1 /**
2  * Scaffolding file used to store all the setups needed to run
3  * tests automatically generated by EvoSuite
4  * Fri Jan 12 15:31:41 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 Sequence_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.Sequence";
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(Sequence_ESTest_scaffolding.class.getClassLoader() ,
85       "org.biojava.bio.seq.AcceptNoneFilter",
86       "uk.ac.sanger.artemis.components.LogViewer$1",
87       "net.sf.cglib.core.EmitUtils$ArrayDelimiters",
88       "org.biojava.bio.symbol.FuzzyLocation$1",
89       "com.ibatis.common.jdbc.SimpleDataSource$SimplePooledConnection",
90       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.ConditionalTagHandler",
91       "org.biojava.bio.seq.io.SymbolTokenization$TokenType",
92       "org.biojava.bio.seq.db.IDMaker$ByURN",
93       "org.biojava.bio.seq.ByHierarchy",
94       "org.biojava.bio.seq.ComponentFeature$Template",
95       "org.apache.log4j.AppenderSkeleton",
96       "com.ibatis.sqlmap.client.extensions.ParameterSetter",
97       "org.biojava.utils.stax.SAX2StAXAdaptor",
98       "uk.ac.sanger.artemis.io.SimpleDocumentFeature",
99       "uk.ac.sanger.artemis.sequence.BasePatternFormatException",
100       "com.sshtools.j2ssh.authentication.PasswordAuthenticationClient",
101       "net.sf.cglib.core.KeyFactory$Generator",
102       "com.sshtools.j2ssh.SshClient",
103       "uk.ac.sanger.artemis.EntryChangeListener",
104       "org.biojava.bio.seq.FeatureFilter$OverlapsLocation",
105       "org.biojava.bio.symbol.DoubleAlphabet$SubDoubleAlphabet",
106       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$AlphabetHandler$1",
107       "uk.ac.sanger.artemis.Selectable",
108       "net.sf.cglib.core.CodeEmitter$State",
109       "org.biojava.bio.seq.io.NameTokenization",
110       "org.biojava.bio.seq.MergeFeatureHolder",
111       "uk.ac.sanger.artemis.io.RangeVector",
112       "uk.ac.sanger.artemis.io.FeatureTable",
113       "org.biojava.bio.seq.FramedFeature$ReadingFrame",
114       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateTagHandler",
115       "org.biojava.bio.seq.io.CharacterTokenization",
116       "org.biojava.bio.seq.homol.SimilarityPairFeature$EmptyPairwiseAlignment",
117       "uk.ac.sanger.artemis.io.PublicDBDocumentEntry",
118       "net.sf.cglib.core.Constants",
119       "uk.ac.sanger.artemis.util.StringVector",
120       "net.sf.cglib.core.AbstractClassGenerator",
121       "org.biojava.bio.seq.Feature$Template",
122       "com.ibatis.common.beans.BaseProbe",
123       "com.sshtools.j2ssh.transport.AsyncService",
124       "com.ibatis.sqlmap.engine.mapping.statement.SelectKeyStatement",
125       "org.gmod.schema.sequence.Synonym",
126       "org.biojava.bio.symbol.SimpleAlphabet",
127       "org.gmod.schema.sequence.FeatureCvTermProp",
128       "org.biojava.bio.seq.io.SequenceBuilderFactory",
129       "org.biojava.bio.seq.FeatureFilter$AnnotationContains",
130       "org.apache.log4j.Hierarchy",
131       "org.biojava.bio.seq.FeatureFilter$ByDescendant",
132       "org.biojava.bio.dp.DotState",
133       "uk.ac.sanger.artemis.sequence.MarkerRange",
134       "org.biojava.utils.Changeable",
135       "org.biojava.bio.symbol.EmptyLocation",
136       "org.biojava.bio.AnnotationType",
137       "net.sf.cglib.asm.MethodWriter",
138       "com.ibatis.common.util.PaginatedList",
139       "uk.ac.sanger.artemis.io.QualifierInfoHash",
140       "com.sshtools.j2ssh.connection.Channel",
141       "net.sf.cglib.core.ClassNameReader$EarlyExitException",
142       "com.ibatis.sqlmap.engine.cache.CacheModel",
143       "org.apache.log4j.spi.OptionHandler",
144       "org.biojava.utils.stax.DelegationManager",
145       "org.biojava.bio.seq.StrandedFeature",
146       "org.biojava.utils.lsid.LifeScienceIdentifier",
147       "net.sf.cglib.core.ReflectUtils",
148       "org.biojava.bio.symbol.FuzzyLocation$InnerRangeResolver",
149       "org.biojava.utils.ChangeVetoException",
150       "org.biojava.bio.symbol.IllegalAlphabetException",
151       "org.biojava.bio.seq.db.SequenceDB",
152       "org.biojava.bio.symbol.DoubleAlphabet$DoubleRange",
153       "com.sshtools.j2ssh.connection.ChannelEventListener",
154       "net.sf.cglib.core.AbstractClassGenerator$1",
155       "uk.ac.sanger.artemis.components.Splash$2",
156       "org.biojava.bio.symbol.AbstractTranslationTable",
157       "org.gmod.schema.dao.GeneralDaoI",
158       "com.ibatis.sqlmap.engine.exchange.DataExchangeFactory",
159       "net.sf.cglib.core.LocalVariablesSorter",
160       "org.apache.log4j.helpers.OptionConverter",
161       "org.gmod.schema.dao.BaseDaoI",
162       "com.ibatis.sqlmap.client.SqlMapExecutor",
163       "org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl",
164       "org.biojava.bio.symbol.Edit",
165       "com.ibatis.sqlmap.client.SqlMapException",
166       "uk.ac.sanger.artemis.io.MiscLineGroup",
167       "uk.ac.sanger.artemis.io.LazyQualifierValue",
168       "com.ibatis.sqlmap.engine.type.SqlTimeTypeHandler",
169       "org.postgresql.largeobject.BlobOutputStream",
170       "org.biojava.bio.symbol.AbstractSymbol",
171       "org.biojava.utils.bytecode.CodeGenerator",
172       "org.biojava.bio.symbol.AbstractSymbolList$SymbolIterator",
173       "org.gmod.schema.cv.CvTerm",
174       "org.biojava.bio.seq.db.IllegalIDException",
175       "uk.ac.sanger.artemis.sequence.SequenceChangeListener",
176       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsGreaterThanTagHandler",
177       "com.sshtools.j2ssh.subsystem.SubsystemMessage",
178       "uk.ac.sanger.artemis.io.InvalidRelationException",
179       "org.biojava.utils.bytecode.CodeMethod",
180       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEqualTagHandler",
181       "org.biojava.bio.seq.impl.FeatureImpl$1",
182       "org.biojava.bio.seq.io.SimpleSequenceBuilder",
183       "com.sshtools.j2ssh.transport.InvalidMessageException",
184       "org.biojava.bio.Annotation",
185       "org.biojava.bio.symbol.IntegerAlphabet$IntegerSymbol",
186       "org.biojava.utils.lsid.LifeScienceIdentifierParseException",
187       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler",
188       "com.sshtools.j2ssh.authentication.AuthenticationProtocolClient",
189       "org.apache.log4j.Category",
190       "uk.ac.sanger.artemis.io.LocationParseException",
191       "org.biojava.utils.ListTools$Mapper",
192       "org.biojava.bio.seq.io.StreamParser",
193       "org.biojava.bio.seq.Up",
194       "org.biojava.bio.seq.FeatureFilter$ByAncestor",
195       "uk.ac.sanger.artemis.util.FastVector",
196       "org.biojava.bio.symbol.SimpleSymbol",
197       "com.ibatis.common.beans.ComplexBeanProbe",
198       "org.apache.log4j.helpers.ThreadLocalMap",
199       "net.sf.cglib.core.KeyFactory$2",
200       "org.biojava.bio.symbol.AbstractSimpleBasisSymbol",
201       "net.sf.cglib.core.KeyFactory$1",
202       "com.sshtools.j2ssh.transport.TransportProtocolEventHandler",
203       "org.gmod.schema.sequence.FeatureDbXRef",
204       "net.sf.cglib.core.ClassInfo",
205       "org.biojava.utils.ChangeEvent",
206       "uk.ac.sanger.artemis.components.variant.AbstractVCFReader",
207       "org.gmod.schema.pub.Pub",
208       "net.sf.cglib.core.ClassEmitter$3",
209       "uk.ac.sanger.artemis.io.ChadoCanonicalGene",
210       "net.sf.cglib.core.EmitUtils$9",
211       "net.sf.cglib.core.ClassEmitter$1",
212       "org.biojava.utils.stax.SAX2StAXAdaptor$S2SDelegationManager",
213       "net.sf.cglib.core.EmitUtils$8",
214       "net.sf.cglib.core.EmitUtils$7",
215       "net.sf.cglib.core.Predicate",
216       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry$IndexContig",
217       "org.biojava.bio.symbol.SimpleCrossProductAlphabet",
218       "net.sf.cglib.core.ClassEmitter",
219       "org.biojava.bio.seq.DNATools",
220       "org.gmod.schema.sequence.FeatureCvTermDbXRef",
221       "com.sshtools.j2ssh.transport.TransportProtocolState",
222       "uk.ac.sanger.artemis.io.GenbankStreamSequence",
223       "net.sf.cglib.core.ClassNameReader",
224       "com.ibatis.sqlmap.engine.cache.CacheController",
225       "net.sf.cglib.core.ClassNameReader$1",
226       "com.ibatis.sqlmap.engine.accessplan.BaseAccessPlan",
227       "org.biojava.bio.BioRuntimeException",
228       "org.biojava.bio.seq.AcceptAllFilter",
229       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.BaseTagHandler",
230       "org.biojava.bio.seq.io.ChunkedSymbolListFactory",
231       "net.sf.cglib.core.Local",
232       "org.biojava.bio.symbol.IntegerAlphabet$SubIntegerAlphabet",
233       "org.biojava.bio.symbol.FuzzyLocation$RangeResolver",
234       "org.biojava.bio.seq.homol.SimilarityPairFeature",
235       "org.gmod.schema.utils.propinterface.PropertyI",
236       "org.biojava.bio.NoneCollectionConstraint",
237       "org.apache.log4j.spi.AppenderAttachable",
238       "com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate",
239       "com.sshtools.j2ssh.SshException",
240       "org.biojava.bio.seq.FeatureFilter$ContainedByLocation",
241       "uk.ac.sanger.artemis.j2ssh.FTProgress",
242       "uk.ac.sanger.artemis.io.GFF3AttributeAggregator",
243       "net.sf.cglib.beans.BulkBean$Generator",
244       "org.gmod.schema.cv.Cv",
245       "uk.ac.sanger.artemis.util.InputStreamProgressListenerVector",
246       "net.sf.cglib.core.DefaultNamingPolicy",
247       "uk.ac.sanger.artemis.util.PushBackException",
248       "com.ibatis.sqlmap.engine.exchange.DataExchange",
249       "com.ibatis.sqlmap.engine.mapping.sql.SqlChild",
250       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.DynamicTagHandler",
251       "com.sshtools.j2ssh.connection.IOChannel",
252       "org.biojava.utils.SingletonList",
253       "org.biojava.bio.symbol.FuzzyLocation$OuterRangeResolver",
254       "org.biojava.bio.symbol.SymbolList",
255       "org.biojava.bio.BioException",
256       "net.sf.cglib.asm.AnnotationVisitor",
257       "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange",
258       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory$1",
259       "com.ibatis.sqlmap.engine.builder.xml.XMLSqlSource",
260       "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMapping",
261       "net.sf.cglib.asm.FieldVisitor",
262       "org.biojava.bio.seq.FramedFeature$Template",
263       "com.ibatis.sqlmap.engine.exchange.BaseDataExchange",
264       "net.sf.cglib.asm.MethodVisitor",
265       "net.sf.cglib.asm.ClassVisitor",
266       "com.sshtools.j2ssh.connection.SshMsgChannelData",
267       "net.sf.cglib.core.DebuggingClassWriter",
268       "net.sf.cglib.core.ClassEmitter$FieldInfo",
269       "uk.ac.sanger.artemis.io.LocationParseNode",
270       "com.ibatis.sqlmap.engine.mapping.statement.MappedStatement",
271       "uk.ac.sanger.artemis.util.WorkingGZIPInputStream",
272       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotPropertyAvailableTagHandler",
273       "org.biojava.utils.ChangeType$1",
274       "org.biojava.bio.symbol.AlphabetManager$WellKnownAlphabet",
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.sequence.BasePattern",
279       "uk.ac.sanger.artemis.io.Key",
280       "org.biojava.bio.OverlayAnnotation",
281       "uk.ac.sanger.artemis.Options",
282       "org.biojava.bio.seq.io.SymbolReader",
283       "org.biojava.bio.seq.impl.SimpleHomologyFeature",
284       "uk.ac.sanger.artemis.io.SimpleDocumentEntry",
285       "org.biojava.bio.symbol.BasisSymbol",
286       "com.ibatis.sqlmap.engine.transaction.Transaction",
287       "org.biojava.bio.seq.FeatureFilter$ByAnnotationType",
288       "com.ibatis.sqlmap.engine.accessplan.PropertyAccessPlan",
289       "uk.ac.sanger.artemis.io.FeatureHeader",
290       "org.biojava.bio.seq.RNATools",
291       "net.sf.cglib.beans.BulkBeanEmitter",
292       "org.biojava.bio.seq.db.AbstractSequenceDB",
293       "uk.ac.sanger.artemis.components.filetree.FileList",
294       "com.sshtools.j2ssh.connection.ConnectionProtocol",
295       "uk.ac.sanger.artemis.chado.Graph",
296       "org.biojava.bio.AnyPropertyConstraint",
297       "org.biojava.bio.seq.io.WordTokenization",
298       "org.biojava.bio.dp.ScoreType$Probability",
299       "com.ibatis.common.beans.GenericProbe",
300       "uk.ac.sanger.artemis.ChangeListener",
301       "net.sf.cglib.core.KeyFactory",
302       "net.sf.cglib.core.GeneratorStrategy",
303       "org.biojava.bio.seq.projection.ReparentContext",
304       "org.apache.log4j.helpers.Loader",
305       "org.biojava.utils.stax.SAX2StAXAdaptor$HandlerBinding",
306       "org.biojava.bio.seq.impl.SimpleFeature",
307       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory",
308       "org.apache.log4j.helpers.FileWatchdog",
309       "org.biojava.bio.CollectionConstraint",
310       "org.biojava.bio.symbol.AbstractSymbolList$ListView",
311       "org.biojava.bio.symbol.AbstractSymbolList$SubList",
312       "uk.ac.sanger.artemis.io.RawStreamSequence",
313       "net.sf.cglib.core.EmitUtils",
314       "org.biojava.bio.seq.GappedSequence",
315       "org.biojava.bio.symbol.Alignment",
316       "org.apache.log4j.MDC",
317       "org.biojava.bio.seq.impl.SimpleRestrictionSite",
318       "net.sf.cglib.core.CollectionUtils",
319       "net.sf.cglib.core.TypeUtils",
320       "uk.ac.sanger.artemis.io.QualifierInfoException",
321       "org.gmod.schema.dao.SequenceDaoI",
322       "org.biojava.bio.seq.FeatureFilter$BySource",
323       "com.ibatis.sqlmap.engine.mapping.result.ResultMapping",
324       "org.biojava.utils.SmallMap",
325       "org.biojava.bio.seq.StrandedFeature$Template",
326       "com.sshtools.j2ssh.transport.HostKeyVerification",
327       "org.biojava.bio.dist.DistributionFactory$DefaultDistributionFactory",
328       "org.biojava.bio.seq.projection.ProjectedFeatureHolder",
329       "org.biojava.bio.symbol.Symbol",
330       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotParameterPresentTagHandler",
331       "org.biojava.bio.seq.RealizingFeatureHolder",
332       "org.biojava.bio.molbio.RestrictionSite$Template",
333       "org.gmod.schema.sequence.FeatureCvTerm",
334       "org.biojava.bio.seq.db.IDMaker",
335       "net.sf.cglib.beans.BulkBeanException",
336       "org.biojava.bio.seq.FramedFeature",
337       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsParameterPresentTagHandler",
338       "org.biojava.bio.seq.AbstractFeatureHolder",
339       "com.ibatis.sqlmap.engine.config.MappedStatementConfig",
340       "org.biojava.utils.ListTools",
341       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEmptyTagHandler",
342       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$AlphabetHandler",
343       "uk.ac.sanger.artemis.io.DatabaseStreamFeature",
344       "org.biojava.bio.seq.FeatureFilter$ByAnnotation",
345       "org.gmod.schema.dao.CvDaoI",
346       "uk.ac.sanger.artemis.util.CacheHashMap",
347       "org.biojava.bio.seq.Feature",
348       "uk.ac.sanger.artemis.io.InvalidKeyException",
349       "org.biojava.bio.seq.FeatureFilter$ByComponentName",
350       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagHandler",
351       "net.sf.cglib.core.EmitUtils$ParameterTyper",
352       "com.ibatis.sqlmap.engine.exchange.ComplexDataExchange",
353       "net.sf.cglib.core.Signature",
354       "com.ibatis.sqlmap.engine.type.SqlTimestampTypeHandler",
355       "org.biojava.bio.dp.WeightMatrixAnnotator",
356       "net.sf.cglib.asm.ByteVector",
357       "uk.ac.sanger.artemis.io.Packing",
358       "org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper",
359       "org.biojava.bio.seq.Sequence",
360       "org.biojava.bio.dp.State",
361       "com.ibatis.sqlmap.engine.mapping.result.Discriminator",
362       "org.biojava.bio.seq.db.IDMaker$ByName",
363       "uk.ac.sanger.artemis.util.ByteBuffer",
364       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNullTagHandler",
365       "uk.ac.sanger.artemis.io.SimpleEntryInformation",
366       "net.sf.cglib.beans.BulkBean$BulkBeanKey",
367       "org.biojava.utils.stax.StAXContentHandlerBase",
368       "com.sshtools.j2ssh.transport.MessageNotAvailableException",
369       "uk.ac.sanger.artemis.io.StreamSequence",
370       "com.ibatis.sqlmap.engine.config.SqlMapConfiguration",
371       "uk.ac.sanger.artemis.io.GFF3AttributeBuilder",
372       "uk.ac.sanger.artemis.io.Range",
373       "net.sf.cglib.asm.Frame",
374       "uk.ac.sanger.artemis.sequence.Bases",
375       "uk.ac.sanger.artemis.components.LogViewer",
376       "org.biojava.bio.seq.db.SequenceDBWrapper",
377       "org.biojava.bio.symbol.AbstractRangeLocation",
378       "uk.ac.sanger.artemis.io.BetweenRange",
379       "uk.ac.sanger.artemis.ExternalProgramMonitor",
380       "com.sshtools.j2ssh.transport.SshMessage",
381       "org.biojava.bio.seq.FeatureFilter$ShadowContainedByLocation",
382       "com.sshtools.j2ssh.util.State",
383       "uk.ac.sanger.artemis.j2ssh.SshLogin",
384       "org.biojava.bio.EmptyAnnotation",
385       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsLessEqualTagHandler",
386       "com.ibatis.sqlmap.engine.type.DateOnlyTypeHandler",
387       "org.apache.log4j.PropertyConfigurator",
388       "uk.ac.sanger.artemis.util.Document",
389       "com.ibatis.sqlmap.client.event.RowHandler",
390       "org.biojava.bio.seq.io.ParseException",
391       "org.biojava.bio.symbol.AlphabetManager",
392       "org.biojava.bio.seq.FeatureFilter$HasAnnotation",
393       "uk.ac.sanger.artemis.components.variant.TabixReader",
394       "uk.ac.sanger.artemis.components.FileViewer",
395       "org.biojava.utils.walker.WalkerFactory",
396       "org.biojava.bio.seq.FeatureRealizer",
397       "org.biojava.utils.bytecode.CodeException",
398       "uk.ac.sanger.artemis.sequence.NoSequenceException",
399       "net.sf.cglib.core.ProcessArrayCallback",
400       "org.biojava.bio.symbol.SparseCrossProductAlphabet",
401       "org.biojava.bio.seq.ComponentFeature",
402       "org.biojava.bio.symbol.AlphabetManager$WellKnownBasisSymbol",
403       "org.biojava.bio.seq.impl.SimpleRemoteFeature",
404       "net.sf.cglib.asm.ClassReader",
405       "org.apache.log4j.spi.LoggerRepository",
406       "com.ibatis.common.beans.ProbeException",
407       "com.sshtools.j2ssh.transport.TransportProtocolException",
408       "uk.ac.sanger.artemis.components.Splash",
409       "com.ibatis.sqlmap.engine.impl.ExtendedSqlMapClient",
410       "uk.ac.sanger.artemis.io.EntryInformationException",
411       "com.ibatis.common.beans.Probe",
412       "net.sf.cglib.core.Transformer",
413       "com.sshtools.j2ssh.authentication.SshMsgUserAuthRequest",
414       "uk.ac.sanger.artemis.io.GFFMisc",
415       "com.ibatis.sqlmap.engine.scope.StatementScope",
416       "org.biojava.bio.dp.SimpleWeightMatrix",
417       "org.biojava.bio.seq.projection.ProjectionContext",
418       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.DynamicSql",
419       "uk.ac.sanger.artemis.chado.IBatisDAO",
420       "org.biojava.bio.seq.FeatureFilter$ByPairwiseScore",
421       "com.ibatis.sqlmap.engine.mapping.result.AutoResultMap",
422       "uk.ac.sanger.artemis.components.filetree.RemoteFileNode",
423       "org.biojava.bio.seq.impl.SimpleSimilarityPairFeature",
424       "org.biojava.bio.symbol.SimpleSymbolList$SSLIOListener",
425       "org.biojava.bio.seq.RemoteFeature$Template",
426       "org.apache.log4j.Level",
427       "org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol",
428       "org.biojava.bio.symbol.AbstractReversibleTranslationTable",
429       "org.biojava.bio.seq.io.SeqIOAdapter",
430       "com.sshtools.j2ssh.authentication.TerminatedStateException",
431       "uk.ac.sanger.artemis.io.EntryInformation",
432       "com.ibatis.sqlmap.engine.type.UnknownTypeHandler",
433       "htsjdk.samtools.util.BlockCompressedInputStream",
434       "org.biojava.bio.seq.io.SeqIOListener",
435       "uk.ac.sanger.artemis.sequence.MarkerChangeListener",
436       "org.biojava.utils.ChangeType",
437       "org.biojava.bio.dp.ScoreType$Odds",
438       "net.sf.cglib.asm.FieldWriter",
439       "uk.ac.sanger.artemis.io.ReadFormatException",
440       "com.sshtools.j2ssh.sftp.SftpSubsystemClient",
441       "com.sshtools.j2ssh.util.InvalidStateException",
442       "org.biojava.utils.ChangeListener",
443       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotNullTagHandler",
444       "org.biojava.bio.seq.FeatureFilter$FrameFilter",
445       "org.biojava.utils.AbstractChangeable",
446       "org.gmod.schema.sequence.FeaturePub",
447       "org.biojava.bio.seq.SimpleFeatureHolder",
448       "uk.ac.sanger.artemis.EntrySourceVector",
449       "net.sf.cglib.core.LocalVariablesSorter$State",
450       "com.ibatis.sqlmap.client.SqlMapTransactionManager",
451       "com.ibatis.sqlmap.engine.config.ResultMapConfig",
452       "org.biojava.bio.symbol.EmptyAlphabet",
453       "org.gmod.schema.analysis.AnalysisFeature",
454       "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMap",
455       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTag",
456       "org.gmod.schema.dao.SchemaDaoI",
457       "org.biojava.bio.seq.CircularView",
458       "uk.ac.sanger.artemis.LastSegmentException",
459       "uk.ac.sanger.artemis.ChangeEvent",
460       "org.gmod.schema.sequence.FeatureRelationship",
461       "org.biojava.bio.seq.SimpleFeatureRealizer",
462       "uk.ac.sanger.artemis.io.GenbankStreamFeature",
463       "uk.ac.sanger.artemis.util.OutOfRangeException",
464       "com.ibatis.sqlmap.engine.scope.SessionScope",
465       "org.postgresql.util.PSQLException",
466       "net.sf.cglib.beans.BulkBean",
467       "org.biojava.bio.seq.FeatureFilter$ByType",
468       "com.ibatis.common.logging.Log",
469       "org.biojava.bio.dp.ScoreType",
470       "com.ibatis.sqlmap.engine.mapping.result.ResultMap",
471       "org.biojava.bio.symbol.SimpleBasisSymbol",
472       "org.biojava.utils.lsid.Identifiable",
473       "org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser",
474       "org.biojava.bio.seq.DNATools$DNAComplementTranslationTable",
475       "uk.ac.sanger.artemis.io.EMBLObject",
476       "org.postgresql.largeobject.LargeObject",
477       "uk.ac.sanger.artemis.chado.GmodDAO",
478       "net.sf.cglib.core.ClassGenerator",
479       "net.sf.cglib.core.ReflectUtils$4",
480       "org.apache.log4j.spi.DefaultRepositorySelector",
481       "uk.ac.sanger.artemis.OptionChangeListener",
482       "com.sshtools.j2ssh.connection.ChannelOutputStream",
483       "net.sf.cglib.core.ReflectUtils$1",
484       "net.sf.cglib.core.ReflectUtils$2",
485       "net.sf.cglib.core.ReflectUtils$3",
486       "uk.ac.sanger.artemis.io.Sequence",
487       "org.biojava.bio.symbol.LocationComparator",
488       "uk.ac.sanger.artemis.components.variant.BCFReader",
489       "uk.ac.sanger.artemis.util.LargeObjectDocument",
490       "uk.ac.sanger.artemis.io.GenbankMisc",
491       "uk.ac.sanger.artemis.chado.JdbcDAO",
492       "net.sf.cglib.core.ObjectSwitchCallback",
493       "org.biojava.utils.bytecode.GeneratedClassLoader",
494       "org.biojava.bio.dist.DistributionFactory",
495       "com.ibatis.sqlmap.engine.cache.CacheKey",
496       "uk.ac.sanger.artemis.io.Location",
497       "org.biojava.utils.stax.StAXContentHandler",
498       "uk.ac.sanger.artemis.io.PublicDBStreamFeature",
499       "net.sf.cglib.core.DefaultGeneratorStrategy",
500       "org.biojava.bio.seq.SequenceAnnotator",
501       "org.apache.log4j.or.ObjectRenderer",
502       "uk.ac.sanger.artemis.util.DatabaseLocationParser",
503       "org.biojava.bio.seq.FeatureFilter$ShadowOverlapsLocation",
504       "net.sf.cglib.core.DebuggingClassWriter$1",
505       "uk.ac.sanger.artemis.io.FastaStreamSequence",
506       "uk.ac.sanger.artemis.io.FeatureEnumeration",
507       "org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper",
508       "com.ibatis.sqlmap.engine.type.DateTypeHandler",
509       "org.biojava.utils.ChangeForwarder",
510       "uk.ac.sanger.artemis.io.StreamFeature",
511       "com.ibatis.common.io.ReaderInputStream",
512       "uk.ac.sanger.artemis.util.ReadOnlyException",
513       "org.biojava.bio.symbol.GappedSymbolList",
514       "org.biojava.bio.seq.FeatureFilter$Or",
515       "com.ibatis.sqlmap.engine.accessplan.MapAccessPlan",
516       "org.biojava.bio.AnnotationType$Abstract",
517       "uk.ac.sanger.artemis.EntryChangeEvent",
518       "org.biojava.utils.walker.Walker",
519       "org.biojava.bio.symbol.HashedAlphabetIndex$HashComparator",
520       "org.biojava.bio.seq.FeatureFilter",
521       "uk.ac.sanger.artemis.Feature",
522       "uk.ac.sanger.artemis.io.EmblDocumentEntry",
523       "org.biojava.bio.seq.homol.HomologyFeature$Template",
524       "com.sshtools.j2ssh.subsystem.SubsystemChannel",
525       "com.ibatis.sqlmap.client.extensions.ResultGetter",
526       "uk.ac.sanger.artemis.io.DocumentFeature",
527       "org.biojava.bio.SimpleAnnotation",
528       "org.biojava.bio.symbol.IntegerAlphabet",
529       "com.sshtools.j2ssh.FileTransferProgress",
530       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotEqualTagHandler",
531       "com.ibatis.sqlmap.engine.transaction.TransactionManager",
532       "com.ibatis.common.jdbc.SimpleDataSource",
533       "org.biojava.bio.seq.impl.FeatureImpl",
534       "org.apache.log4j.spi.LoggerFactory",
535       "org.biojava.bio.symbol.DoubleAlphabet$DoubleSymbol",
536       "org.apache.log4j.spi.Configurator",
537       "org.biojava.bio.PropertyConstraint",
538       "uk.ac.sanger.artemis.io.MSPcrunchStreamFeature",
539       "org.biojava.bio.seq.impl.SimpleFramedFeature",
540       "net.sf.cglib.core.CodeEmitter",
541       "org.gmod.schema.sequence.Feature",
542       "org.biojava.bio.symbol.FiniteAlphabet",
543       "org.biojava.bio.seq.FeatureFilter$OnlyChildren",
544       "org.biojava.bio.seq.homol.SimilarityPairFeature$Template",
545       "org.apache.log4j.PropertyWatchdog",
546       "uk.ac.sanger.artemis.io.KeyVector",
547       "org.biojava.bio.seq.Down",
548       "org.gmod.schema.sequence.FeatureCvTermPub",
549       "org.biojava.bio.Annotatable",
550       "org.gmod.schema.utils.Rankable",
551       "com.ibatis.sqlmap.engine.accessplan.ComplexAccessPlan",
552       "net.sf.cglib.core.ProcessSwitchCallback",
553       "com.ibatis.sqlmap.engine.mapping.sql.Sql",
554       "uk.ac.sanger.artemis.components.FileViewer$2",
555       "com.ibatis.common.beans.ProbeFactory",
556       "com.ibatis.common.beans.ClassInfo",
557       "uk.ac.sanger.artemis.FeatureVector",
558       "org.biojava.bio.seq.io.SequenceBuilderBase",
559       "uk.ac.sanger.artemis.io.EmblStreamSequence",
560       "org.biojava.utils.stax.StringElementHandlerBase",
561       "com.ibatis.sqlmap.engine.scope.ErrorContext",
562       "org.biojava.bio.seq.io.CrossProductTokenization",
563       "org.biojava.utils.walker.Visitor",
564       "org.biojava.bio.symbol.IntegerAlphabet$IntegerArray",
565       "org.biojava.bio.seq.FeatureFilter$StrandFilter",
566       "com.ibatis.sqlmap.engine.config.SqlSource",
567       "org.biojava.bio.symbol.FundamentalAtomicSymbol",
568       "org.biojava.bio.seq.FeatureHolder",
569       "net.sf.cglib.asm.Edge",
570       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler$MappingHandler",
571       "org.biojava.utils.ChangeForwarder$Retyper",
572       "org.gmod.schema.dao.OrganismDaoI",
573       "com.ibatis.sqlmap.engine.mapping.sql.stat.StaticSql",
574       "net.sf.cglib.asm.ClassWriter",
575       "org.biojava.bio.seq.io.SymbolTokenization",
576       "com.sshtools.j2ssh.session.SessionChannelClient",
577       "htsjdk.samtools.util.LocationAware",
578       "uk.ac.sanger.artemis.io.QualifierInfo",
579       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry$1",
580       "com.ibatis.common.resources.Resources",
581       "org.biojava.utils.Unchangeable",
582       "org.apache.log4j.Priority",
583       "org.biojava.bio.symbol.FuzzyLocation",
584       "org.biojava.bio.CardinalityConstraint",
585       "net.sf.cglib.core.AbstractClassGenerator$Source",
586       "org.biojava.bio.dp.SimpleDotState",
587       "org.apache.log4j.LogManager",
588       "org.gmod.schema.sequence.FeatureLoc",
589       "org.biojava.bio.symbol.AlphabetIndex",
590       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler",
591       "org.biojava.bio.seq.FeatureHolder$EmptyFeatureHolder",
592       "com.ibatis.common.logging.jakarta.JakartaCommonsLoggingImpl",
593       "org.biojava.bio.seq.FeatureFilter$OnlyDescendants",
594       "uk.ac.sanger.artemis.io.DocumentEntry",
595       "org.biojava.bio.seq.FeatureFilter$ByFeature",
596       "org.biojava.bio.symbol.EmptySymbolList",
597       "uk.ac.sanger.artemis.io.BlastStreamFeature",
598       "org.apache.log4j.DefaultCategoryFactory",
599       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagHandlerFactory",
600       "org.postgresql.core.Logger",
601       "org.apache.log4j.or.RendererMap",
602       "com.ibatis.sqlmap.engine.mapping.sql.simple.SimpleDynamicSql",
603       "uk.ac.sanger.artemis.io.OutOfDateException",
604       "uk.ac.sanger.artemis.ExternalProgram",
605       "com.sshtools.j2ssh.transport.Service",
606       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateContext",
607       "uk.ac.sanger.artemis.io.EmblMisc",
608       "org.gmod.schema.pub.PubDbXRef",
609       "com.ibatis.sqlmap.engine.type.SqlDateTypeHandler",
610       "org.biojava.bio.symbol.AbstractAlphabet",
611       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsPropertyAvailableTagHandler",
612       "org.biojava.bio.seq.FeatureFilter$ByClass",
613       "org.gmod.schema.general.DbXRef",
614       "uk.ac.sanger.artemis.io.PartialSequence",
615       "org.biojava.bio.seq.FeatureFilter$ByParent",
616       "org.biojava.bio.dp.WeightMatrix",
617       "org.biojava.utils.ChangeListener$AlwaysVetoListener",
618       "uk.ac.sanger.artemis.chado.SqlMapClientWrapper",
619       "org.biojava.bio.symbol.DummySymbolList",
620       "org.biojava.bio.symbol.AlphabetManager$SizeQueen",
621       "uk.ac.sanger.artemis.Entry",
622       "org.biojava.bio.symbol.HashedAlphabetIndex",
623       "org.biojava.utils.ClassTools",
624       "net.sf.cglib.core.Customizer",
625       "uk.ac.sanger.artemis.io.EmblStreamFeature",
626       "uk.ac.sanger.artemis.io.QualifierParseException",
627       "org.biojava.bio.seq.impl.ViewSequence",
628       "org.biojava.utils.cache.WeakValueHashMap",
629       "org.biojava.bio.symbol.IllegalSymbolException",
630       "uk.ac.sanger.artemis.ExternalProgramVector",
631       "com.ibatis.sqlmap.engine.type.TypeHandler",
632       "com.ibatis.sqlmap.engine.mapping.parameter.InlineParameterMapParser",
633       "org.apache.log4j.CategoryKey",
634       "uk.ac.sanger.artemis.io.Qualifier",
635       "uk.ac.sanger.artemis.util.InputStreamProgressListener",
636       "org.biojava.bio.AnnotationType$Impl",
637       "org.biojava.bio.seq.RemoteFeature",
638       "com.ibatis.sqlmap.engine.type.JdbcTypeRegistry",
639       "org.apache.log4j.helpers.OnlyOnceErrorHandler",
640       "org.biojava.bio.symbol.TranslationTable",
641       "uk.ac.sanger.artemis.sequence.MarkerRangeVector",
642       "uk.ac.sanger.artemis.io.DocumentEntryAutosaveThread",
643       "org.biojava.bio.symbol.CrossProductAlphabetIndex",
644       "com.ibatis.sqlmap.engine.execution.BatchException",
645       "com.sshtools.j2ssh.sftp.FileAttributes",
646       "org.biojava.bio.seq.impl.SimpleStrandedFeature",
647       "uk.ac.sanger.artemis.sequence.Marker",
648       "org.biojava.bio.seq.Feature$ByLocationComparator",
649       "org.biojava.bio.symbol.DoubleAlphabet",
650       "org.postgresql.largeobject.BlobInputStream",
651       "org.apache.log4j.ProvisionNode",
652       "com.sshtools.j2ssh.authentication.SshAuthenticationClient",
653       "uk.ac.sanger.artemis.io.GFFDocumentEntry",
654       "org.biojava.bio.symbol.AbstractSymbolList$EditTranslater",
655       "com.ibatis.sqlmap.engine.mapping.result.ResultObjectFactory",
656       "uk.ac.sanger.artemis.io.GFFStreamFeature",
657       "org.biojava.bio.seq.impl.SimpleSequence",
658       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler",
659       "org.biojava.bio.symbol.AtomicSymbol",
660       "com.sshtools.j2ssh.transport.MessageStoreEOFException",
661       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsGreaterEqualTagHandler",
662       "org.biojava.bio.dist.Distribution",
663       "org.biojava.bio.seq.FeatureFilter$BySequenceName",
664       "org.apache.log4j.spi.RootLogger",
665       "org.biojava.bio.BioError",
666       "com.ibatis.common.beans.Invoker",
667       "net.sf.cglib.asm.Type",
668       "org.biojava.bio.seq.FilterUtils$FilterTransformer",
669       "org.apache.log4j.spi.ErrorHandler",
670       "com.ibatis.sqlmap.engine.accessplan.EnhancedPropertyAccessPlan",
671       "org.biojava.bio.seq.db.ViewingSequenceDB",
672       "net.sf.cglib.core.MethodInfo",
673       "uk.ac.sanger.artemis.ExternalProgramException",
674       "uk.ac.sanger.artemis.io.QualifierVector",
675       "org.apache.log4j.spi.RendererSupport",
676       "org.biojava.bio.symbol.SymbolListFactory",
677       "org.biojava.bio.seq.OptimizableFilter",
678       "uk.ac.sanger.artemis.components.variant.TabixReader$Iterator",
679       "com.ibatis.sqlmap.engine.execution.SqlExecutor",
680       "uk.ac.sanger.artemis.FeatureChangeListener",
681       "uk.ac.sanger.artemis.util.FileDocument",
682       "uk.ac.sanger.artemis.FeatureChangeEvent",
683       "net.sf.cglib.core.Block",
684       "org.biojava.bio.symbol.AlphabetManager$GapSymbol",
685       "com.ibatis.sqlmap.engine.mapping.sql.SqlText",
686       "net.sf.cglib.asm.Opcodes",
687       "uk.ac.sanger.artemis.io.LocationParseNodeVector",
688       "uk.ac.sanger.artemis.io.LineGroup",
689       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagContext",
690       "com.ibatis.sqlmap.engine.type.TimeOnlyTypeHandler",
691       "org.biojava.bio.symbol.AbstractLocation",
692       "org.biojava.bio.CollectionConstraint$AllValuesIn",
693       "com.ibatis.sqlmap.engine.mapping.statement.RowHandlerCallback",
694       "org.postgresql.Driver",
695       "org.biojava.utils.ChangeSupport",
696       "org.biojava.bio.NonePropertyConstraint",
697       "org.biojava.bio.seq.io.AlternateTokenization",
698       "com.ibatis.sqlmap.engine.accessplan.AccessPlanFactory",
699       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.DynamicParent",
700       "org.biojava.bio.molbio.RestrictionSite",
701       "org.biojava.bio.seq.StrandedFeature$Strand",
702       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry",
703       "org.biojava.bio.symbol.AlphabetManager$1",
704       "org.apache.log4j.Logger",
705       "org.biojava.bio.dp.ScoreType$NullModel",
706       "org.biojava.bio.symbol.IntegerAlphabet$1",
707       "com.ibatis.sqlmap.engine.mapping.statement.ExecuteListener",
708       "org.biojava.bio.seq.homol.HomologyFeature",
709       "uk.ac.sanger.artemis.EntryGroup",
710       "uk.ac.sanger.artemis.io.Feature",
711       "com.ibatis.sqlmap.engine.mapping.statement.SelectStatement",
712       "org.biojava.bio.AbstractAnnotation",
713       "org.biojava.bio.symbol.ManyToOneTranslationTable",
714       "com.ibatis.sqlmap.engine.transaction.TransactionException",
715       "com.sshtools.j2ssh.authentication.AuthenticationProtocolListener",
716       "org.apache.log4j.helpers.LogLog",
717       "uk.ac.sanger.artemis.io.QualifierInfoVector",
718       "org.biojava.bio.seq.SequenceIterator",
719       "com.ibatis.common.logging.LogFactory",
720       "org.biojava.bio.seq.io.SimpleSequenceBuilder$SSBFactory",
721       "com.ibatis.sqlmap.engine.type.BaseTypeHandler",
722       "org.biojava.bio.seq.db.SequenceDBLite",
723       "org.apache.log4j.spi.RepositorySelector",
724       "org.biojava.utils.ListTools$SeriesList",
725       "org.biojava.bio.symbol.SimpleSymbolList",
726       "uk.ac.sanger.artemis.io.GFF3AttributeBuilder$1",
727       "com.ibatis.common.beans.DomProbe",
728       "com.ibatis.sqlmap.engine.type.CustomTypeHandler",
729       "org.biojava.utils.ChangeListener$LoggingListener",
730       "org.biojava.bio.seq.db.HashSequenceDB",
731       "net.sf.cglib.core.NamingPolicy",
732       "org.biojava.bio.symbol.SingletonAlphabet",
733       "org.biojava.bio.SmallAnnotation",
734       "org.biojava.bio.seq.io.SimpleSequenceBuilder$1",
735       "org.biojava.bio.symbol.ReversibleTranslationTable",
736       "uk.ac.sanger.artemis.io.Entry",
737       "net.sf.cglib.asm.Item",
738       "uk.ac.sanger.artemis.util.LinePushBackReader",
739       "org.apache.log4j.or.DefaultRenderer",
740       "uk.ac.sanger.artemis.util.ProgressInputStream",
741       "com.ibatis.common.jdbc.exception.NestedSQLException",
742       "com.ibatis.sqlmap.engine.builder.xml.SqlMapClasspathEntityResolver",
743       "com.ibatis.sqlmap.engine.accessplan.AccessPlan",
744       "org.biojava.bio.seq.FeatureFilter$ByChild",
745       "org.biojava.bio.seq.io.SequenceBuilder",
746       "net.sf.cglib.asm.Attribute",
747       "net.sf.cglib.asm.ClassAdapter",
748       "uk.ac.sanger.artemis.io.FeatureVector",
749       "net.sf.cglib.asm.MethodAdapter",
750       "org.biojava.bio.symbol.LinearAlphabetIndex",
751       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler$1",
752       "com.ibatis.sqlmap.client.extensions.TypeHandlerCallback",
753       "org.apache.commons.logging.impl.Log4JLogger",
754       "org.biojava.bio.symbol.Location",
755       "org.gmod.schema.organism.Organism",
756       "org.gmod.schema.general.Db",
757       "com.ibatis.sqlmap.engine.config.CacheModelConfig",
758       "com.ibatis.sqlmap.engine.impl.SqlMapSessionImpl",
759       "org.apache.log4j.Appender",
760       "org.biojava.bio.symbol.SimpleReversibleTranslationTable",
761       "org.biojava.bio.symbol.Alphabet",
762       "com.ibatis.sqlmap.engine.config.ParameterMapConfig",
763       "org.biojava.bio.symbol.AbstractSymbolList$EditScreener",
764       "org.biojava.utils.ListTools$5",
765       "net.sf.cglib.core.CodeGenerationException",
766       "org.biojava.bio.seq.Frame",
767       "uk.ac.sanger.artemis.chado.ChadoTransaction",
768       "com.sshtools.j2ssh.transport.SshMsgServiceAccept",
769       "org.biojava.utils.AssertionFailure",
770       "uk.ac.sanger.artemis.FeaturePredicate",
771       "com.sshtools.j2ssh.authentication.AuthenticationProtocolException",
772       "uk.ac.sanger.artemis.Logger",
773       "org.biojava.bio.seq.IsTopLevel",
774       "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl",
775       "com.ibatis.sqlmap.client.SqlMapSession",
776       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotEmptyTagHandler",
777       "org.gmod.schema.sequence.FeatureSynonym",
778       "org.apache.log4j.spi.LoggingEvent",
779       "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol",
780       "com.ibatis.sqlmap.engine.mapping.statement.CachingStatement",
781       "uk.ac.sanger.artemis.io.QualifierLazyLoading",
782       "org.biojava.bio.symbol.FuzzyLocation$AverageRangeResolver",
783       "uk.ac.sanger.artemis.util.DatabaseDocument",
784       "uk.ac.sanger.artemis.FeatureEnumeration",
785       "net.sf.cglib.asm.Label",
786       "org.biojava.bio.symbol.AbstractSymbolList",
787       "uk.ac.sanger.artemis.io.StreamFeatureTable",
788       "org.gmod.schema.dao.PubDaoI",
789       "org.biojava.bio.symbol.RangeLocation"
790     );
791   }
792 
resetClasses()793   private static void resetClasses() {
794     org.evosuite.runtime.classhandling.ClassResetter.getInstance().setClassLoader(Sequence_ESTest_scaffolding.class.getClassLoader());
795 
796     org.evosuite.runtime.classhandling.ClassStateSupport.resetClasses(
797       "uk.ac.sanger.artemis.io.LineGroup",
798       "uk.ac.sanger.artemis.io.Packing",
799       "org.apache.log4j.Category",
800       "org.apache.log4j.Logger",
801       "org.apache.log4j.Priority",
802       "org.apache.log4j.Level",
803       "org.apache.log4j.or.RendererMap",
804       "org.apache.log4j.helpers.OptionConverter",
805       "org.apache.log4j.helpers.Loader",
806       "org.apache.log4j.helpers.LogLog",
807       "org.apache.log4j.PropertyConfigurator",
808       "org.apache.log4j.LogManager",
809       "org.apache.log4j.CategoryKey",
810       "org.apache.log4j.ProvisionNode",
811       "uk.ac.sanger.artemis.util.DatabaseDocument",
812       "uk.ac.sanger.artemis.util.DatabaseLocationParser",
813       "org.apache.log4j.MDC",
814       "uk.ac.sanger.artemis.chado.GmodDAO",
815       "uk.ac.sanger.artemis.chado.IBatisDAO",
816       "uk.ac.sanger.artemis.chado.SqlMapClientWrapper",
817       "com.ibatis.common.resources.Resources",
818       "com.ibatis.common.beans.ComplexBeanProbe",
819       "com.ibatis.common.beans.GenericProbe",
820       "com.ibatis.common.beans.ProbeFactory",
821       "com.ibatis.sqlmap.engine.config.SqlMapConfiguration",
822       "com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate",
823       "com.ibatis.sqlmap.engine.execution.SqlExecutor",
824       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory$1",
825       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory",
826       "com.ibatis.sqlmap.engine.type.UnknownTypeHandler",
827       "com.ibatis.sqlmap.engine.type.DateTypeHandler",
828       "com.ibatis.sqlmap.engine.type.DateOnlyTypeHandler",
829       "com.ibatis.sqlmap.engine.type.TimeOnlyTypeHandler",
830       "com.ibatis.sqlmap.engine.type.SqlDateTypeHandler",
831       "com.ibatis.sqlmap.engine.type.SqlTimeTypeHandler",
832       "com.ibatis.sqlmap.engine.type.SqlTimestampTypeHandler",
833       "com.ibatis.sqlmap.engine.exchange.ComplexDataExchange",
834       "com.ibatis.common.logging.LogFactory",
835       "org.apache.commons.logging.impl.Log4JLogger",
836       "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl",
837       "com.ibatis.sqlmap.engine.builder.xml.SqlMapClasspathEntityResolver",
838       "com.ibatis.common.beans.ClassInfo",
839       "com.ibatis.sqlmap.engine.accessplan.AccessPlanFactory",
840       "com.ibatis.common.jdbc.SimpleDataSource",
841       "org.postgresql.Driver",
842       "com.ibatis.sqlmap.engine.mapping.result.ResultMap",
843       "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange",
844       "net.sf.cglib.core.TypeUtils",
845       "net.sf.cglib.asm.Type",
846       "net.sf.cglib.core.KeyFactory",
847       "net.sf.cglib.core.AbstractClassGenerator",
848       "net.sf.cglib.core.KeyFactory$Generator",
849       "net.sf.cglib.core.DefaultGeneratorStrategy",
850       "net.sf.cglib.core.DefaultNamingPolicy",
851       "net.sf.cglib.asm.ClassWriter",
852       "net.sf.cglib.core.DebuggingClassWriter",
853       "net.sf.cglib.core.ClassEmitter",
854       "net.sf.cglib.core.ReflectUtils",
855       "net.sf.cglib.core.EmitUtils",
856       "net.sf.cglib.core.Constants",
857       "net.sf.cglib.core.CodeEmitter",
858       "net.sf.cglib.asm.Frame",
859       "net.sf.cglib.asm.ClassReader",
860       "net.sf.cglib.core.ClassNameReader$EarlyExitException",
861       "net.sf.cglib.core.ClassNameReader",
862       "net.sf.cglib.beans.BulkBean",
863       "org.biojava.bio.symbol.DoubleAlphabet",
864       "org.biojava.bio.symbol.AlphabetManager$GapSymbol",
865       "org.biojava.bio.symbol.AlphabetManager$SizeQueen",
866       "org.biojava.bio.symbol.IntegerAlphabet",
867       "org.biojava.bio.symbol.SimpleSymbol",
868       "org.biojava.bio.symbol.AbstractSimpleBasisSymbol",
869       "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol",
870       "org.biojava.utils.ChangeType",
871       "org.biojava.bio.EmptyAnnotation",
872       "org.biojava.bio.Annotation",
873       "org.biojava.bio.symbol.EmptyAlphabet",
874       "org.biojava.bio.symbol.Alphabet",
875       "org.biojava.bio.AbstractAnnotation",
876       "org.biojava.bio.SimpleAnnotation",
877       "org.biojava.utils.ListTools",
878       "org.biojava.utils.SingletonList",
879       "org.biojava.bio.SmallAnnotation",
880       "org.biojava.utils.lsid.LifeScienceIdentifier",
881       "org.biojava.utils.SmallMap",
882       "org.biojava.bio.symbol.AlphabetManager$WellKnownBasisSymbol",
883       "org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol",
884       "org.biojava.bio.symbol.FundamentalAtomicSymbol",
885       "org.biojava.utils.ChangeListener",
886       "org.biojava.utils.ChangeSupport",
887       "org.biojava.bio.Annotatable",
888       "org.biojava.bio.symbol.AbstractAlphabet",
889       "org.biojava.bio.symbol.SingletonAlphabet",
890       "org.biojava.bio.symbol.SimpleAlphabet",
891       "org.biojava.bio.symbol.AlphabetManager$WellKnownAlphabet",
892       "org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper",
893       "org.biojava.bio.seq.io.CharacterTokenization",
894       "org.biojava.bio.symbol.SimpleBasisSymbol",
895       "org.biojava.bio.seq.io.AlternateTokenization",
896       "org.biojava.bio.symbol.AlphabetManager",
897       "org.biojava.bio.dist.DistributionFactory$DefaultDistributionFactory",
898       "org.biojava.bio.dist.DistributionFactory",
899       "org.biojava.bio.dp.SimpleWeightMatrix",
900       "org.biojava.bio.dp.ScoreType$Probability",
901       "org.biojava.bio.dp.ScoreType$Odds",
902       "org.biojava.bio.dp.ScoreType$NullModel",
903       "org.biojava.bio.dp.ScoreType",
904       "org.biojava.bio.dp.WeightMatrixAnnotator",
905       "org.biojava.bio.seq.impl.ViewSequence",
906       "uk.ac.sanger.artemis.io.FeatureVector",
907       "uk.ac.sanger.artemis.util.StringVector",
908       "uk.ac.sanger.artemis.components.Splash",
909       "uk.ac.sanger.artemis.util.FastVector",
910       "uk.ac.sanger.artemis.io.KeyVector",
911       "uk.ac.sanger.artemis.io.Key",
912       "uk.ac.sanger.artemis.io.QualifierInfo",
913       "uk.ac.sanger.artemis.ExternalProgram",
914       "uk.ac.sanger.artemis.Options",
915       "uk.ac.sanger.artemis.io.PublicDBDocumentEntry",
916       "org.biojava.bio.symbol.AbstractLocation",
917       "org.biojava.bio.symbol.AbstractRangeLocation",
918       "org.biojava.bio.symbol.FuzzyLocation$InnerRangeResolver",
919       "org.biojava.bio.symbol.FuzzyLocation$OuterRangeResolver",
920       "org.biojava.bio.symbol.FuzzyLocation$AverageRangeResolver",
921       "org.biojava.bio.symbol.FuzzyLocation",
922       "org.biojava.bio.seq.homol.SimilarityPairFeature",
923       "org.postgresql.largeobject.LargeObject",
924       "org.biojava.bio.seq.SimpleFeatureRealizer",
925       "org.biojava.bio.seq.impl.FeatureImpl$1",
926       "org.biojava.bio.seq.impl.FeatureImpl",
927       "org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper",
928       "org.biojava.bio.symbol.SimpleSymbolList",
929       "org.biojava.bio.seq.io.SymbolTokenization",
930       "org.biojava.bio.BioException",
931       "org.biojava.bio.symbol.IllegalSymbolException",
932       "org.biojava.bio.BioError",
933       "org.biojava.bio.seq.DNATools",
934       "uk.ac.sanger.artemis.util.ByteBuffer",
935       "org.biojava.bio.seq.io.SequenceBuilderBase",
936       "org.biojava.bio.seq.io.SimpleSequenceBuilder$SSBFactory",
937       "org.biojava.bio.seq.io.SimpleSequenceBuilder",
938       "org.biojava.bio.seq.io.ChunkedSymbolListFactory",
939       "org.biojava.bio.symbol.EmptySymbolList",
940       "org.biojava.bio.seq.impl.SimpleSequence",
941       "org.biojava.bio.seq.CircularView",
942       "org.biojava.bio.seq.SimpleFeatureHolder",
943       "org.biojava.bio.seq.AcceptAllFilter",
944       "org.biojava.bio.seq.AcceptNoneFilter",
945       "org.biojava.bio.seq.IsTopLevel",
946       "org.biojava.utils.walker.WalkerFactory",
947       "org.biojava.bio.seq.FeatureFilter$OnlyChildren",
948       "org.biojava.bio.seq.FeatureFilter",
949       "org.biojava.bio.seq.MergeFeatureHolder",
950       "org.biojava.bio.seq.projection.ProjectedFeatureHolder",
951       "org.biojava.bio.seq.projection.ReparentContext",
952       "uk.ac.sanger.artemis.io.RangeVector",
953       "uk.ac.sanger.artemis.j2ssh.SshLogin",
954       "net.sf.cglib.beans.BulkBean$Generator",
955       "net.sf.cglib.beans.BulkBeanEmitter",
956       "com.ibatis.sqlmap.engine.type.JdbcTypeRegistry",
957       "com.ibatis.sqlmap.engine.mapping.parameter.InlineParameterMapParser",
958       "com.ibatis.sqlmap.engine.builder.xml.XMLSqlSource",
959       "com.ibatis.sqlmap.engine.config.MappedStatementConfig",
960       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.DynamicSql",
961       "com.ibatis.sqlmap.engine.mapping.sql.simple.SimpleDynamicSql",
962       "com.ibatis.sqlmap.engine.cache.CacheKey",
963       "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMapping",
964       "com.ibatis.sqlmap.engine.cache.CacheModel",
965       "com.ibatis.sqlmap.engine.accessplan.ComplexAccessPlan",
966       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.ConditionalTagHandler",
967       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEmptyTagHandler",
968       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNullTagHandler",
969       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsPropertyAvailableTagHandler",
970       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateTagHandler",
971       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagHandlerFactory",
972       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry",
973       "uk.ac.sanger.artemis.util.CacheHashMap",
974       "uk.ac.sanger.artemis.components.filetree.RemoteFileNode",
975       "org.biojava.bio.symbol.IntegerAlphabet$IntegerArray",
976       "org.biojava.bio.dp.SimpleDotState",
977       "org.biojava.bio.seq.db.IDMaker$ByURN",
978       "org.biojava.bio.seq.db.IDMaker$ByName",
979       "org.biojava.bio.seq.db.IDMaker",
980       "org.biojava.bio.seq.db.HashSequenceDB",
981       "uk.ac.sanger.artemis.sequence.BasePattern",
982       "uk.ac.sanger.artemis.components.filetree.FileList",
983       "org.biojava.bio.seq.FeatureHolder",
984       "org.biojava.bio.symbol.SymbolList",
985       "org.biojava.bio.seq.db.SequenceDBWrapper",
986       "org.biojava.bio.seq.db.ViewingSequenceDB",
987       "org.biojava.bio.OverlayAnnotation",
988       "org.biojava.bio.seq.FeatureFilter$ByAnnotationType",
989       "org.biojava.bio.seq.FeatureFilter$HasAnnotation",
990       "org.biojava.bio.PropertyConstraint",
991       "org.biojava.bio.symbol.EmptyLocation",
992       "org.biojava.bio.symbol.RangeLocation",
993       "org.biojava.bio.symbol.LocationComparator",
994       "org.biojava.bio.symbol.Location",
995       "org.biojava.bio.CardinalityConstraint",
996       "org.biojava.bio.CollectionConstraint",
997       "org.biojava.bio.AnnotationType",
998       "org.biojava.bio.seq.FeatureFilter$Or",
999       "com.ibatis.sqlmap.engine.config.ParameterMapConfig",
1000       "com.ibatis.common.beans.ProbeException",
1001       "com.ibatis.sqlmap.engine.accessplan.PropertyAccessPlan",
1002       "net.sf.cglib.beans.BulkBeanException",
1003       "uk.ac.sanger.artemis.io.SimpleDocumentFeature",
1004       "uk.ac.sanger.artemis.io.PublicDBStreamFeature",
1005       "uk.ac.sanger.artemis.io.LocationParseNodeVector",
1006       "uk.ac.sanger.artemis.io.LocationParseNode",
1007       "uk.ac.sanger.artemis.io.QualifierVector",
1008       "org.biojava.bio.seq.Feature$Template",
1009       "org.biojava.bio.seq.StrandedFeature$Template",
1010       "org.biojava.bio.seq.ComponentFeature$Template",
1011       "uk.ac.sanger.artemis.io.GFFStreamFeature",
1012       "org.biojava.bio.symbol.DummySymbolList",
1013       "org.biojava.bio.seq.io.WordTokenization",
1014       "org.biojava.bio.seq.io.NameTokenization",
1015       "org.biojava.bio.symbol.AbstractSymbolList$SymbolIterator",
1016       "org.biojava.bio.symbol.Edit",
1017       "org.biojava.utils.ChangeVetoException"
1018     );
1019   }
1020 }
1021