Summary

Test suite

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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