStreamSequence0 = new RawStreamSequence("");
2: Bases bases0 = new Bases(rawStreamSequence0);
3: Strand strand0 = bases0.getReverseStrand();
4: strand0.getStrandBases();
5: assertEquals(2, strand0.getDirection());
Test case 61
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("jMQ/n?Z-5GP<}b3F0U");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: Strand strand0 = bases0.getReverseStrand();
4: strand0.makeMarkerRangeFromRawPositions(1, 5);
5: assertEquals(2, strand0.getDirection());
Test case 62
1: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence("vi.-mWH3Q");
2: Bases bases0 = new Bases(genbankStreamSequence0);
3: Strand strand0 = new Strand(bases0, 1);
4: Marker marker0 = strand0.makeMarkerFromRawPosition(5);
5: MarkerRange markerRange0 = new MarkerRange(marker0);
6: String string0 = Strand.markerRangeBases(markerRange0);
7: assertEquals("k", string0);
8: assertEquals(2, strand0.getDirection());
Test case 63
1: FastaStreamSequence fastaStreamSequence0 = new FastaStreamSequence("");
2: Bases bases0 = new Bases(fastaStreamSequence0);
3: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
4: bases0.addBases(1, 1, "vTgt!f:6B&i!%@?LS");
5: SimpleGotoEventSource simpleGotoEventSource0 = new SimpleGotoEventSource(simpleEntryGroup0);
6: MarkerRange markerRange0 = simpleGotoEventSource0.gotoBase(1);
7: MarkerRange[] markerRangeArray0 = Strand.getOpenReadingFrameRanges(markerRange0, 2, (-5), 0);
8: assertNotNull(markerRangeArray0);