1 /**
2  * Scaffolding file used to store all the setups needed to run
3  * tests automatically generated by EvoSuite
4  * Fri Jan 12 14:42:41 GMT 2018
5  */
6 
7 package uk.ac.sanger.artemis.io;
8 
9 import org.evosuite.runtime.annotation.EvoSuiteClassExclude;
10 import org.junit.BeforeClass;
11 import org.junit.Before;
12 import org.junit.After;
13 import org.junit.AfterClass;
14 import org.evosuite.runtime.sandbox.Sandbox;
15 import org.evosuite.runtime.sandbox.Sandbox.SandboxMode;
16 
17 @EvoSuiteClassExclude
18 public class EmblStreamFeature_ESTest_scaffolding {
19 
20   @org.junit.Rule
21   public org.evosuite.runtime.vnet.NonFunctionalRequirementRule nfr = new org.evosuite.runtime.vnet.NonFunctionalRequirementRule();
22 
23   private static final java.util.Properties defaultProperties = (java.util.Properties) java.lang.System.getProperties().clone();
24 
25   private org.evosuite.runtime.thread.ThreadStopper threadStopper =  new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);
26 
27 
28   @BeforeClass
initEvoSuiteFramework()29   public static void initEvoSuiteFramework() {
30     org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.io.EmblStreamFeature";
31     org.evosuite.runtime.GuiSupport.initialize();
32     org.evosuite.runtime.RuntimeSettings.maxNumberOfThreads = 100;
33     org.evosuite.runtime.RuntimeSettings.maxNumberOfIterationsPerLoop = 10000;
34     org.evosuite.runtime.RuntimeSettings.mockSystemIn = true;
35     org.evosuite.runtime.RuntimeSettings.sandboxMode = org.evosuite.runtime.sandbox.Sandbox.SandboxMode.RECOMMENDED;
36     org.evosuite.runtime.sandbox.Sandbox.initializeSecurityManagerForSUT();
37     org.evosuite.runtime.classhandling.JDKClassResetter.init();
38     setSystemProperties();
39     initializeClasses();
40     org.evosuite.runtime.Runtime.getInstance().resetRuntime();
41   }
42 
43   @AfterClass
clearEvoSuiteFramework()44   public static void clearEvoSuiteFramework(){
45     Sandbox.resetDefaultSecurityManager();
46     java.lang.System.setProperties((java.util.Properties) defaultProperties.clone());
47   }
48 
49   @Before
initTestCase()50   public void initTestCase(){
51     threadStopper.storeCurrentThreads();
52     threadStopper.startRecordingTime();
53     org.evosuite.runtime.jvm.ShutdownHookHandler.getInstance().initHandler();
54     org.evosuite.runtime.sandbox.Sandbox.goingToExecuteSUTCode();
55     setSystemProperties();
56     org.evosuite.runtime.GuiSupport.setHeadless();
57     org.evosuite.runtime.Runtime.getInstance().resetRuntime();
58     org.evosuite.runtime.agent.InstrumentingAgent.activate();
59   }
60 
61   @After
doneWithTestCase()62   public void doneWithTestCase(){
63     threadStopper.killAndJoinClientThreads();
64     org.evosuite.runtime.jvm.ShutdownHookHandler.getInstance().safeExecuteAddedHooks();
65     org.evosuite.runtime.classhandling.JDKClassResetter.reset();
66     resetClasses();
67     org.evosuite.runtime.sandbox.Sandbox.doneWithExecutingSUTCode();
68     org.evosuite.runtime.agent.InstrumentingAgent.deactivate();
69     org.evosuite.runtime.GuiSupport.restoreHeadlessMode();
70   }
71 
setSystemProperties()72   public static void setSystemProperties() {
73 
74     java.lang.System.setProperties((java.util.Properties) defaultProperties.clone());
75     java.lang.System.setProperty("file.encoding", "UTF-8");
76     java.lang.System.setProperty("java.awt.headless", "true");
77     java.lang.System.setProperty("user.country", "GB");
78     java.lang.System.setProperty("user.language", "en");
79     java.lang.System.setProperty("user.timezone", "Europe/London");
80     java.lang.System.setProperty("log4j.configuration", "SUT.log4j.properties");
81   }
82 
initializeClasses()83   private static void initializeClasses() {
84     org.evosuite.runtime.classhandling.ClassStateSupport.initializeClasses(EmblStreamFeature_ESTest_scaffolding.class.getClassLoader() ,
85       "uk.ac.sanger.artemis.components.LogViewer$1",
86       "org.biojava.bio.seq.AcceptNoneFilter",
87       "net.sf.cglib.core.EmitUtils$ArrayDelimiters",
88       "com.ibatis.common.jdbc.SimpleDataSource$SimplePooledConnection",
89       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.ConditionalTagHandler",
90       "org.biojava.bio.seq.io.SymbolTokenization$TokenType",
91       "org.biojava.bio.seq.ByHierarchy",
92       "org.biojava.bio.seq.ComponentFeature$Template",
93       "org.apache.log4j.AppenderSkeleton",
94       "com.ibatis.sqlmap.client.extensions.ParameterSetter",
95       "com.sshtools.j2ssh.connection.SshMsgRequestFailure",
96       "org.biojava.utils.stax.SAX2StAXAdaptor",
97       "uk.ac.sanger.artemis.io.SimpleDocumentFeature",
98       "uk.ac.sanger.artemis.sequence.BasePatternFormatException",
99       "com.sshtools.j2ssh.sftp.SshFxpRmdir",
100       "com.sshtools.j2ssh.authentication.PasswordAuthenticationClient",
101       "net.sf.cglib.core.KeyFactory$Generator",
102       "com.sshtools.j2ssh.SshClient",
103       "uk.ac.sanger.artemis.EntryChangeListener",
104       "org.biojava.ontology.Term",
105       "org.biojava.utils.ListTools$Triplet",
106       "org.biojava.bio.symbol.DoubleAlphabet$SubDoubleAlphabet",
107       "uk.ac.sanger.artemis.sequence.AminoAcidSequence",
108       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$AlphabetHandler$1",
109       "uk.ac.sanger.artemis.Selectable",
110       "org.biojava.bio.seq.io.NameTokenization",
111       "net.sf.cglib.core.CodeEmitter$State",
112       "uk.ac.sanger.artemis.io.FeatureTable",
113       "uk.ac.sanger.artemis.io.RangeVector",
114       "org.biojava.bio.seq.FramedFeature$ReadingFrame",
115       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateTagHandler",
116       "org.biojava.bio.seq.io.CharacterTokenization",
117       "org.biojava.bio.seq.homol.SimilarityPairFeature$EmptyPairwiseAlignment",
118       "uk.ac.sanger.artemis.io.PublicDBDocumentEntry",
119       "uk.ac.sanger.artemis.util.StringVector",
120       "net.sf.cglib.core.Constants",
121       "net.sf.cglib.core.AbstractClassGenerator",
122       "org.biojava.bio.seq.Feature$Template",
123       "com.ibatis.common.beans.BaseProbe",
124       "com.sshtools.j2ssh.transport.AsyncService",
125       "com.ibatis.sqlmap.engine.mapping.statement.SelectKeyStatement",
126       "org.gmod.schema.sequence.Synonym",
127       "org.biojava.bio.symbol.SimpleAlphabet",
128       "org.biojava.bio.seq.io.SequenceBuilderFactory",
129       "org.gmod.schema.sequence.FeatureCvTermProp",
130       "org.apache.log4j.Hierarchy",
131       "htsjdk.samtools.seekablestream.SeekableFileStream",
132       "uk.ac.sanger.artemis.sequence.MarkerRange",
133       "org.biojava.utils.Changeable",
134       "org.biojava.bio.symbol.EmptyLocation",
135       "net.sf.cglib.asm.MethodWriter",
136       "com.ibatis.common.util.PaginatedList",
137       "uk.ac.sanger.artemis.io.QualifierInfoHash",
138       "com.sshtools.j2ssh.connection.Channel",
139       "net.sf.cglib.core.ClassNameReader$EarlyExitException",
140       "com.ibatis.sqlmap.engine.cache.CacheModel",
141       "org.apache.log4j.spi.OptionHandler",
142       "org.biojava.bio.symbol.SimpleManyToOneTranslationTable",
143       "org.biojava.utils.stax.DelegationManager",
144       "org.biojava.bio.seq.StrandedFeature",
145       "org.biojava.utils.lsid.LifeScienceIdentifier",
146       "net.sf.cglib.core.ReflectUtils",
147       "org.biojava.utils.ChangeVetoException",
148       "org.biojava.bio.symbol.IllegalAlphabetException",
149       "org.biojava.bio.symbol.DoubleAlphabet$DoubleRange",
150       "htsjdk.samtools.seekablestream.SeekableStream",
151       "uk.ac.sanger.artemis.sequence.MarkerInternal",
152       "com.sshtools.j2ssh.connection.ChannelEventListener",
153       "net.sf.cglib.core.AbstractClassGenerator$1",
154       "org.biojava.bio.symbol.AbstractTranslationTable",
155       "uk.ac.sanger.artemis.components.Splash$2",
156       "org.gmod.schema.dao.GeneralDaoI",
157       "com.ibatis.sqlmap.engine.exchange.DataExchangeFactory",
158       "net.sf.cglib.core.LocalVariablesSorter",
159       "org.apache.log4j.helpers.OptionConverter",
160       "org.gmod.schema.dao.BaseDaoI",
161       "com.ibatis.sqlmap.client.SqlMapExecutor",
162       "org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl",
163       "org.biojava.bio.symbol.Edit",
164       "com.ibatis.sqlmap.client.SqlMapException",
165       "uk.ac.sanger.artemis.io.MiscLineGroup",
166       "uk.ac.sanger.artemis.io.LazyQualifierValue",
167       "com.ibatis.sqlmap.engine.type.SqlTimeTypeHandler",
168       "org.postgresql.largeobject.BlobOutputStream",
169       "org.biojava.bio.symbol.AbstractSymbol",
170       "org.biojava.utils.bytecode.CodeGenerator",
171       "org.gmod.schema.cv.CvTerm",
172       "uk.ac.sanger.artemis.sequence.SequenceChangeListener",
173       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsGreaterThanTagHandler",
174       "com.sshtools.j2ssh.subsystem.SubsystemMessage",
175       "uk.ac.sanger.artemis.io.InvalidRelationException",
176       "org.biojava.utils.bytecode.CodeMethod",
177       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEqualTagHandler",
178       "org.biojava.bio.seq.impl.FeatureImpl$1",
179       "org.biojava.bio.seq.io.SimpleSequenceBuilder",
180       "com.sshtools.j2ssh.transport.InvalidMessageException",
181       "org.biojava.bio.Annotation",
182       "org.biojava.bio.symbol.IntegerAlphabet$IntegerSymbol",
183       "org.biojava.utils.lsid.LifeScienceIdentifierParseException",
184       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler",
185       "com.sshtools.j2ssh.authentication.AuthenticationProtocolClient",
186       "org.apache.log4j.Category",
187       "uk.ac.sanger.artemis.io.LocationParseException",
188       "org.biojava.utils.ListTools$Mapper",
189       "htsjdk.samtools.SAMException",
190       "org.biojava.bio.seq.io.StreamParser",
191       "uk.ac.sanger.artemis.util.FastVector",
192       "org.biojava.bio.symbol.SimpleSymbol",
193       "com.ibatis.common.beans.ComplexBeanProbe",
194       "org.apache.log4j.helpers.ThreadLocalMap",
195       "net.sf.cglib.core.KeyFactory$2",
196       "org.biojava.bio.symbol.AbstractSimpleBasisSymbol",
197       "net.sf.cglib.core.KeyFactory$1",
198       "com.sshtools.j2ssh.transport.TransportProtocolEventHandler",
199       "org.gmod.schema.sequence.FeatureDbXRef",
200       "net.sf.cglib.core.ClassInfo",
201       "org.biojava.utils.ChangeEvent",
202       "uk.ac.sanger.artemis.components.variant.AbstractVCFReader",
203       "org.gmod.schema.pub.Pub",
204       "uk.ac.sanger.artemis.io.ChadoCanonicalGene",
205       "net.sf.cglib.core.ClassEmitter$3",
206       "net.sf.cglib.core.EmitUtils$9",
207       "net.sf.cglib.core.ClassEmitter$1",
208       "org.biojava.utils.stax.SAX2StAXAdaptor$S2SDelegationManager",
209       "net.sf.cglib.core.EmitUtils$8",
210       "net.sf.cglib.core.EmitUtils$7",
211       "net.sf.cglib.core.Predicate",
212       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry$IndexContig",
213       "org.biojava.bio.symbol.SimpleCrossProductAlphabet",
214       "net.sf.cglib.core.ClassEmitter",
215       "org.biojava.bio.seq.DNATools",
216       "org.gmod.schema.sequence.FeatureCvTermDbXRef",
217       "org.biojava.bio.seq.FramedFeature$1",
218       "com.sshtools.j2ssh.transport.TransportProtocolState",
219       "org.biojava.bio.symbol.AbstractManyToOneTranslationTable",
220       "uk.ac.sanger.artemis.io.GenbankStreamSequence",
221       "net.sf.cglib.core.ClassNameReader",
222       "com.sshtools.j2ssh.connection.ChannelInputStream",
223       "com.ibatis.sqlmap.engine.cache.CacheController",
224       "net.sf.cglib.core.ClassNameReader$1",
225       "com.ibatis.sqlmap.engine.accessplan.BaseAccessPlan",
226       "htsjdk.samtools.util.RuntimeIOException",
227       "org.biojava.bio.BioRuntimeException",
228       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.BaseTagHandler",
229       "org.biojava.bio.seq.AcceptAllFilter",
230       "org.biojava.bio.seq.io.ChunkedSymbolListFactory",
231       "net.sf.cglib.core.Local",
232       "org.biojava.bio.symbol.IntegerAlphabet$SubIntegerAlphabet",
233       "org.biojava.bio.seq.homol.SimilarityPairFeature",
234       "org.gmod.schema.utils.propinterface.PropertyI",
235       "org.apache.log4j.spi.AppenderAttachable",
236       "com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate",
237       "com.sshtools.j2ssh.SshException",
238       "uk.ac.sanger.artemis.j2ssh.FTProgress",
239       "uk.ac.sanger.artemis.io.GFF3AttributeAggregator",
240       "net.sf.cglib.beans.BulkBean$Generator",
241       "org.gmod.schema.cv.Cv",
242       "uk.ac.sanger.artemis.util.InputStreamProgressListenerVector",
243       "com.sshtools.j2ssh.sftp.SshFxpRename",
244       "net.sf.cglib.core.DefaultNamingPolicy",
245       "uk.ac.sanger.artemis.util.PushBackException",
246       "com.ibatis.sqlmap.engine.exchange.DataExchange",
247       "com.ibatis.sqlmap.engine.mapping.sql.SqlChild",
248       "org.biojava.utils.ParseErrorListener",
249       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.DynamicTagHandler",
250       "com.sshtools.j2ssh.connection.IOChannel",
251       "org.biojava.utils.SingletonList",
252       "org.biojava.bio.symbol.SymbolList",
253       "org.biojava.bio.BioException",
254       "net.sf.cglib.asm.AnnotationVisitor",
255       "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange",
256       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory$1",
257       "com.ibatis.sqlmap.engine.builder.xml.XMLSqlSource",
258       "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMapping",
259       "net.sf.cglib.asm.FieldVisitor",
260       "org.biojava.bio.seq.FramedFeature$Template",
261       "com.ibatis.sqlmap.engine.exchange.BaseDataExchange",
262       "net.sf.cglib.asm.MethodVisitor",
263       "net.sf.cglib.asm.ClassVisitor",
264       "com.sshtools.j2ssh.connection.SshMsgChannelData",
265       "net.sf.cglib.core.DebuggingClassWriter",
266       "net.sf.cglib.core.ClassEmitter$FieldInfo",
267       "uk.ac.sanger.artemis.io.LocationParseNode",
268       "com.ibatis.sqlmap.engine.mapping.statement.MappedStatement",
269       "uk.ac.sanger.artemis.util.WorkingGZIPInputStream",
270       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotPropertyAvailableTagHandler",
271       "org.biojava.utils.ChangeType$1",
272       "org.biojava.bio.symbol.AlphabetManager$WellKnownAlphabet",
273       "org.biojava.bio.seq.io.AbstractGenEmblFileFormer",
274       "com.sshtools.j2ssh.connection.SshMsgRequestSuccess",
275       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsLessThanTagHandler",
276       "com.ibatis.sqlmap.client.SqlMapClient",
277       "uk.ac.sanger.artemis.io.ComparableFeature",
278       "uk.ac.sanger.artemis.io.Key",
279       "uk.ac.sanger.artemis.Options",
280       "org.biojava.bio.seq.io.SymbolReader",
281       "org.biojava.bio.seq.impl.SimpleHomologyFeature",
282       "uk.ac.sanger.artemis.io.SimpleDocumentEntry",
283       "org.biojava.bio.symbol.BasisSymbol",
284       "com.ibatis.sqlmap.engine.transaction.Transaction",
285       "com.ibatis.sqlmap.engine.accessplan.PropertyAccessPlan",
286       "com.sshtools.j2ssh.connection.ChannelFactory",
287       "uk.ac.sanger.artemis.io.FeatureHeader",
288       "org.biojava.bio.seq.RNATools",
289       "net.sf.cglib.beans.BulkBeanEmitter",
290       "com.sshtools.j2ssh.connection.ConnectionProtocol",
291       "com.sshtools.j2ssh.connection.SshMsgChannelOpenConfirmation",
292       "uk.ac.sanger.artemis.chado.Graph",
293       "org.biojava.bio.seq.io.WordTokenization",
294       "com.ibatis.common.beans.GenericProbe",
295       "uk.ac.sanger.artemis.ChangeListener",
296       "uk.ac.sanger.artemis.io.FeatureTree",
297       "net.sf.cglib.core.KeyFactory",
298       "net.sf.cglib.core.GeneratorStrategy",
299       "org.apache.log4j.helpers.Loader",
300       "uk.ac.sanger.artemis.sequence.MarkerChangeEvent",
301       "org.biojava.utils.stax.SAX2StAXAdaptor$HandlerBinding",
302       "org.biojava.bio.seq.impl.SimpleFeature",
303       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory",
304       "org.apache.log4j.helpers.FileWatchdog",
305       "org.biojava.bio.symbol.AbstractSymbolList$ListView",
306       "uk.ac.sanger.artemis.io.RawStreamSequence",
307       "org.biojava.bio.seq.GappedSequence",
308       "net.sf.cglib.core.EmitUtils",
309       "org.biojava.bio.symbol.Alignment",
310       "org.apache.log4j.MDC",
311       "org.biojava.bio.seq.impl.SimpleRestrictionSite",
312       "net.sf.cglib.core.CollectionUtils",
313       "uk.ac.sanger.artemis.io.QualifierInfoException",
314       "net.sf.cglib.core.TypeUtils",
315       "org.gmod.schema.dao.SequenceDaoI",
316       "com.sshtools.j2ssh.sftp.MessageRequestId",
317       "com.ibatis.sqlmap.engine.mapping.result.ResultMapping",
318       "org.biojava.utils.SmallMap",
319       "org.biojava.bio.seq.StrandedFeature$Template",
320       "com.sshtools.j2ssh.transport.HostKeyVerification",
321       "org.biojava.bio.symbol.Symbol",
322       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotParameterPresentTagHandler",
323       "org.biojava.bio.seq.RealizingFeatureHolder",
324       "org.biojava.bio.molbio.RestrictionSite$Template",
325       "org.gmod.schema.sequence.FeatureCvTerm",
326       "net.sf.cglib.beans.BulkBeanException",
327       "org.biojava.bio.seq.FramedFeature",
328       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsParameterPresentTagHandler",
329       "org.biojava.bio.seq.AbstractFeatureHolder",
330       "com.ibatis.sqlmap.engine.config.MappedStatementConfig",
331       "org.biojava.utils.ListTools",
332       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEmptyTagHandler",
333       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$AlphabetHandler",
334       "uk.ac.sanger.artemis.io.DatabaseStreamFeature",
335       "org.gmod.schema.dao.CvDaoI",
336       "uk.ac.sanger.artemis.util.CacheHashMap",
337       "org.biojava.bio.seq.Feature",
338       "uk.ac.sanger.artemis.io.InvalidKeyException",
339       "uk.ac.sanger.artemis.util.FTPSeekableStream",
340       "com.ibatis.common.xml.NodeletException",
341       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagHandler",
342       "net.sf.cglib.core.EmitUtils$ParameterTyper",
343       "com.ibatis.sqlmap.engine.exchange.ComplexDataExchange",
344       "net.sf.cglib.core.Signature",
345       "com.ibatis.sqlmap.engine.type.SqlTimestampTypeHandler",
346       "net.sf.cglib.asm.ByteVector",
347       "org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper",
348       "uk.ac.sanger.artemis.io.LocationLexer",
349       "org.biojava.bio.seq.Sequence",
350       "com.ibatis.sqlmap.engine.mapping.result.Discriminator",
351       "uk.ac.sanger.artemis.util.ByteBuffer",
352       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNullTagHandler",
353       "com.sshtools.j2ssh.connection.InvalidChannelException",
354       "uk.ac.sanger.artemis.io.SimpleEntryInformation",
355       "net.sf.cglib.beans.BulkBean$BulkBeanKey",
356       "org.biojava.utils.stax.StAXContentHandlerBase",
357       "com.sshtools.j2ssh.transport.MessageNotAvailableException",
358       "uk.ac.sanger.artemis.io.StreamSequence",
359       "com.ibatis.sqlmap.engine.config.SqlMapConfiguration",
360       "uk.ac.sanger.artemis.io.GFF3AttributeBuilder",
361       "uk.ac.sanger.artemis.io.Range",
362       "net.sf.cglib.asm.Frame",
363       "uk.ac.sanger.artemis.sequence.Bases",
364       "uk.ac.sanger.artemis.components.LogViewer",
365       "org.biojava.bio.symbol.AbstractRangeLocation",
366       "uk.ac.sanger.artemis.io.BetweenRange",
367       "uk.ac.sanger.artemis.ExternalProgramMonitor",
368       "com.sshtools.j2ssh.transport.SshMessage",
369       "com.sshtools.j2ssh.util.State",
370       "uk.ac.sanger.artemis.j2ssh.SshLogin",
371       "org.biojava.bio.EmptyAnnotation",
372       "org.biojava.bio.program.phred.PhredFormat",
373       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsLessEqualTagHandler",
374       "com.ibatis.sqlmap.engine.type.DateOnlyTypeHandler",
375       "org.apache.log4j.PropertyConfigurator",
376       "uk.ac.sanger.artemis.util.Document",
377       "org.biojava.bio.seq.io.ParseException",
378       "com.ibatis.sqlmap.client.event.RowHandler",
379       "org.biojava.bio.symbol.AlphabetManager",
380       "uk.ac.sanger.artemis.components.variant.TabixReader",
381       "uk.ac.sanger.artemis.components.FileViewer",
382       "org.biojava.utils.walker.WalkerFactory",
383       "org.biojava.bio.seq.FeatureRealizer",
384       "org.biojava.utils.bytecode.CodeException",
385       "uk.ac.sanger.artemis.sequence.NoSequenceException",
386       "net.sf.cglib.core.ProcessArrayCallback",
387       "org.biojava.bio.seq.io.SequenceFormat",
388       "org.biojava.bio.symbol.SparseCrossProductAlphabet",
389       "org.biojava.bio.seq.ComponentFeature",
390       "org.biojava.bio.symbol.AlphabetManager$WellKnownBasisSymbol",
391       "org.biojava.bio.seq.impl.SimpleRemoteFeature",
392       "net.sf.cglib.asm.ClassReader",
393       "org.apache.log4j.spi.LoggerRepository",
394       "com.ibatis.common.beans.ProbeException",
395       "com.sshtools.j2ssh.transport.TransportProtocolException",
396       "uk.ac.sanger.artemis.components.Splash",
397       "com.ibatis.sqlmap.engine.impl.ExtendedSqlMapClient",
398       "uk.ac.sanger.artemis.io.EntryInformationException",
399       "com.ibatis.common.beans.Probe",
400       "net.sf.cglib.core.Transformer",
401       "com.sshtools.j2ssh.authentication.SshMsgUserAuthRequest",
402       "uk.ac.sanger.artemis.io.GFFMisc",
403       "com.ibatis.sqlmap.engine.scope.StatementScope",
404       "htsjdk.samtools.FileTruncatedException",
405       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.DynamicSql",
406       "uk.ac.sanger.artemis.chado.IBatisDAO",
407       "com.ibatis.sqlmap.engine.mapping.result.AutoResultMap",
408       "uk.ac.sanger.artemis.components.filetree.RemoteFileNode",
409       "org.biojava.bio.seq.impl.SimpleSimilarityPairFeature",
410       "org.biojava.bio.symbol.SimpleSymbolList$SSLIOListener",
411       "org.biojava.bio.seq.RemoteFeature$Template",
412       "org.apache.log4j.Level",
413       "uk.ac.sanger.artemis.io.FuzzyRange",
414       "org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol",
415       "org.biojava.bio.symbol.AbstractReversibleTranslationTable",
416       "org.biojava.bio.seq.io.SeqIOAdapter",
417       "com.sshtools.j2ssh.authentication.TerminatedStateException",
418       "uk.ac.sanger.artemis.io.EntryInformation",
419       "org.biojava.bio.symbol.SimpleGeneticCodeTable",
420       "com.ibatis.sqlmap.engine.type.UnknownTypeHandler",
421       "htsjdk.samtools.util.BlockCompressedInputStream",
422       "org.biojava.bio.seq.io.SeqIOListener",
423       "uk.ac.sanger.artemis.sequence.MarkerChangeListener",
424       "org.biojava.utils.ChangeType",
425       "net.sf.cglib.asm.FieldWriter",
426       "uk.ac.sanger.artemis.io.ReadFormatException",
427       "com.sshtools.j2ssh.sftp.SftpSubsystemClient",
428       "com.sshtools.j2ssh.util.InvalidStateException",
429       "org.biojava.utils.ChangeListener",
430       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotNullTagHandler",
431       "org.biojava.utils.AbstractChangeable",
432       "org.biojava.bio.seq.SimpleFeatureHolder",
433       "org.gmod.schema.sequence.FeaturePub",
434       "uk.ac.sanger.artemis.EntrySourceVector",
435       "net.sf.cglib.core.LocalVariablesSorter$State",
436       "com.ibatis.sqlmap.client.SqlMapTransactionManager",
437       "com.ibatis.sqlmap.engine.config.ResultMapConfig",
438       "org.biojava.bio.symbol.EmptyAlphabet",
439       "com.sshtools.j2ssh.sftp.SshFxpReadlink",
440       "org.gmod.schema.analysis.AnalysisFeature",
441       "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMap",
442       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTag",
443       "org.gmod.schema.dao.SchemaDaoI",
444       "uk.ac.sanger.artemis.LastSegmentException",
445       "uk.ac.sanger.artemis.ChangeEvent",
446       "org.biojava.bio.seq.SimpleFeatureRealizer",
447       "org.gmod.schema.sequence.FeatureRelationship",
448       "uk.ac.sanger.artemis.io.GenbankStreamFeature",
449       "uk.ac.sanger.artemis.util.OutOfRangeException",
450       "com.ibatis.sqlmap.engine.scope.SessionScope",
451       "org.postgresql.util.PSQLException",
452       "net.sf.cglib.beans.BulkBean",
453       "com.ibatis.common.logging.Log",
454       "org.biojava.bio.symbol.SimpleBasisSymbol",
455       "com.ibatis.sqlmap.engine.mapping.result.ResultMap",
456       "org.biojava.utils.lsid.Identifiable",
457       "org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser",
458       "org.biojava.bio.seq.DNATools$DNAComplementTranslationTable",
459       "uk.ac.sanger.artemis.io.EMBLObject",
460       "org.postgresql.largeobject.LargeObject",
461       "uk.ac.sanger.artemis.sequence.Strand",
462       "uk.ac.sanger.artemis.chado.GmodDAO",
463       "net.sf.cglib.core.ClassGenerator",
464       "net.sf.cglib.core.ReflectUtils$4",
465       "org.apache.log4j.spi.DefaultRepositorySelector",
466       "uk.ac.sanger.artemis.OptionChangeListener",
467       "com.sshtools.j2ssh.connection.ChannelOutputStream",
468       "net.sf.cglib.core.ReflectUtils$1",
469       "net.sf.cglib.core.ReflectUtils$2",
470       "com.sshtools.j2ssh.sftp.SshFxpSymlink",
471       "net.sf.cglib.core.ReflectUtils$3",
472       "uk.ac.sanger.artemis.io.Sequence",
473       "org.biojava.bio.symbol.LocationComparator",
474       "uk.ac.sanger.artemis.components.variant.BCFReader",
475       "uk.ac.sanger.artemis.util.LargeObjectDocument",
476       "uk.ac.sanger.artemis.io.GenbankMisc",
477       "uk.ac.sanger.artemis.chado.JdbcDAO",
478       "net.sf.cglib.core.ObjectSwitchCallback",
479       "org.biojava.utils.bytecode.GeneratedClassLoader",
480       "com.ibatis.sqlmap.engine.cache.CacheKey",
481       "uk.ac.sanger.artemis.io.Location",
482       "org.biojava.utils.stax.StAXContentHandler",
483       "uk.ac.sanger.artemis.io.PublicDBStreamFeature",
484       "net.sf.cglib.core.DefaultGeneratorStrategy",
485       "org.apache.log4j.or.ObjectRenderer",
486       "uk.ac.sanger.artemis.util.DatabaseLocationParser",
487       "net.sf.cglib.core.DebuggingClassWriter$1",
488       "uk.ac.sanger.artemis.io.FastaStreamSequence",
489       "uk.ac.sanger.artemis.io.FeatureEnumeration",
490       "org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper",
491       "com.ibatis.sqlmap.engine.type.DateTypeHandler",
492       "org.biojava.utils.ChangeForwarder",
493       "uk.ac.sanger.artemis.io.StreamFeature",
494       "com.ibatis.common.io.ReaderInputStream",
495       "uk.ac.sanger.artemis.util.ReadOnlyException",
496       "org.biojava.bio.symbol.GappedSymbolList",
497       "com.ibatis.sqlmap.engine.accessplan.MapAccessPlan",
498       "uk.ac.sanger.artemis.EntryChangeEvent",
499       "org.biojava.bio.symbol.HashedAlphabetIndex$HashComparator",
500       "org.biojava.bio.seq.FeatureFilter",
501       "com.sshtools.j2ssh.sftp.SshFxpClose",
502       "uk.ac.sanger.artemis.Feature",
503       "uk.ac.sanger.artemis.io.EmblDocumentEntry",
504       "org.biojava.utils.cache.KeyedWeakReference",
505       "org.biojava.bio.seq.homol.HomologyFeature$Template",
506       "com.sshtools.j2ssh.subsystem.SubsystemChannel",
507       "com.ibatis.sqlmap.client.extensions.ResultGetter",
508       "uk.ac.sanger.artemis.io.DocumentFeature",
509       "org.biojava.bio.SimpleAnnotation",
510       "com.sshtools.j2ssh.FileTransferProgress",
511       "org.biojava.bio.symbol.IntegerAlphabet",
512       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotEqualTagHandler",
513       "com.ibatis.sqlmap.engine.transaction.TransactionManager",
514       "com.ibatis.common.jdbc.SimpleDataSource",
515       "org.biojava.bio.seq.impl.FeatureImpl",
516       "org.apache.log4j.spi.LoggerFactory",
517       "org.biojava.bio.symbol.DoubleAlphabet$DoubleSymbol",
518       "org.apache.log4j.spi.Configurator",
519       "uk.ac.sanger.artemis.io.MSPcrunchStreamFeature",
520       "org.biojava.bio.seq.impl.SimpleFramedFeature",
521       "org.biojava.bio.seq.io.ReferenceAnnotation",
522       "net.sf.cglib.core.CodeEmitter",
523       "org.biojava.bio.symbol.FiniteAlphabet",
524       "org.gmod.schema.sequence.Feature",
525       "org.biojava.bio.seq.FeatureFilter$OnlyChildren",
526       "org.biojava.bio.seq.homol.SimilarityPairFeature$Template",
527       "org.apache.log4j.PropertyWatchdog",
528       "uk.ac.sanger.artemis.io.KeyVector",
529       "org.gmod.schema.sequence.FeatureProp",
530       "org.gmod.schema.sequence.FeatureCvTermPub",
531       "org.biojava.bio.Annotatable",
532       "org.gmod.schema.utils.Rankable",
533       "com.ibatis.sqlmap.engine.accessplan.ComplexAccessPlan",
534       "net.sf.cglib.core.ProcessSwitchCallback",
535       "com.ibatis.sqlmap.engine.mapping.sql.Sql",
536       "org.biojava.utils.ParseErrorEvent",
537       "uk.ac.sanger.artemis.components.FileViewer$2",
538       "org.biojava.bio.seq.io.EmblLikeFormat",
539       "com.ibatis.common.beans.ProbeFactory",
540       "com.ibatis.common.beans.ClassInfo",
541       "uk.ac.sanger.artemis.FeatureVector",
542       "org.biojava.bio.seq.io.SequenceBuilderBase",
543       "uk.ac.sanger.artemis.io.EmblStreamSequence",
544       "org.biojava.utils.stax.StringElementHandlerBase",
545       "org.biojava.bio.seq.io.CrossProductTokenization",
546       "com.ibatis.sqlmap.engine.scope.ErrorContext",
547       "com.ibatis.sqlmap.engine.config.SqlSource",
548       "org.biojava.bio.seq.FeatureHolder",
549       "org.biojava.bio.symbol.FundamentalAtomicSymbol",
550       "net.sf.cglib.asm.Edge",
551       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler$MappingHandler",
552       "org.biojava.utils.ChangeForwarder$Retyper",
553       "org.gmod.schema.dao.OrganismDaoI",
554       "com.ibatis.sqlmap.engine.mapping.sql.stat.StaticSql",
555       "org.biojava.bio.seq.io.SymbolTokenization",
556       "net.sf.cglib.asm.ClassWriter",
557       "com.sshtools.j2ssh.session.SessionChannelClient",
558       "htsjdk.samtools.util.LocationAware",
559       "uk.ac.sanger.artemis.io.QualifierInfo",
560       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry$1",
561       "org.biojava.utils.Unchangeable",
562       "com.ibatis.common.resources.Resources",
563       "org.apache.log4j.Priority",
564       "net.sf.cglib.core.AbstractClassGenerator$Source",
565       "org.biojava.bio.seq.RNATools$RNAComplementTranslationTable",
566       "org.apache.log4j.LogManager",
567       "org.biojava.bio.symbol.AlphabetIndex",
568       "org.gmod.schema.sequence.FeatureLoc",
569       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler",
570       "org.biojava.bio.seq.FeatureHolder$EmptyFeatureHolder",
571       "com.sshtools.j2ssh.connection.SshMsgChannelFailure",
572       "com.ibatis.common.logging.jakarta.JakartaCommonsLoggingImpl",
573       "uk.ac.sanger.artemis.io.DocumentEntry",
574       "org.biojava.bio.symbol.SimpleAtomicSymbol",
575       "org.biojava.bio.symbol.EmptySymbolList",
576       "uk.ac.sanger.artemis.io.BlastStreamFeature",
577       "org.apache.log4j.DefaultCategoryFactory",
578       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagHandlerFactory",
579       "org.postgresql.core.Logger",
580       "org.apache.log4j.or.RendererMap",
581       "com.ibatis.sqlmap.engine.mapping.sql.simple.SimpleDynamicSql",
582       "uk.ac.sanger.artemis.io.OutOfDateException",
583       "uk.ac.sanger.artemis.ExternalProgram",
584       "com.sshtools.j2ssh.transport.Service",
585       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateContext",
586       "uk.ac.sanger.artemis.io.EmblMisc",
587       "org.gmod.schema.pub.PubDbXRef",
588       "com.ibatis.sqlmap.engine.type.SqlDateTypeHandler",
589       "org.biojava.bio.symbol.AbstractAlphabet",
590       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsPropertyAvailableTagHandler",
591       "org.gmod.schema.general.DbXRef",
592       "uk.ac.sanger.artemis.io.PartialSequence",
593       "org.biojava.utils.ChangeListener$AlwaysVetoListener",
594       "uk.ac.sanger.artemis.chado.SqlMapClientWrapper",
595       "org.biojava.bio.symbol.AlphabetManager$SizeQueen",
596       "uk.ac.sanger.artemis.Entry",
597       "org.biojava.bio.symbol.HashedAlphabetIndex",
598       "org.biojava.utils.ClassTools",
599       "net.sf.cglib.core.Customizer",
600       "uk.ac.sanger.artemis.io.EmblStreamFeature",
601       "uk.ac.sanger.artemis.io.QualifierParseException",
602       "org.biojava.utils.cache.WeakValueHashMap",
603       "org.biojava.bio.symbol.IllegalSymbolException",
604       "uk.ac.sanger.artemis.ExternalProgramVector",
605       "com.ibatis.sqlmap.engine.type.TypeHandler",
606       "com.ibatis.sqlmap.engine.mapping.parameter.InlineParameterMapParser",
607       "org.apache.log4j.CategoryKey",
608       "uk.ac.sanger.artemis.io.Qualifier",
609       "uk.ac.sanger.artemis.util.InputStreamProgressListener",
610       "com.sshtools.j2ssh.sftp.SshFxpRemove",
611       "uk.ac.sanger.artemis.io.LocationLexer$TokenEnumeration",
612       "com.sshtools.j2ssh.connection.SshMsgChannelExtendedData",
613       "org.biojava.bio.seq.RemoteFeature",
614       "com.ibatis.sqlmap.engine.type.JdbcTypeRegistry",
615       "htsjdk.samtools.seekablestream.SeekableBufferedStream",
616       "org.apache.log4j.helpers.OnlyOnceErrorHandler",
617       "org.biojava.bio.symbol.TranslationTable",
618       "htsjdk.samtools.seekablestream.SeekableHTTPStream",
619       "uk.ac.sanger.artemis.io.DocumentEntryAutosaveThread",
620       "org.biojava.bio.symbol.CrossProductAlphabetIndex",
621       "com.ibatis.sqlmap.engine.execution.BatchException",
622       "org.biojava.bio.seq.impl.SimpleStrandedFeature",
623       "uk.ac.sanger.artemis.sequence.Marker",
624       "org.biojava.bio.seq.Feature$ByLocationComparator",
625       "org.biojava.bio.symbol.DoubleAlphabet",
626       "org.postgresql.largeobject.BlobInputStream",
627       "org.apache.log4j.ProvisionNode",
628       "com.sshtools.j2ssh.authentication.SshAuthenticationClient",
629       "com.sshtools.j2ssh.connection.SshMsgChannelOpenFailure",
630       "uk.ac.sanger.artemis.io.GFFDocumentEntry",
631       "org.biojava.bio.symbol.AbstractSymbolList$EditTranslater",
632       "com.ibatis.sqlmap.engine.mapping.result.ResultObjectFactory",
633       "uk.ac.sanger.artemis.io.GFFStreamFeature",
634       "org.biojava.bio.seq.impl.SimpleSequence",
635       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler",
636       "org.biojava.bio.symbol.AtomicSymbol",
637       "com.sshtools.j2ssh.transport.MessageStoreEOFException",
638       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsGreaterEqualTagHandler",
639       "org.biojava.bio.dist.Distribution",
640       "org.apache.log4j.spi.RootLogger",
641       "org.biojava.bio.BioError",
642       "com.ibatis.common.beans.Invoker",
643       "net.sf.cglib.asm.Type",
644       "org.apache.log4j.spi.ErrorHandler",
645       "com.ibatis.sqlmap.engine.accessplan.EnhancedPropertyAccessPlan",
646       "uk.ac.sanger.artemis.ExternalProgramException",
647       "net.sf.cglib.core.MethodInfo",
648       "uk.ac.sanger.artemis.io.QualifierVector",
649       "org.apache.log4j.spi.RendererSupport",
650       "org.biojava.bio.symbol.SymbolListFactory",
651       "uk.ac.sanger.artemis.components.variant.TabixReader$Iterator",
652       "org.biojava.bio.seq.OptimizableFilter",
653       "uk.ac.sanger.artemis.util.FileDocument",
654       "uk.ac.sanger.artemis.FeatureChangeListener",
655       "com.ibatis.sqlmap.engine.execution.SqlExecutor",
656       "uk.ac.sanger.artemis.FeatureChangeEvent",
657       "org.biojava.bio.symbol.AlphabetManager$GapSymbol",
658       "net.sf.cglib.core.Block",
659       "com.ibatis.sqlmap.engine.mapping.sql.SqlText",
660       "net.sf.cglib.asm.Opcodes",
661       "uk.ac.sanger.artemis.io.LocationParseNodeVector",
662       "uk.ac.sanger.artemis.io.LineGroup",
663       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagContext",
664       "com.ibatis.sqlmap.engine.type.TimeOnlyTypeHandler",
665       "org.biojava.bio.symbol.AbstractLocation",
666       "com.ibatis.sqlmap.engine.mapping.statement.RowHandlerCallback",
667       "org.postgresql.Driver",
668       "org.apache.commons.net.ftp.FTPConnectionClosedException",
669       "org.biojava.utils.ChangeSupport",
670       "org.biojava.bio.seq.io.AlternateTokenization",
671       "com.ibatis.sqlmap.engine.accessplan.AccessPlanFactory",
672       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.DynamicParent",
673       "org.biojava.bio.molbio.RestrictionSite",
674       "org.biojava.bio.seq.StrandedFeature$Strand",
675       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry",
676       "org.biojava.bio.seq.io.SeqFileFormer",
677       "org.biojava.bio.symbol.AlphabetManager$1",
678       "org.apache.log4j.Logger",
679       "com.ibatis.sqlmap.engine.mapping.statement.ExecuteListener",
680       "org.biojava.bio.seq.homol.HomologyFeature",
681       "uk.ac.sanger.artemis.EntryGroup",
682       "uk.ac.sanger.artemis.io.Feature",
683       "org.biojava.bio.AbstractAnnotation",
684       "org.biojava.bio.symbol.ManyToOneTranslationTable",
685       "com.ibatis.sqlmap.engine.mapping.statement.SelectStatement",
686       "com.ibatis.sqlmap.engine.transaction.TransactionException",
687       "com.sshtools.j2ssh.authentication.AuthenticationProtocolListener",
688       "org.apache.log4j.helpers.LogLog",
689       "uk.ac.sanger.artemis.io.QualifierInfoVector",
690       "org.biojava.bio.seq.io.SwissprotFileFormer",
691       "com.ibatis.common.logging.LogFactory",
692       "org.biojava.bio.seq.io.SimpleSequenceBuilder$SSBFactory",
693       "com.ibatis.sqlmap.engine.type.BaseTypeHandler",
694       "org.apache.log4j.spi.RepositorySelector",
695       "org.biojava.utils.ListTools$SeriesList",
696       "org.biojava.bio.symbol.SimpleSymbolList",
697       "uk.ac.sanger.artemis.io.GFF3AttributeBuilder$1",
698       "com.ibatis.common.beans.DomProbe",
699       "com.ibatis.sqlmap.engine.type.CustomTypeHandler",
700       "org.biojava.utils.ChangeListener$LoggingListener",
701       "net.sf.cglib.core.NamingPolicy",
702       "org.biojava.bio.symbol.SingletonAlphabet",
703       "org.biojava.bio.SmallAnnotation",
704       "org.biojava.bio.seq.io.SimpleSequenceBuilder$1",
705       "org.biojava.bio.symbol.ReversibleTranslationTable",
706       "uk.ac.sanger.artemis.io.Entry",
707       "net.sf.cglib.asm.Item",
708       "uk.ac.sanger.artemis.util.LinePushBackReader",
709       "org.biojava.utils.ParseErrorSource",
710       "org.apache.log4j.or.DefaultRenderer",
711       "uk.ac.sanger.artemis.util.ProgressInputStream",
712       "com.ibatis.common.jdbc.exception.NestedSQLException",
713       "com.ibatis.sqlmap.engine.builder.xml.SqlMapClasspathEntityResolver",
714       "com.ibatis.sqlmap.engine.accessplan.AccessPlan",
715       "org.biojava.bio.seq.io.SequenceBuilder",
716       "net.sf.cglib.asm.Attribute",
717       "net.sf.cglib.asm.ClassAdapter",
718       "uk.ac.sanger.artemis.io.FeatureVector",
719       "org.biojava.bio.symbol.LinearAlphabetIndex",
720       "net.sf.cglib.asm.MethodAdapter",
721       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler$1",
722       "com.ibatis.sqlmap.client.extensions.TypeHandlerCallback",
723       "org.apache.commons.logging.impl.Log4JLogger",
724       "org.biojava.bio.symbol.Location",
725       "org.gmod.schema.organism.Organism",
726       "org.gmod.schema.general.Db",
727       "com.ibatis.sqlmap.engine.config.CacheModelConfig",
728       "com.ibatis.sqlmap.engine.impl.SqlMapSessionImpl",
729       "org.apache.log4j.Appender",
730       "org.biojava.bio.symbol.SimpleReversibleTranslationTable",
731       "org.biojava.bio.symbol.Alphabet",
732       "org.biojava.bio.symbol.AbstractSymbolList$EditScreener",
733       "com.ibatis.sqlmap.engine.config.ParameterMapConfig",
734       "org.biojava.bio.seq.io.EmblFileFormer",
735       "org.biojava.utils.ListTools$5",
736       "net.sf.cglib.core.CodeGenerationException",
737       "org.biojava.bio.seq.Frame",
738       "uk.ac.sanger.artemis.chado.ChadoTransaction",
739       "com.sshtools.j2ssh.transport.SshMsgServiceAccept",
740       "org.biojava.utils.AssertionFailure",
741       "uk.ac.sanger.artemis.FeaturePredicate",
742       "com.sshtools.j2ssh.authentication.AuthenticationProtocolException",
743       "uk.ac.sanger.artemis.Logger",
744       "org.biojava.bio.seq.IsTopLevel",
745       "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl",
746       "com.ibatis.sqlmap.client.SqlMapSession",
747       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotEmptyTagHandler",
748       "org.gmod.schema.sequence.FeatureSynonym",
749       "org.apache.log4j.spi.LoggingEvent",
750       "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol",
751       "com.ibatis.sqlmap.engine.mapping.statement.CachingStatement",
752       "uk.ac.sanger.artemis.io.QualifierLazyLoading",
753       "uk.ac.sanger.artemis.util.DatabaseDocument",
754       "uk.ac.sanger.artemis.FeatureEnumeration",
755       "org.biojava.bio.symbol.AbstractSymbolList",
756       "net.sf.cglib.asm.Label",
757       "uk.ac.sanger.artemis.io.StreamFeatureTable",
758       "org.gmod.schema.dao.PubDaoI",
759       "org.biojava.bio.symbol.RangeLocation"
760     );
761   }
762 
resetClasses()763   private static void resetClasses() {
764     org.evosuite.runtime.classhandling.ClassResetter.getInstance().setClassLoader(EmblStreamFeature_ESTest_scaffolding.class.getClassLoader());
765 
766     org.evosuite.runtime.classhandling.ClassStateSupport.resetClasses(
767       "uk.ac.sanger.artemis.io.LineGroup",
768       "uk.ac.sanger.artemis.io.SimpleDocumentFeature",
769       "uk.ac.sanger.artemis.io.PublicDBStreamFeature",
770       "uk.ac.sanger.artemis.io.Key",
771       "uk.ac.sanger.artemis.io.LocationParseNodeVector",
772       "uk.ac.sanger.artemis.io.LocationParseNode",
773       "uk.ac.sanger.artemis.io.QualifierVector",
774       "uk.ac.sanger.artemis.components.filetree.RemoteFileNode",
775       "uk.ac.sanger.artemis.util.FastVector",
776       "org.biojava.bio.AbstractAnnotation",
777       "org.biojava.bio.SimpleAnnotation",
778       "org.biojava.bio.seq.SimpleFeatureRealizer",
779       "org.biojava.bio.seq.impl.FeatureImpl$1",
780       "org.biojava.bio.seq.impl.FeatureImpl",
781       "org.biojava.bio.symbol.AlphabetManager$GapSymbol",
782       "org.biojava.bio.symbol.AlphabetManager$SizeQueen",
783       "org.biojava.bio.symbol.IntegerAlphabet",
784       "org.biojava.bio.symbol.DoubleAlphabet",
785       "org.biojava.bio.symbol.SimpleSymbol",
786       "org.biojava.bio.symbol.AbstractSimpleBasisSymbol",
787       "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol",
788       "org.biojava.utils.ChangeType",
789       "org.biojava.bio.EmptyAnnotation",
790       "org.biojava.bio.Annotation",
791       "org.biojava.bio.symbol.EmptyAlphabet",
792       "org.biojava.bio.symbol.Alphabet",
793       "org.biojava.utils.ListTools",
794       "org.biojava.utils.SingletonList",
795       "org.biojava.bio.SmallAnnotation",
796       "org.biojava.utils.lsid.LifeScienceIdentifier",
797       "org.biojava.utils.SmallMap",
798       "org.biojava.bio.symbol.AlphabetManager$WellKnownBasisSymbol",
799       "org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol",
800       "org.biojava.bio.symbol.FundamentalAtomicSymbol",
801       "org.biojava.utils.ChangeListener",
802       "org.biojava.utils.ChangeSupport",
803       "org.biojava.bio.Annotatable",
804       "org.biojava.bio.symbol.AbstractAlphabet",
805       "org.biojava.bio.symbol.SingletonAlphabet",
806       "org.biojava.bio.symbol.SimpleAlphabet",
807       "org.biojava.bio.symbol.AlphabetManager$WellKnownAlphabet",
808       "org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper",
809       "org.biojava.bio.seq.io.CharacterTokenization",
810       "org.biojava.bio.symbol.SimpleBasisSymbol",
811       "org.biojava.bio.seq.io.AlternateTokenization",
812       "org.biojava.bio.symbol.AlphabetManager",
813       "org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper",
814       "org.biojava.bio.symbol.SimpleSymbolList",
815       "org.biojava.bio.seq.io.SymbolTokenization",
816       "org.biojava.bio.symbol.SimpleReversibleTranslationTable",
817       "org.biojava.bio.symbol.SimpleCrossProductAlphabet",
818       "org.biojava.utils.ListTools$Triplet",
819       "org.biojava.bio.symbol.SimpleAtomicSymbol",
820       "org.biojava.bio.seq.io.WordTokenization",
821       "org.biojava.bio.seq.io.NameTokenization",
822       "org.biojava.bio.symbol.SimpleManyToOneTranslationTable",
823       "org.biojava.bio.symbol.SimpleGeneticCodeTable",
824       "org.biojava.bio.symbol.AbstractSymbolList$ListView",
825       "org.biojava.bio.BioException",
826       "org.biojava.bio.symbol.IllegalSymbolException",
827       "org.biojava.bio.BioError",
828       "org.biojava.bio.seq.RNATools",
829       "org.biojava.bio.seq.DNATools",
830       "uk.ac.sanger.artemis.io.PublicDBDocumentEntry",
831       "org.apache.log4j.Category",
832       "org.apache.log4j.Logger",
833       "org.apache.log4j.Priority",
834       "org.apache.log4j.Level",
835       "org.apache.log4j.or.RendererMap",
836       "org.apache.log4j.helpers.OptionConverter",
837       "org.apache.log4j.helpers.Loader",
838       "org.apache.log4j.helpers.LogLog",
839       "org.apache.log4j.PropertyConfigurator",
840       "org.apache.log4j.LogManager",
841       "org.apache.log4j.CategoryKey",
842       "org.apache.log4j.ProvisionNode",
843       "uk.ac.sanger.artemis.util.DatabaseDocument",
844       "uk.ac.sanger.artemis.util.StringVector",
845       "uk.ac.sanger.artemis.components.Splash",
846       "uk.ac.sanger.artemis.io.KeyVector",
847       "uk.ac.sanger.artemis.io.QualifierInfo",
848       "uk.ac.sanger.artemis.ExternalProgram",
849       "uk.ac.sanger.artemis.Options",
850       "uk.ac.sanger.artemis.io.RangeVector",
851       "org.biojava.bio.seq.io.SequenceBuilderBase",
852       "org.biojava.bio.seq.io.SimpleSequenceBuilder$SSBFactory",
853       "org.biojava.bio.seq.io.SimpleSequenceBuilder",
854       "org.biojava.bio.seq.io.ChunkedSymbolListFactory",
855       "org.biojava.bio.symbol.EmptySymbolList",
856       "org.biojava.bio.seq.impl.SimpleSequence",
857       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry",
858       "uk.ac.sanger.artemis.util.CacheHashMap",
859       "uk.ac.sanger.artemis.util.ByteBuffer",
860       "uk.ac.sanger.artemis.util.DatabaseLocationParser",
861       "org.apache.log4j.MDC",
862       "uk.ac.sanger.artemis.chado.GmodDAO",
863       "uk.ac.sanger.artemis.chado.IBatisDAO",
864       "uk.ac.sanger.artemis.chado.SqlMapClientWrapper",
865       "com.ibatis.common.resources.Resources",
866       "com.ibatis.common.beans.ComplexBeanProbe",
867       "com.ibatis.common.beans.GenericProbe",
868       "com.ibatis.common.beans.ProbeFactory",
869       "com.ibatis.sqlmap.engine.config.SqlMapConfiguration",
870       "com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate",
871       "com.ibatis.sqlmap.engine.execution.SqlExecutor",
872       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory$1",
873       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory",
874       "com.ibatis.sqlmap.engine.type.UnknownTypeHandler",
875       "com.ibatis.sqlmap.engine.type.DateTypeHandler",
876       "com.ibatis.sqlmap.engine.type.DateOnlyTypeHandler",
877       "com.ibatis.sqlmap.engine.type.TimeOnlyTypeHandler",
878       "com.ibatis.sqlmap.engine.type.SqlDateTypeHandler",
879       "com.ibatis.sqlmap.engine.type.SqlTimeTypeHandler",
880       "com.ibatis.sqlmap.engine.type.SqlTimestampTypeHandler",
881       "com.ibatis.sqlmap.engine.exchange.ComplexDataExchange",
882       "com.ibatis.common.logging.LogFactory",
883       "org.apache.commons.logging.impl.Log4JLogger",
884       "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl",
885       "com.ibatis.sqlmap.engine.builder.xml.SqlMapClasspathEntityResolver",
886       "com.ibatis.common.beans.ClassInfo",
887       "com.ibatis.sqlmap.engine.accessplan.AccessPlanFactory",
888       "com.ibatis.common.jdbc.SimpleDataSource",
889       "org.postgresql.Driver",
890       "com.ibatis.sqlmap.engine.mapping.result.ResultMap",
891       "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange",
892       "net.sf.cglib.core.TypeUtils",
893       "net.sf.cglib.asm.Type",
894       "net.sf.cglib.core.KeyFactory",
895       "net.sf.cglib.core.AbstractClassGenerator",
896       "net.sf.cglib.core.KeyFactory$Generator",
897       "net.sf.cglib.core.DefaultGeneratorStrategy",
898       "net.sf.cglib.core.DefaultNamingPolicy",
899       "net.sf.cglib.asm.ClassWriter",
900       "net.sf.cglib.core.DebuggingClassWriter",
901       "net.sf.cglib.core.ClassEmitter",
902       "net.sf.cglib.core.ReflectUtils",
903       "net.sf.cglib.core.EmitUtils",
904       "net.sf.cglib.core.Constants",
905       "net.sf.cglib.core.CodeEmitter",
906       "net.sf.cglib.asm.Frame",
907       "net.sf.cglib.asm.ClassReader",
908       "net.sf.cglib.core.ClassNameReader$EarlyExitException",
909       "net.sf.cglib.core.ClassNameReader",
910       "net.sf.cglib.beans.BulkBean",
911       "net.sf.cglib.beans.BulkBean$Generator",
912       "net.sf.cglib.beans.BulkBeanEmitter",
913       "com.ibatis.sqlmap.engine.type.JdbcTypeRegistry",
914       "com.ibatis.sqlmap.engine.mapping.parameter.InlineParameterMapParser",
915       "com.ibatis.sqlmap.engine.builder.xml.XMLSqlSource",
916       "com.ibatis.sqlmap.engine.config.MappedStatementConfig",
917       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.DynamicSql",
918       "com.ibatis.sqlmap.engine.mapping.sql.simple.SimpleDynamicSql",
919       "com.ibatis.sqlmap.engine.cache.CacheKey",
920       "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMapping",
921       "com.ibatis.sqlmap.engine.cache.CacheModel",
922       "com.ibatis.sqlmap.engine.accessplan.ComplexAccessPlan",
923       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.ConditionalTagHandler",
924       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEmptyTagHandler",
925       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNullTagHandler",
926       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsPropertyAvailableTagHandler",
927       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateTagHandler",
928       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagHandlerFactory",
929       "com.ibatis.sqlmap.engine.accessplan.PropertyAccessPlan",
930       "com.ibatis.sqlmap.engine.config.ParameterMapConfig",
931       "com.ibatis.common.beans.ProbeException",
932       "net.sf.cglib.beans.BulkBeanException",
933       "uk.ac.sanger.artemis.io.FeatureVector",
934       "com.ibatis.common.xml.NodeletException",
935       "uk.ac.sanger.artemis.io.ReadFormatException",
936       "uk.ac.sanger.artemis.io.LocationParseException",
937       "uk.ac.sanger.artemis.io.GFFStreamFeature",
938       "uk.ac.sanger.artemis.sequence.Marker",
939       "uk.ac.sanger.artemis.util.OutOfRangeException",
940       "uk.ac.sanger.artemis.j2ssh.SshLogin",
941       "org.gmod.schema.organism.Organism",
942       "uk.ac.sanger.artemis.io.MSPcrunchStreamFeature",
943       "org.gmod.schema.sequence.Feature",
944       "uk.ac.sanger.artemis.sequence.Strand",
945       "org.biojava.bio.seq.Feature",
946       "org.postgresql.largeobject.LargeObject",
947       "org.biojava.bio.seq.Feature$Template",
948       "org.biojava.bio.seq.StrandedFeature$Template",
949       "org.biojava.bio.seq.FramedFeature$Template",
950       "org.biojava.bio.seq.impl.SimpleFeature",
951       "org.biojava.bio.seq.impl.SimpleStrandedFeature",
952       "org.biojava.bio.seq.ComponentFeature$Template",
953       "org.biojava.bio.program.phred.PhredFormat",
954       "uk.ac.sanger.artemis.io.FeatureTree",
955       "org.biojava.bio.seq.io.EmblLikeFormat"
956     );
957   }
958 }
959