Test case 1
1: SimpleEntryInformation simpleEntryInformation0 = (SimpleEntryInformation)SimpleEntryInformation.getDefaultEntryInformation();
2: String string0 = null;
3: MockFile mockFile0 = new MockFile((String) null, (String) null);
4: FileDocument fileDocument0 = new FileDocument(mockFile0);
5: IndexedGFFDocumentEntry indexedGFFDocumentEntry0 = new IndexedGFFDocumentEntry(fileDocument0);
6: boolean boolean0 = false;
7: MSPcrunchDocumentEntry mSPcrunchDocumentEntry0 = new MSPcrunchDocumentEntry(indexedGFFDocumentEntry0, boolean0);
8: mSPcrunchDocumentEntry0.setDirtyFlag();
9: GFFDocumentEntry gFFDocumentEntry0 = new GFFDocumentEntry(mSPcrunchDocumentEntry0, boolean0);
10: int int0 = 1272;
11: Feature feature0 = gFFDocumentEntry0.getFeatureAtIndex(int0);
12: Feature feature1 = indexedGFFDocumentEntry0.forcedAdd(feature0);
13: ReadAndWriteEntry.addAllKeysQualifiers(simpleEntryInformation0, feature1);
14: ReadAndWriteEntry readAndWriteEntry0 = new ReadAndWriteEntry();
15: RepositorySelector repositorySelector0 = mock(RepositorySelector.class, new ViolatedAssumptionAnswer());
16: String string1 = "All terms must be from the same ontology: ";
17: TextArea textArea0 = new TextArea(string1);
18: LogManager.setRepositorySelector(repositorySelector0, textArea0);
19: DatabaseEntrySource databaseEntrySource0 = ReadAndWriteEntry.getEntrySource();
20: String string2 = ReadAndWriteEntry.getFeatureId(databaseEntrySource0, string0);
21: ReadAndWriteEntry.readEntryFromDatabase(string0);
22: fileDocument0.getOutputStream();
23: String string3 = "cC5{P5w.Xa";
24: ReadAndWriteEntry.readEntryFromDatabase(string3);
25: DatabaseEntrySource databaseEntrySource1 = ReadAndWriteEntry.getEntrySource();
26: ReadAndWriteEntry.readEntryFromDatabase(string2, databaseEntrySource1);
27: String string4 = "rU&_/%o(ln[W";
28: ReadAndWriteEntry.getFeatureId(databaseEntrySource0, string4);
29: ReadAndWriteEntry.getFeatureId(databaseEntrySource0, string4);
30: ReadAndWriteEntry.addAllKeysQualifiers(simpleEntryInformation0, feature1);
31: String string5 = "o~\\%o";
32: ReadAndWriteEntry.readEntryFromDatabase(string5);
33: ReadAndWriteEntry.addAllKeysQualifiers(simpleEntryInformation0, feature0);
Test case 2
1: ReadAndWriteEntry readAndWriteEntry0 = new ReadAndWriteEntry();
2: RemoteFileNode remoteFileNode0 = new RemoteFileNode(true);
3: RemoteFileDocument remoteFileDocument0 = new RemoteFileDocument(remoteFileNode0);
4: remoteFileNode0.getPreviousSibling();
5: IndexedGFFDocumentEntry indexedGFFDocumentEntry0 = new IndexedGFFDocumentEntry(remoteFileDocument0);
6: EntryInformation entryInformation0 = indexedGFFDocumentEntry0.getEntryInformation();
7: remoteFileDocument0.getWriter();
8: SimpleEntryInformation simpleEntryInformation0 = new SimpleEntryInformation(entryInformation0);
9: simpleEntryInformation0.getSortedValidKeys();
10: String string0 = "Trp";
11: ReadAndWriteEntry.addQualifierToEntryInfo(simpleEntryInformation0, string0);
12: boolean boolean0 = true;
13: LogLog.setQuietMode(boolean0);
14: String string1 = "Ij/5";
15: DatabaseDocument.TRANSCRIPT = string1;
16: ReadAndWriteEntry.getEntrySource();
17: ReadAndWriteEntry.getEntrySource();
18: EntryInformation entryInformation1 = SimpleEntryInformation.getDefaultEntryInformation();
19: Sequence sequence0 = null;
20: BioJavaEntry bioJavaEntry0 = new BioJavaEntry(sequence0);
21: String string2 = "";
22: Key key0 = new Key(string2);
23: int int0 = 5;
24: Range range0 = new Range(int0, int0);
25: Location location0 = new Location(range0);
26: int int1 = (-860);
27: Location location1 = location0.reverseComplement(int0, int1);
28: Range range1 = new Range(int1);
29: Location location2 = location1.addRange(range1);
30: FramedFeature.Template framedFeature_Template0 = new FramedFeature.Template();
31: SimpleFramedFeature simpleFramedFeature0 = new SimpleFramedFeature(sequence0, sequence0, framedFeature_Template0);
32: BioJavaFeature bioJavaFeature0 = new BioJavaFeature(simpleFramedFeature0, bioJavaEntry0);
33: QualifierVector qualifierVector0 = bioJavaFeature0.getQualifiers();
34: Feature feature0 = bioJavaEntry0.createFeature(key0, location2, qualifierVector0);
35: ReadAndWriteEntry.addAllKeysQualifiers(entryInformation1, feature0);
36: ReadAndWriteEntry.getEntrySource();
Test case 3
1: BlastEntryInformation blastEntryInformation0 = new BlastEntryInformation();
2: Key key0 = new Key("p`jy~s");
3: blastEntryInformation0.isValidKey(key0);
4: SimpleEntryInformation simpleEntryInformation0 = new SimpleEntryInformation(blastEntryInformation0);
5: blastEntryInformation0.getSortedValidKeys();
6: InputStreamProgressListener inputStreamProgressListener0 = mock(InputStreamProgressListener.class, new ViolatedAssumptionAnswer());
7: ReadAndWriteEntry.getEntrySource();
8: ReadAndWriteEntry.addQualifierToEntryInfo(blastEntryInformation0, "-z\t[y|n] gzip output, default is y");
9: String string0 = BorderLayout.LINE_END;
10: assertEquals("After", string0);
Test case 4
1: SimpleEntryInformation simpleEntryInformation0 = (SimpleEntryInformation)SimpleEntryInformation.getDefaultEntryInformation();
2: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
3: ReadAndWriteEntry.addAllKeysQualifiers(simpleEntryInformation0, emblStreamFeature0);
4: ReadAndWriteEntry.getEntrySource();
5: ReadAndWriteEntry.readEntryFromDatabase("updateFeatureLoc", (DatabaseEntrySource) null);
6: ReadAndWriteEntry.getEntrySource();
Test case 5
1: SimpleEntryInformation simpleEntryInformation0 = (SimpleEntryInformation)SimpleEntryInformation.getDefaultEntryInformation();
2: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
3: ReadAndWriteEntry.addAllKeysQualifiers(simpleEntryInformation0, emblStreamFeature0);
4: assertFalse(simpleEntryInformation0.useEMBLFormat());
Test case 6
1: ReadAndWriteEntry.readEntryFromDatabase("");
2: ReadAndWriteEntry.getEntrySource();
3: String string0 = "ASCIDIAN_MITOCHONDRIAL";
4: Entry entry0 = ReadAndWriteEntry.readEntryFromDatabase(string0);
5: EntryInformation entryInformation0 = entry0.getEntryInformation();
6: SimpleEntryInformation simpleEntryInformation0 = new SimpleEntryInformation(entryInformation0);
7: simpleEntryInformation0.getSortedValidKeys();
8: SimpleEntryInformation.getDefaultEntryInformation();
9: EmblStreamFeature emblStreamFeature0 = new EmblStreamFeature();
10: ReadAndWriteEntry.addAllKeysQualifiers(simpleEntryInformation0, emblStreamFeature0);
11: ReadAndWriteEntry.addAllKeysQualifiers(entryInformation0, emblStreamFeature0);
12: ReadAndWriteEntry.readEntryFromDatabase(string0);
Test case 7
1: ReadAndWriteEntry.getEntrySource();
2: ReadAndWriteEntry.readEntryFromDatabase(";@(5KWNQ:muP2C+o_", (DatabaseEntrySource) null);
Test case 8
1: System.setCurrentTimeMillis((-3912L));
2: DatabaseEntrySource databaseEntrySource0 = new DatabaseEntrySource();
3: databaseEntrySource0.setLocation(false);
4: ReadAndWriteEntry.readEntryFromDatabase("", databaseEntrySource0);
Test case 9
1: System.setCurrentTimeMillis((-3912L));
2: DatabaseEntrySource databaseEntrySource0 = new DatabaseEntrySource();
3: assertTrue(databaseEntrySource0.isFullEntrySource());
4: assertEquals("Database", databaseEntrySource0.getSourceName());
5: assertNull(databaseEntrySource0.getLocation());
6: assertFalse(databaseEntrySource0.isReadOnly());
7: assertNotNull(databaseEntrySource0);
8:
9: boolean boolean0 = databaseEntrySource0.setLocation(false);
10: assertTrue(databaseEntrySource0.isFullEntrySource());
11: assertEquals("Database", databaseEntrySource0.getSourceName());
12: assertFalse(databaseEntrySource0.isReadOnly());
13: assertEquals("jdbc:postgresql://localhost:5432/chado?user=", databaseEntrySource0.getLocation());
14: assertTrue(boolean0);
15:
16: ReadAndWriteEntry.readEntryFromDatabase("", databaseEntrySource0);
Test case 10
1: ReadAndWriteEntry readAndWriteEntry0 = new ReadAndWriteEntry();
2: assertNotNull(readAndWriteEntry0);
3:
4: URL uRL0 = Loader.getResource("");
5: assertEquals("", uRL0.getAuthority());
6: assertEquals("file", uRL0.getProtocol());
7: assertEquals("", uRL0.getHost());
8: assertNull(uRL0.getUserInfo());
9: assertEquals((-1), uRL0.getPort());
10: assertEquals((-1), uRL0.getDefaultPort());
11: assertNull(uRL0.getRef());
12: assertNull(uRL0.getQuery());
13: assertNotNull(uRL0);
14:
15: SimpleEntryInformation simpleEntryInformation0 = (SimpleEntryInformation)SimpleEntryInformation.getDefaultEntryInformation();
16: assertFalse(simpleEntryInformation0.useEMBLFormat());
17: assertNotNull(simpleEntryInformation0);
18:
19: ReadAndWriteEntry.addQualifierToEntryInfo(simpleEntryInformation0, (String) null);
Test case 11
1: DatabaseEntrySource databaseEntrySource0 = ReadAndWriteEntry.getEntrySource();
2: assertNull(databaseEntrySource0);
3:
4: ReadAndWriteEntry.getFeatureId((DatabaseEntrySource) null, "K3H");
Test case 12
1: DatabaseEntrySource databaseEntrySource0 = new DatabaseEntrySource();
2: assertNull(databaseEntrySource0.getLocation());
3: assertFalse(databaseEntrySource0.isReadOnly());
4: assertEquals("Database", databaseEntrySource0.getSourceName());
5: assertTrue(databaseEntrySource0.isFullEntrySource());
6: assertNotNull(databaseEntrySource0);
7:
8: ReadAndWriteEntry.getFeatureId(databaseEntrySource0, (String) null);
Test case 13
1: DatabaseEntrySource databaseEntrySource0 = ReadAndWriteEntry.getEntrySource();
2: assertNull(databaseEntrySource0);
3:
4: ReadAndWriteEntry readAndWriteEntry0 = new ReadAndWriteEntry();
5: assertNotNull(readAndWriteEntry0);
6:
7: UI.UIMode uI_UIMode0 = UI.UIMode.CONSOLE;
8: UI.mode = uI_UIMode0;
9: LogLog.setInternalDebugging(false);
10: MSPcrunchEntryInformation mSPcrunchEntryInformation0 = new MSPcrunchEntryInformation();
11: assertFalse(mSPcrunchEntryInformation0.useEMBLFormat());
12: assertNotNull(mSPcrunchEntryInformation0);
13:
14: QualifierInfoHash qualifierInfoHash0 = mSPcrunchEntryInformation0.getAllQualifierInfo();
15: assertFalse(mSPcrunchEntryInformation0.useEMBLFormat());
16: assertNull(qualifierInfoHash0);
17:
18: ReadAndWriteEntry.addQualifierToEntryInfo(mSPcrunchEntryInformation0, "<W]ezc");
19: assertFalse(mSPcrunchEntryInformation0.useEMBLFormat());
20:
21: ReadAndWriteEntry.readEntryFromDatabase("O1_wVQDA6uf");
Test case 14
1: BlastEntryInformation blastEntryInformation0 = new BlastEntryInformation();
2: assertFalse(blastEntryInformation0.useEMBLFormat());
3: assertNotNull(blastEntryInformation0);
4:
5: Key key0 = new Key((String) null);
6: assertNull(key0.toString());
7: assertNull(key0.getKeyString());
8: assertNotNull(key0);
9:
10: boolean boolean0 = blastEntryInformation0.isValidQualifier(key0, "qQ}yO8&VCbc8Qx/");
11: assertFalse(blastEntryInformation0.useEMBLFormat());
12: assertNull(key0.toString());
13: assertNull(key0.getKeyString());
14: assertTrue(boolean0);
15:
16: boolean boolean1 = blastEntryInformation0.isRequiredQualifier(key0, "qQ}yO8&VCbc8Qx/");
17: assertFalse(blastEntryInformation0.useEMBLFormat());
18: assertNull(key0.toString());
19: assertNull(key0.getKeyString());
20: assertFalse(boolean1 == boolean0);
21: assertFalse(boolean1);
22:
23: ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene();
24: assertEquals(0, chadoCanonicalGene0.getSrcfeature_id());
25: assertEquals(0, chadoCanonicalGene0.getSeqlen());
26: assertNotNull(chadoCanonicalGene0);
27:
28: boolean boolean2 = blastEntryInformation0.isRequiredQualifier(key0, "-08-");
29: assertFalse(blastEntryInformation0.useEMBLFormat());
30: assertNull(key0.toString());
31: assertNull(key0.getKeyString());
32: assertFalse(boolean2 == boolean0);
33: assertTrue(boolean2 == boolean1);
34: assertFalse(boolean2);
35:
36: Feature feature0 = chadoCanonicalGene0.getProteinOfTranscript("");
37: assertEquals(0, chadoCanonicalGene0.getSrcfeature_id());
38: assertEquals(0, chadoCanonicalGene0.getSeqlen());
39: assertNull(feature0);
40:
41: ReadAndWriteEntry.addAllKeysQualifiers(blastEntryInformation0, (Feature) null);
Test case 15
1: DatabaseEntrySource databaseEntrySource0 = new DatabaseEntrySource();
2: assertEquals("Database", databaseEntrySource0.getSourceName());
3: assertNull(databaseEntrySource0.getLocation());
4: assertTrue(databaseEntrySource0.isFullEntrySource());
5: assertFalse(databaseEntrySource0.isReadOnly());
6: assertNotNull(databaseEntrySource0);
7:
8: ReadAndWriteEntry.readEntryFromDatabase("zym~;19 uoZBm", databaseEntrySource0);
Test case 16
1: DatabaseEntrySource databaseEntrySource0 = new DatabaseEntrySource();
2: assertEquals("Database", databaseEntrySource0.getSourceName());
3: assertNull(databaseEntrySource0.getLocation());
4: assertFalse(databaseEntrySource0.isReadOnly());
5: assertTrue(databaseEntrySource0.isFullEntrySource());
6: assertNotNull(databaseEntrySource0);
7:
8: SystemInUtil.addInputLine("");
9: boolean boolean0 = databaseEntrySource0.setLocation(false);
10: assertEquals("Database", databaseEntrySource0.getSourceName());
11: assertFalse(databaseEntrySource0.isReadOnly());
12: assertTrue(databaseEntrySource0.isFullEntrySource());
13: assertEquals("jdbc:postgresql://localhost:5432/chado?user=", databaseEntrySource0.getLocation());
14: assertTrue(boolean0);
15:
16: InputStreamProgressListener inputStreamProgressListener0 = mock(InputStreamProgressListener.class, new ViolatedAssumptionAnswer());
17: ReadAndWriteEntry.readEntryFromDatabase("", databaseEntrySource0);
18: ReadAndWriteEntry readAndWriteEntry0 = new ReadAndWriteEntry();
19: SimpleEntryInformation simpleEntryInformation0 = new SimpleEntryInformation();
20: SimpleEntryInformation simpleEntryInformation1 = new SimpleEntryInformation(simpleEntryInformation0);
21: String string0 = null;
22: ReadAndWriteEntry.addQualifierToEntryInfo(simpleEntryInformation1, string0);
23: String string1 = "pjJ";
24: ReadAndWriteEntry.readEntryFromDatabase(string1);
25: String string2 = "52XfJ";
26: ReadAndWriteEntry.addQualifierToEntryInfo(simpleEntryInformation0, string2);
Test case 17
1: DatabaseEntrySource databaseEntrySource0 = new DatabaseEntrySource();
2: assertFalse(databaseEntrySource0.isReadOnly());
3: assertNull(databaseEntrySource0.getLocation());
4: assertTrue(databaseEntrySource0.isFullEntrySource());
5: assertEquals("Database", databaseEntrySource0.getSourceName());
6: assertNotNull(databaseEntrySource0);
7:
8: boolean boolean0 = databaseEntrySource0.setLocation(false);
9: assertFalse(databaseEntrySource0.isReadOnly());
10: assertEquals("jdbc:postgresql://localhost:5432/chado?user=", databaseEntrySource0.getLocation());
11: assertTrue(databaseEntrySource0.isFullEntrySource());
12: assertEquals("Database", databaseEntrySource0.getSourceName());
13: assertTrue(boolean0);
14:
15: InputStreamProgressListener inputStreamProgressListener0 = mock(InputStreamProgressListener.class, new ViolatedAssumptionAnswer());
16: ReadAndWriteEntry readAndWriteEntry0 = new ReadAndWriteEntry();
17: assertNotNull(readAndWriteEntry0);
18:
19: ReadAndWriteEntry.getFeatureId(databaseEntrySource0, "-_BV.-#'sO|");
Source Code
1: No source found for uk.ac.sanger.artemis.io.ReadAndWriteEntry
EvoSuite Parameters
- TARGET_CLASS: uk.ac.sanger.artemis.io.ReadAndWriteEntry
- Size: 17
- Length: 155
- criterion: LINE;BRANCH;EXCEPTION;WEAKMUTATION;OUTPUT;METHOD;METHODNOEXCEPTION;CBRANCH
- Coverage: 0.36517715714239535
- BranchCoverage: 0.20754716981132076
- MethodCoverage: 0.875
- OutputCoverage: 0.07142857142857142
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