Test case 1
1: ArtemisUtils artemisUtils0 = new ArtemisUtils();
2: String string0 = "";
3: StringVector stringVector0 = new StringVector("");
4: String string1 = ArtemisUtils.getString(stringVector0, "");
5: ArtemisUtils.getString(stringVector0, "");
6: int int0 = 2211;
7: JPasswordField jPasswordField0 = new JPasswordField("", 2211);
8: IBatisDAO iBatisDAO0 = new IBatisDAO(jPasswordField0);
9: Feature feature0 = iBatisDAO0.getFeatureById(int0);
10: Cv cv0 = new Cv();
11: String string2 = "H<H";
12: cv0.setName(string2);
13: DbXRef dbXRef0 = null;
14: String string3 = "";
15: CvTerm cvTerm0 = new CvTerm(cv0, dbXRef0, string3, string1);
16: boolean boolean0 = true;
17: FeatureCvTerm featureCvTerm0 = iBatisDAO0.getFeatureCvTermByFeatureAndCvTerm(feature0, cvTerm0, boolean0);
18: ArtemisUtils.inserFeatureCvTerm(iBatisDAO0, featureCvTerm0);
19: ArtemisUtils.getCurrentSchema();
20: String string4 = ArtemisUtils.getCurrentSchema();
21: ArtemisUtils.getString(stringVector0, string3);
22: ArtemisUtils.inserFeatureCvTerm(iBatisDAO0, featureCvTerm0);
23: ArtemisUtils.getCurrentSchema();
24: LargeObject largeObject0 = mock(LargeObject.class, new ViolatedAssumptionAnswer());
25: LargeObjectDocument largeObjectDocument0 = new LargeObjectDocument(string4, string0, largeObject0);
26: IndexedGFFDocumentEntry indexedGFFDocumentEntry0 = new IndexedGFFDocumentEntry(largeObjectDocument0);
27: String string5 = "L?.*&1[Bs-hqT_6L,";
28: Key key0 = new Key(string5);
29: int int1 = 963;
30: Range range0 = new Range(int1);
31: Location location0 = new Location(range0);
32: QualifierVector qualifierVector0 = new QualifierVector();
33: ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene();
34: DatabaseInferredFeature databaseInferredFeature0 = new DatabaseInferredFeature(key0, location0, qualifierVector0, chadoCanonicalGene0);
35: uk.ac.sanger.artemis.io.Feature feature1 = indexedGFFDocumentEntry0.add(databaseInferredFeature0);
36: GFFStreamFeature gFFStreamFeature0 = new GFFStreamFeature(feature1);
37: boolean boolean1 = false;
38: ArtemisUtils.getMatchFeatureWithFeatureRelations(string0, string4, string2, gFFStreamFeature0, boolean1);
Test case 2
1: String string0 = "P<)M!Zn|4OX";
2: String string1 = "";
3: String string2 = "Features have been added or removed";
4: String string3 = "zgHxNbr";
5: GFFStreamFeature gFFStreamFeature0 = new GFFStreamFeature("zgHxNbr");
6: boolean boolean0 = false;
7: gFFStreamFeature0.setVisible(boolean0);
8: Hashtable<String, Range> hashtable0 = gFFStreamFeature0.getSegmentRangeStore();
9: boolean boolean1 = true;
10: Feature feature0 = ArtemisUtils.getMatchFeatureWithFeatureRelations(string0, string1, string2, gFFStreamFeature0, boolean1);
11: String string4 = ArtemisUtils.getCurrentSchema();
12: ArtemisUtils artemisUtils0 = new ArtemisUtils();
13: ArtemisUtils.getAnalysisFeature(string4, string3, gFFStreamFeature0);
14: int int0 = (-1431);
15: JPasswordField jPasswordField0 = new JPasswordField(int0);
16: JdbcDAO jdbcDAO0 = new JdbcDAO(string3, jPasswordField0);
17: IBatisDAO iBatisDAO0 = new IBatisDAO(jPasswordField0);
18: Cv cv0 = new Cv();
19: Db db0 = new Db();
20: String string5 = "SwTH{Sl,@z&)=1*Nr&";
21: jdbcDAO0.getFeatureDbXRefsByFeatureUniquename(string5);
22: DbXRef dbXRef0 = new DbXRef(db0, string2);
23: CvTerm cvTerm0 = new CvTerm(cv0, dbXRef0, string1, string1);
24: boolean boolean2 = true;
25: String string6 = "EMPTY_ANNOTATION";
26: gFFStreamFeature0.setSegmentRangeStore(hashtable0);
27: db0.setUrl(string6);
28: FeatureCvTerm featureCvTerm0 = iBatisDAO0.getFeatureCvTermByFeatureAndCvTerm(feature0, cvTerm0, boolean2);
29: ArtemisUtils.deleteFeatureCvTerm(jdbcDAO0, featureCvTerm0);
30: ArtemisUtils.deleteFeatureCvTerm(iBatisDAO0, featureCvTerm0);
31: ArtemisUtils.getMatchFeatureWithFeatureRelations(string4, string2, string2, gFFStreamFeature0, boolean0);
32: String string7 = "zF4xBo1V6;,;qC\\\\";
33: String string8 = "";
34: GFFStreamFeature gFFStreamFeature1 = null;
35: ArtemisUtils.getMatchFeatureWithFeatureRelations(string7, string2, string8, gFFStreamFeature1, boolean0);
36: BlastEntryInformation blastEntryInformation0 = new BlastEntryInformation();
37: Key key0 = Key.CDS;
38: StringVector stringVector0 = blastEntryInformation0.getRequiredQualifiers(key0);
39: ArtemisUtils.getString(stringVector0, string8);
Test case 3
1: String string0 = "org.biojava.bio.seq.FeatureFilter$OverlapsLocation";
2: String string1 = "KqY*W1)Z}YHJ}?y\\";
3: SimilarityPairFeature.Template similarityPairFeature_Template0 = new SimilarityPairFeature.Template();
4: SimpleFeature simpleFeature0 = new SimpleFeature((Sequence) null, (FeatureHolder) null, similarityPairFeature_Template0);
5: String string2 = "Q7{(cTBvf";
6: String string3 = "";
7: SimpleAssembly simpleAssembly0 = new SimpleAssembly(string2, string3);
8: BioJavaEntry bioJavaEntry0 = new BioJavaEntry(simpleAssembly0);
9: BioJavaFeature bioJavaFeature0 = new BioJavaFeature(simpleFeature0, bioJavaEntry0);
10: Key key0 = bioJavaFeature0.getKey();
11: String string4 = null;
12: Location location0 = new Location(string4);
13: int int0 = 0;
14: Range range0 = new Range(int0, int0);
15: Location location1 = location0.removeRange(range0);
16: Location location2 = location1.truncate(range0);
17: QualifierVector qualifierVector0 = bioJavaFeature0.getQualifiers();
18: ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene();
19: DatabaseInferredFeature databaseInferredFeature0 = new DatabaseInferredFeature(key0, location2, qualifierVector0, chadoCanonicalGene0);
20: boolean boolean0 = false;
21: ArtemisUtils.getMatchFeatureWithFeatureRelations(string0, string0, string1, databaseInferredFeature0, boolean0);
22: GenbankStreamSequence genbankStreamSequence0 = new GenbankStreamSequence(string0);
23: Bases bases0 = new Bases(genbankStreamSequence0);
24: SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup(bases0);
25: Entry entry0 = simpleEntryGroup0.elementAt(bases0.REVERSE);
26: Feature feature0 = entry0.createFeature();
27: String string5 = "` T27o4!I@((l1n.";
28: feature0.getFirstCodingBaseMarker();
29: char char0 = 's';
30: Bases.getIndexOfBase(char0);
31: StringVector stringVector0 = feature0.getValuesOfQualifier(string5);
32: ArtemisUtils.getString(stringVector0, string2);
33: ArtemisUtils artemisUtils0 = new ArtemisUtils();
34: ArtemisUtils.getCurrentSchema();
35: String string6 = "Szi{ertG6i_SF ;";
36: ArtemisUtils.getString(stringVector0, string6);
Test case 4
1: String[] stringArray0 = new String[4];
2: stringArray0[0] = "rank";
3: stringArray0[1] = "oCH";
4: stringArray0[2] = "feature_id";
5: stringArray0[3] = "FeatureCvTermDbXRefs not the same - ignore ";
6: StringVector stringVector0 = new StringVector(stringArray0);
7: String string0 = ArtemisUtils.getString(stringVector0, "feature_id");
8: assertEquals("feature_id", string0);
Test case 5
1: StringVector stringVector0 = new StringVector((String[]) null);
2: String string0 = "";
3: boolean boolean0 = stringVector0.add(string0);
4: StringVector stringVector1 = null;
5: stringVector0.add(stringVector1);
6: String string1 = "insertAnalysis";
7: boolean boolean1 = stringVector0.add(string1);
8: String string2 = null;
9: String string3 = ArtemisUtils.getString(stringVector0, string2);
10: String string4 = "f$N-^l";
11: GFFStreamFeature gFFStreamFeature0 = null;
12: ArtemisUtils.getAnalysisFeature(string0, string4, gFFStreamFeature0);
13: String string5 = " PeOw2*F9MQ%hB4g|";
14: String string6 = ")rO_7I&C2n}a\"{B_L";
15: Feature feature0 = ArtemisUtils.getMatchFeatureWithFeatureRelations(string3, string5, string6, gFFStreamFeature0, boolean1);
16: String string7 = ArtemisUtils.getCurrentSchema();
17: JPasswordField jPasswordField0 = null;
18: IBatisDAO iBatisDAO0 = new IBatisDAO(jPasswordField0);
19: int int0 = 7;
20: String string8 = " -> ";
21: stringVector0.add(int0, string8);
22: JPasswordField jPasswordField1 = new JPasswordField(string7, int0);
23: JdbcDAO jdbcDAO0 = new JdbcDAO(string0, jPasswordField1);
24: String string9 = "";
25: CvTerm cvTerm0 = iBatisDAO0.getGoCvTermByAcc(string9);
26: String string10 = "";
27: jdbcDAO0.getFeaturesByUniqueName(string10);
28: FeatureCvTerm featureCvTerm0 = jdbcDAO0.getFeatureCvTermByFeatureAndCvTerm(feature0, cvTerm0, boolean1);
29: ArtemisUtils.deleteFeatureCvTerm(iBatisDAO0, featureCvTerm0);
30: String string11 = " rank = ";
31: ArtemisUtils.getMatchFeatureWithFeatureRelations(string11, string5, string4, gFFStreamFeature0, boolean0);
32: ArtemisUtils.getString(stringVector1, string11);
Test case 6
1: String string0 = ArtemisUtils.getCurrentSchema();
2: String string1 = ArtemisUtils.getCurrentSchema();
3: StringVector stringVector0 = null;
4: String string2 = null;
5: ArtemisUtils.getString(stringVector0, string2);
6: GmodDAO gmodDAO0 = null;
7: String string3 = "";
8: int int0 = 0;
9: JPasswordField jPasswordField0 = new JPasswordField(int0);
10: JdbcDAO jdbcDAO0 = new JdbcDAO(string3, jPasswordField0);
11: int int1 = 5;
12: CvTerm cvTerm0 = jdbcDAO0.getCvTermById(int1);
13: String string4 = "";
14: GenbankStreamFeature genbankStreamFeature0 = new GenbankStreamFeature();
15: boolean boolean0 = false;
16: GFFStreamFeature gFFStreamFeature0 = new GFFStreamFeature(genbankStreamFeature0, boolean0);
17: boolean boolean1 = true;
18: Feature feature0 = ArtemisUtils.getMatchFeatureWithFeatureRelations(string3, string4, string1, gFFStreamFeature0, boolean1);
19: Pub pub0 = new Pub(string2);
20: int int2 = (-2230);
21: FeatureCvTerm featureCvTerm0 = new FeatureCvTerm(cvTerm0, feature0, pub0, boolean0, int2);
22: ArtemisUtils.inserFeatureCvTerm(gmodDAO0, featureCvTerm0);
23: IBatisDAO iBatisDAO0 = new IBatisDAO(jPasswordField0);
24: boolean boolean2 = true;
25: FeatureCvTerm featureCvTerm1 = iBatisDAO0.getFeatureCvTermByFeatureAndCvTerm(feature0, cvTerm0, boolean2);
26: ArtemisUtils.deleteFeatureCvTerm(jdbcDAO0, featureCvTerm1);
27: ArtemisUtils.getString(stringVector0, string2);
28: ArtemisUtils.getCurrentSchema();
29: ArtemisUtils.getString(stringVector0, string1);
30: String string5 = "`vdz!O<&df>deO";
31: ArtemisUtils.getAnalysisFeature(string5, string0, gFFStreamFeature0);
32: IBatisDAO iBatisDAO1 = new IBatisDAO(jPasswordField0);
33: ArtemisUtils.deleteFeatureCvTerm(iBatisDAO1, featureCvTerm0);
Test case 7
1: String string0 = ArtemisUtils.getCurrentSchema();
2: int int0 = 7;
3: JPasswordField jPasswordField0 = new JPasswordField(int0);
4: JdbcDAO jdbcDAO0 = new JdbcDAO(string0, jPasswordField0);
5: int int1 = (-383);
6: int int2 = 4624;
7: TextArea textArea0 = new TextArea(string0, int1, int2, int2);
8: jdbcDAO0.merge(textArea0);
9: IBatisDAO iBatisDAO0 = new IBatisDAO(jPasswordField0);
10: int int3 = 199;
11: Feature feature0 = jdbcDAO0.getFeatureById(int3);
12: CvTerm cvTerm0 = DatabaseDocument.getCvTermByCvTermName(string0);
13: boolean boolean0 = false;
14: FeatureCvTerm featureCvTerm0 = iBatisDAO0.getFeatureCvTermByFeatureAndCvTerm(feature0, cvTerm0, boolean0);
15: ArtemisUtils.inserFeatureCvTerm(jdbcDAO0, featureCvTerm0);
16: ArtemisUtils.deleteFeatureCvTerm(jdbcDAO0, featureCvTerm0);
17: ArtemisUtils.inserFeatureCvTerm(iBatisDAO0, featureCvTerm0);
Test case 8
1: ArtemisUtils.getMatchFeatureWithFeatureRelations((String) null, "", (String) null, (GFFStreamFeature) null, true);
Test case 9
1: StringVector stringVector0 = SelectionViewer.getBaseSummary("h$@k.x\"-[f*VP5U3");
2: stringVector0.add("");
3: ArtemisUtils.getString(stringVector0, "AoV=/#e1b\"Hft");
4: FileDescriptor fileDescriptor0 = new FileDescriptor();
5: MockFileReader mockFileReader0 = new MockFileReader(fileDescriptor0);
6: LinePushBackReader linePushBackReader0 = new LinePushBackReader(mockFileReader0);
7: EmblStreamFeature.readFromStream(linePushBackReader0);
Test case 10
1: BlastEntryInformation blastEntryInformation0 = new BlastEntryInformation();
2: Key key0 = Key.CDS;
3: blastEntryInformation0.getValidQualifierNames(key0);
4: String string0 = "~B+`P#%pi;\\u";
5: ArtemisUtils.getString((StringVector) null, string0);
Test case 11
1: StringVector stringVector0 = new StringVector();
2: StringVector stringVector1 = new StringVector(stringVector0);
3: stringVector1.retainAll(stringVector0);
4: stringVector1.add("MH`rS");
5: stringVector0.add(stringVector1);
6: ArtemisUtils.getString(stringVector1, "");
7: JPasswordField jPasswordField0 = new JPasswordField(" -> ", 0);
8: JdbcDAO jdbcDAO0 = new JdbcDAO("MH`rS", jPasswordField0);
Test case 12
1: StringVector stringVector0 = SelectionViewer.getBaseSummary("%2C");
2: ArtemisUtils.getString(stringVector0, "%2C");
3: Key key0 = new Key("%2C");
4: Range range0 = new Range(2894);
5: Location location0 = new Location(range0);
6: Location location1 = location0.copy();
7: Location location2 = location1.changeRange(range0, range0);
8: ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene();
9: DatabaseInferredFeature databaseInferredFeature0 = new DatabaseInferredFeature(key0, location2, (QualifierVector) null, chadoCanonicalGene0);
10: ArtemisUtils.getMatchFeatureWithFeatureRelations("%2C", "", "", databaseInferredFeature0, true);
Test case 13
1: Key key0 = new Key("");
2: Range range0 = new Range(125, 125);
3: Location location0 = new Location(range0);
4: QualifierVector qualifierVector0 = new QualifierVector();
5: GFFStreamFeature gFFStreamFeature0 = new GFFStreamFeature(key0, location0, qualifierVector0);
6: DatabaseStreamFeature databaseStreamFeature0 = new DatabaseStreamFeature(gFFStreamFeature0);
7: ArtemisUtils.getAnalysisFeature("", "", databaseStreamFeature0);