1 /**
2  * Scaffolding file used to store all the setups needed to run
3  * tests automatically generated by EvoSuite
4  * Fri Jan 12 15:03:09 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 IndexFastaStream_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.IndexFastaStream";
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(IndexFastaStream_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.db.IDMaker$ByURN",
92       "org.biojava.bio.seq.ByHierarchy",
93       "org.biojava.bio.seq.ComponentFeature$Template",
94       "org.apache.log4j.AppenderSkeleton",
95       "com.ibatis.sqlmap.client.extensions.ParameterSetter",
96       "org.biojava.utils.stax.SAX2StAXAdaptor",
97       "uk.ac.sanger.artemis.io.SimpleDocumentFeature",
98       "uk.ac.sanger.artemis.sequence.BasePatternFormatException",
99       "net.sf.cglib.core.KeyFactory$Generator",
100       "uk.ac.sanger.artemis.io.MSPcrunchDocumentEntry",
101       "uk.ac.sanger.artemis.EntryChangeListener",
102       "org.biojava.ontology.Term",
103       "org.biojava.utils.ListTools$Triplet",
104       "org.biojava.bio.symbol.DoubleAlphabet$SubDoubleAlphabet",
105       "uk.ac.sanger.artemis.sequence.AminoAcidSequence",
106       "org.biojava.bio.symbol.AlphabetManager$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.FeatureTable",
112       "htsjdk.samtools.reference.ReferenceSequenceFileFactory",
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       "htsjdk.samtools.reference.ReferenceSequenceFileFactory$1",
120       "uk.ac.sanger.artemis.util.StringVector",
121       "net.sf.cglib.core.Constants",
122       "net.sf.cglib.core.AbstractClassGenerator",
123       "org.biojava.bio.seq.Feature$Template",
124       "com.ibatis.common.beans.BaseProbe",
125       "com.ibatis.sqlmap.engine.mapping.statement.SelectKeyStatement",
126       "org.gmod.schema.sequence.Synonym",
127       "org.biojava.bio.symbol.PointLocation",
128       "org.biojava.bio.symbol.SimpleAlphabet",
129       "org.gmod.schema.sequence.FeatureCvTermProp",
130       "org.biojava.bio.seq.io.SequenceBuilderFactory",
131       "org.apache.log4j.Hierarchy",
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       "net.sf.cglib.core.ClassNameReader$EarlyExitException",
139       "com.ibatis.sqlmap.engine.cache.CacheModel",
140       "org.apache.log4j.spi.OptionHandler",
141       "org.biojava.bio.symbol.SimpleManyToOneTranslationTable",
142       "org.biojava.utils.stax.DelegationManager",
143       "org.biojava.bio.seq.StrandedFeature",
144       "org.biojava.utils.lsid.LifeScienceIdentifier",
145       "net.sf.cglib.core.ReflectUtils",
146       "org.biojava.bio.symbol.FuzzyLocation$InnerRangeResolver",
147       "org.biojava.utils.ChangeVetoException",
148       "org.biojava.bio.symbol.IllegalAlphabetException",
149       "org.biojava.bio.seq.db.SequenceDB",
150       "htsjdk.samtools.reference.AbstractFastaSequenceFile",
151       "org.biojava.bio.symbol.DoubleAlphabet$DoubleRange",
152       "htsjdk.samtools.seekablestream.SeekableStream",
153       "org.biojava.bio.symbol.BetweenLocation",
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.gmod.schema.cv.CvTerm",
173       "org.biojava.bio.seq.db.IllegalIDException",
174       "uk.ac.sanger.artemis.sequence.SequenceChangeListener",
175       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsGreaterThanTagHandler",
176       "uk.ac.sanger.artemis.io.InvalidRelationException",
177       "org.biojava.utils.bytecode.CodeMethod",
178       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEqualTagHandler",
179       "org.biojava.bio.seq.impl.FeatureImpl$1",
180       "org.biojava.bio.seq.io.SimpleSequenceBuilder",
181       "org.biojava.bio.Annotation",
182       "org.biojava.bio.symbol.IntegerAlphabet$IntegerSymbol",
183       "org.biojava.utils.lsid.LifeScienceIdentifierParseException",
184       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler",
185       "org.biojava.bio.seq.io.SimpleAssemblyBuilder$1",
186       "org.apache.log4j.Category",
187       "uk.ac.sanger.artemis.io.LocationParseException",
188       "org.biojava.utils.ListTools$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       "org.gmod.schema.sequence.FeatureDbXRef",
199       "net.sf.cglib.core.ClassInfo",
200       "org.biojava.utils.ChangeEvent",
201       "uk.ac.sanger.artemis.components.variant.AbstractVCFReader",
202       "org.gmod.schema.pub.Pub",
203       "uk.ac.sanger.artemis.io.ChadoCanonicalGene",
204       "net.sf.cglib.core.ClassEmitter$3",
205       "net.sf.cglib.core.EmitUtils$9",
206       "net.sf.cglib.core.ClassEmitter$1",
207       "org.biojava.utils.stax.SAX2StAXAdaptor$S2SDelegationManager",
208       "net.sf.cglib.core.EmitUtils$8",
209       "net.sf.cglib.core.EmitUtils$7",
210       "net.sf.cglib.core.Predicate",
211       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry$IndexContig",
212       "org.biojava.bio.symbol.SimpleCrossProductAlphabet",
213       "net.sf.cglib.core.ClassEmitter",
214       "org.biojava.bio.seq.DNATools",
215       "org.gmod.schema.sequence.FeatureCvTermDbXRef",
216       "org.biojava.bio.symbol.AbstractManyToOneTranslationTable",
217       "uk.ac.sanger.artemis.io.GenbankStreamSequence",
218       "net.sf.cglib.core.ClassNameReader",
219       "org.biojava.bio.seq.io.ProteinRefSeqFileFormer",
220       "org.biojava.bio.seq.io.SimpleAssemblyBuilder",
221       "com.ibatis.sqlmap.engine.cache.CacheController",
222       "com.sshtools.j2ssh.io.UnsignedInteger32",
223       "org.biojava.bio.molbio.RestrictionEnzyme",
224       "net.sf.cglib.core.ClassNameReader$1",
225       "com.ibatis.sqlmap.engine.accessplan.BaseAccessPlan",
226       "org.biojava.bio.BioRuntimeException",
227       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.BaseTagHandler",
228       "org.biojava.bio.seq.AcceptAllFilter",
229       "org.biojava.bio.seq.io.ChunkedSymbolListFactory",
230       "net.sf.cglib.core.Local",
231       "org.biojava.bio.symbol.IntegerAlphabet$SubIntegerAlphabet",
232       "org.biojava.bio.seq.homol.SimilarityPairFeature",
233       "org.biojava.bio.symbol.FuzzyLocation$RangeResolver",
234       "org.gmod.schema.utils.propinterface.PropertyI",
235       "org.apache.log4j.spi.AppenderAttachable",
236       "com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate",
237       "uk.ac.sanger.artemis.j2ssh.FTProgress",
238       "uk.ac.sanger.artemis.io.GFF3AttributeAggregator",
239       "net.sf.cglib.beans.BulkBean$Generator",
240       "org.gmod.schema.cv.Cv",
241       "uk.ac.sanger.artemis.util.InputStreamProgressListenerVector",
242       "net.sf.cglib.core.DefaultNamingPolicy",
243       "uk.ac.sanger.artemis.util.PushBackException",
244       "com.ibatis.sqlmap.engine.exchange.DataExchange",
245       "com.ibatis.sqlmap.engine.mapping.sql.SqlChild",
246       "org.biojava.utils.ParseErrorListener",
247       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.DynamicTagHandler",
248       "org.biojava.utils.SingletonList",
249       "org.biojava.bio.seq.db.BioIndex$IndexFileAsList",
250       "org.biojava.bio.symbol.FuzzyLocation$OuterRangeResolver",
251       "org.biojava.bio.symbol.SymbolList",
252       "org.biojava.bio.BioException",
253       "net.sf.cglib.asm.AnnotationVisitor",
254       "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange",
255       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory$1",
256       "com.ibatis.sqlmap.engine.builder.xml.XMLSqlSource",
257       "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMapping",
258       "net.sf.cglib.asm.FieldVisitor",
259       "org.biojava.bio.seq.FramedFeature$Template",
260       "org.biojava.bio.symbol.FuzzyPointLocation$MaxPointResolver",
261       "com.ibatis.sqlmap.engine.exchange.BaseDataExchange",
262       "net.sf.cglib.asm.MethodVisitor",
263       "net.sf.cglib.asm.ClassVisitor",
264       "net.sf.cglib.core.DebuggingClassWriter",
265       "net.sf.cglib.core.ClassEmitter$FieldInfo",
266       "uk.ac.sanger.artemis.io.LocationParseNode",
267       "uk.ac.sanger.artemis.util.WorkingGZIPInputStream",
268       "com.ibatis.sqlmap.engine.mapping.statement.MappedStatement",
269       "org.biojava.bio.symbol.FuzzyPointLocation",
270       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotPropertyAvailableTagHandler",
271       "htsjdk.samtools.reference.ReferenceSequenceFile",
272       "org.biojava.utils.ChangeType$1",
273       "org.biojava.bio.symbol.AlphabetManager$WellKnownAlphabet",
274       "org.biojava.bio.seq.io.AbstractGenEmblFileFormer",
275       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsLessThanTagHandler",
276       "com.ibatis.sqlmap.client.SqlMapClient",
277       "uk.ac.sanger.artemis.io.ComparableFeature",
278       "org.biojava.bio.seq.io.GenbankXmlFormat",
279       "uk.ac.sanger.artemis.io.Key",
280       "uk.ac.sanger.artemis.Options",
281       "org.biojava.bio.seq.io.SymbolReader",
282       "org.biojava.bio.seq.impl.SimpleHomologyFeature",
283       "uk.ac.sanger.artemis.io.SimpleDocumentEntry",
284       "org.biojava.bio.symbol.BasisSymbol",
285       "com.ibatis.sqlmap.engine.transaction.Transaction",
286       "com.ibatis.sqlmap.engine.accessplan.PropertyAccessPlan",
287       "uk.ac.sanger.artemis.io.FeatureHeader",
288       "org.biojava.bio.seq.RNATools",
289       "net.sf.cglib.beans.BulkBeanEmitter",
290       "org.biojava.bio.seq.db.AbstractSequenceDB",
291       "uk.ac.sanger.artemis.components.filetree.FileList",
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       "org.biojava.utils.stax.SAX2StAXAdaptor$HandlerBinding",
301       "org.biojava.bio.seq.impl.SimpleFeature",
302       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory",
303       "org.apache.log4j.helpers.FileWatchdog",
304       "org.biojava.bio.symbol.AbstractSymbolList$ListView",
305       "uk.ac.sanger.artemis.io.RawStreamSequence",
306       "net.sf.cglib.core.EmitUtils",
307       "org.biojava.bio.seq.GappedSequence",
308       "org.biojava.bio.symbol.Alignment",
309       "org.apache.log4j.MDC",
310       "org.biojava.bio.seq.impl.SimpleRestrictionSite",
311       "net.sf.cglib.core.CollectionUtils",
312       "uk.ac.sanger.artemis.io.QualifierInfoException",
313       "net.sf.cglib.core.TypeUtils",
314       "org.gmod.schema.dao.SequenceDaoI",
315       "uk.ac.sanger.artemis.sequence.SequenceChangeEvent",
316       "com.ibatis.sqlmap.engine.mapping.result.ResultMapping",
317       "org.biojava.utils.SmallMap",
318       "org.biojava.bio.seq.StrandedFeature$Template",
319       "org.biojava.bio.symbol.Symbol",
320       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotParameterPresentTagHandler",
321       "org.biojava.bio.molbio.RestrictionSite$Template",
322       "org.biojava.bio.seq.RealizingFeatureHolder",
323       "com.sshtools.j2ssh.io.UnsignedInteger64",
324       "org.gmod.schema.sequence.FeatureCvTerm",
325       "org.biojava.bio.seq.db.IDMaker",
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       "uk.ac.sanger.artemis.io.ReadListener",
338       "org.biojava.bio.seq.Feature",
339       "uk.ac.sanger.artemis.io.InvalidKeyException",
340       "com.ibatis.common.xml.NodeletException",
341       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagHandler",
342       "net.sf.cglib.core.EmitUtils$ParameterTyper",
343       "com.ibatis.sqlmap.engine.exchange.ComplexDataExchange",
344       "net.sf.cglib.core.Signature",
345       "com.ibatis.sqlmap.engine.type.SqlTimestampTypeHandler",
346       "net.sf.cglib.asm.ByteVector",
347       "uk.ac.sanger.artemis.io.Packing",
348       "org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper",
349       "org.biojava.bio.seq.Sequence",
350       "com.ibatis.sqlmap.engine.mapping.result.Discriminator",
351       "org.biojava.bio.seq.db.IDMaker$ByName",
352       "uk.ac.sanger.artemis.util.ByteBuffer",
353       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNullTagHandler",
354       "org.biojava.bio.seq.io.FastaFormat",
355       "uk.ac.sanger.artemis.io.SimpleEntryInformation",
356       "net.sf.cglib.beans.BulkBean$BulkBeanKey",
357       "org.biojava.utils.stax.StAXContentHandlerBase",
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.seq.io.FeatureTableParser",
366       "org.biojava.bio.symbol.AbstractRangeLocation",
367       "uk.ac.sanger.artemis.io.BetweenRange",
368       "uk.ac.sanger.artemis.ExternalProgramMonitor",
369       "org.biojava.bio.EmptyAnnotation",
370       "org.biojava.bio.program.phred.PhredFormat",
371       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsLessEqualTagHandler",
372       "com.ibatis.sqlmap.engine.type.DateOnlyTypeHandler",
373       "org.apache.log4j.PropertyConfigurator",
374       "uk.ac.sanger.artemis.util.Document",
375       "org.biojava.bio.seq.db.BioIndex$1",
376       "com.ibatis.sqlmap.client.event.RowHandler",
377       "org.biojava.bio.seq.io.ParseException",
378       "org.biojava.bio.symbol.AlphabetManager",
379       "uk.ac.sanger.artemis.components.variant.TabixReader",
380       "uk.ac.sanger.artemis.components.FileViewer",
381       "org.biojava.utils.walker.WalkerFactory",
382       "org.biojava.bio.seq.FeatureRealizer",
383       "org.biojava.utils.bytecode.CodeException",
384       "uk.ac.sanger.artemis.sequence.NoSequenceException",
385       "net.sf.cglib.core.ProcessArrayCallback",
386       "org.biojava.bio.seq.io.SequenceFormat",
387       "org.biojava.bio.symbol.SparseCrossProductAlphabet",
388       "org.biojava.bio.seq.ComponentFeature",
389       "org.biojava.bio.symbol.AlphabetManager$WellKnownBasisSymbol",
390       "org.biojava.bio.seq.impl.SimpleRemoteFeature",
391       "uk.ac.sanger.artemis.io.BioJavaEntry",
392       "net.sf.cglib.asm.ClassReader",
393       "org.apache.log4j.spi.LoggerRepository",
394       "com.ibatis.common.beans.ProbeException",
395       "uk.ac.sanger.artemis.components.Splash",
396       "com.ibatis.sqlmap.engine.impl.ExtendedSqlMapClient",
397       "uk.ac.sanger.artemis.io.EntryInformationException",
398       "com.ibatis.common.beans.Probe",
399       "net.sf.cglib.core.Transformer",
400       "uk.ac.sanger.artemis.io.GFFMisc",
401       "com.ibatis.sqlmap.engine.scope.StatementScope",
402       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.DynamicSql",
403       "org.biojava.bio.seq.io.EmblProcessor",
404       "uk.ac.sanger.artemis.chado.IBatisDAO",
405       "com.ibatis.sqlmap.engine.mapping.result.AutoResultMap",
406       "org.biojava.bio.seq.db.BioIndex$Commitable",
407       "uk.ac.sanger.artemis.components.filetree.RemoteFileNode",
408       "org.biojava.bio.seq.impl.SimpleSimilarityPairFeature",
409       "org.biojava.bio.symbol.SimpleSymbolList$SSLIOListener",
410       "org.biojava.bio.seq.RemoteFeature$Template",
411       "org.biojava.bio.seq.io.GenbankXmlFormat$GenbankXmlHandler",
412       "org.apache.log4j.Level",
413       "org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol",
414       "org.biojava.bio.symbol.AbstractReversibleTranslationTable",
415       "org.biojava.bio.seq.io.SeqIOAdapter",
416       "uk.ac.sanger.artemis.io.EntryInformation",
417       "com.ibatis.sqlmap.engine.type.UnknownTypeHandler",
418       "org.biojava.bio.symbol.SimpleGeneticCodeTable",
419       "htsjdk.samtools.util.BlockCompressedInputStream",
420       "uk.ac.sanger.artemis.sequence.MarkerChangeListener",
421       "org.biojava.bio.seq.io.SeqIOListener",
422       "org.biojava.utils.ChangeType",
423       "org.biojava.bio.seq.db.BioIndex",
424       "net.sf.cglib.asm.FieldWriter",
425       "uk.ac.sanger.artemis.io.ReadFormatException",
426       "org.biojava.utils.ChangeListener",
427       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotNullTagHandler",
428       "org.biojava.utils.AbstractChangeable",
429       "org.gmod.schema.sequence.FeaturePub",
430       "org.biojava.bio.seq.SimpleFeatureHolder",
431       "uk.ac.sanger.artemis.EntrySourceVector",
432       "net.sf.cglib.core.LocalVariablesSorter$State",
433       "com.ibatis.sqlmap.client.SqlMapTransactionManager",
434       "com.ibatis.sqlmap.engine.config.ResultMapConfig",
435       "org.biojava.bio.symbol.EmptyAlphabet",
436       "org.gmod.schema.analysis.AnalysisFeature",
437       "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMap",
438       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTag",
439       "org.gmod.schema.dao.SchemaDaoI",
440       "uk.ac.sanger.artemis.LastSegmentException",
441       "uk.ac.sanger.artemis.ChangeEvent",
442       "org.gmod.schema.sequence.FeatureRelationship",
443       "org.biojava.bio.seq.SimpleFeatureRealizer",
444       "uk.ac.sanger.artemis.io.GenbankStreamFeature",
445       "uk.ac.sanger.artemis.util.OutOfRangeException",
446       "com.ibatis.sqlmap.engine.scope.SessionScope",
447       "org.postgresql.util.PSQLException",
448       "net.sf.cglib.beans.BulkBean",
449       "com.ibatis.common.logging.Log",
450       "com.ibatis.sqlmap.engine.mapping.result.ResultMap",
451       "org.biojava.bio.symbol.SimpleBasisSymbol",
452       "org.biojava.utils.lsid.Identifiable",
453       "org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser",
454       "org.biojava.bio.seq.DNATools$DNAComplementTranslationTable",
455       "uk.ac.sanger.artemis.io.EMBLObject",
456       "org.postgresql.largeobject.LargeObject",
457       "uk.ac.sanger.artemis.sequence.Strand",
458       "uk.ac.sanger.artemis.chado.GmodDAO",
459       "net.sf.cglib.core.ClassGenerator",
460       "net.sf.cglib.core.ReflectUtils$4",
461       "org.apache.log4j.spi.DefaultRepositorySelector",
462       "uk.ac.sanger.artemis.OptionChangeListener",
463       "net.sf.cglib.core.ReflectUtils$1",
464       "net.sf.cglib.core.ReflectUtils$2",
465       "net.sf.cglib.core.ReflectUtils$3",
466       "uk.ac.sanger.artemis.io.Sequence",
467       "org.biojava.bio.symbol.LocationComparator",
468       "uk.ac.sanger.artemis.components.variant.BCFReader",
469       "org.biojava.bio.symbol.FuzzyPointLocation$AveragePointResolver",
470       "uk.ac.sanger.artemis.util.LargeObjectDocument",
471       "uk.ac.sanger.artemis.io.GenbankMisc",
472       "uk.ac.sanger.artemis.chado.JdbcDAO",
473       "net.sf.cglib.core.ObjectSwitchCallback",
474       "org.biojava.utils.bytecode.GeneratedClassLoader",
475       "com.ibatis.sqlmap.engine.cache.CacheKey",
476       "uk.ac.sanger.artemis.io.Location",
477       "org.biojava.utils.stax.StAXContentHandler",
478       "uk.ac.sanger.artemis.io.PublicDBStreamFeature",
479       "net.sf.cglib.core.DefaultGeneratorStrategy",
480       "org.apache.log4j.or.ObjectRenderer",
481       "uk.ac.sanger.artemis.util.DatabaseLocationParser",
482       "net.sf.cglib.core.DebuggingClassWriter$1",
483       "uk.ac.sanger.artemis.io.FastaStreamSequence",
484       "uk.ac.sanger.artemis.io.FeatureEnumeration",
485       "org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper",
486       "com.ibatis.sqlmap.engine.type.DateTypeHandler",
487       "org.biojava.utils.ChangeForwarder",
488       "uk.ac.sanger.artemis.io.StreamFeature",
489       "com.ibatis.common.io.ReaderInputStream",
490       "uk.ac.sanger.artemis.util.ReadOnlyException",
491       "org.biojava.bio.symbol.GappedSymbolList",
492       "com.ibatis.sqlmap.engine.accessplan.MapAccessPlan",
493       "uk.ac.sanger.artemis.EntryChangeEvent",
494       "org.biojava.bio.symbol.HashedAlphabetIndex$HashComparator",
495       "org.biojava.bio.seq.FeatureFilter",
496       "uk.ac.sanger.artemis.Feature",
497       "uk.ac.sanger.artemis.io.EmblDocumentEntry",
498       "org.biojava.utils.cache.KeyedWeakReference",
499       "org.biojava.bio.seq.homol.HomologyFeature$Template",
500       "com.ibatis.sqlmap.client.extensions.ResultGetter",
501       "uk.ac.sanger.artemis.io.DocumentFeature",
502       "org.biojava.bio.SimpleAnnotation",
503       "org.biojava.bio.symbol.IntegerAlphabet",
504       "com.sshtools.j2ssh.FileTransferProgress",
505       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotEqualTagHandler",
506       "com.ibatis.sqlmap.engine.transaction.TransactionManager",
507       "com.ibatis.common.jdbc.SimpleDataSource",
508       "org.biojava.bio.seq.impl.FeatureImpl",
509       "org.apache.log4j.spi.LoggerFactory",
510       "org.biojava.bio.symbol.DoubleAlphabet$DoubleSymbol",
511       "org.apache.log4j.spi.Configurator",
512       "uk.ac.sanger.artemis.io.MSPcrunchStreamFeature",
513       "org.biojava.bio.seq.impl.SimpleFramedFeature",
514       "org.biojava.bio.seq.io.ReferenceAnnotation",
515       "net.sf.cglib.core.CodeEmitter",
516       "org.biojava.bio.seq.io.GenbankFileFormer",
517       "org.gmod.schema.sequence.Feature",
518       "org.biojava.bio.symbol.FiniteAlphabet",
519       "org.biojava.bio.seq.FeatureFilter$OnlyChildren",
520       "org.biojava.bio.seq.homol.SimilarityPairFeature$Template",
521       "uk.ac.sanger.artemis.io.KeyVector",
522       "org.apache.log4j.PropertyWatchdog",
523       "org.gmod.schema.sequence.FeatureCvTermPub",
524       "org.biojava.bio.Annotatable",
525       "org.gmod.schema.utils.Rankable",
526       "uk.ac.sanger.artemis.io.MSPcrunchEntryInformation",
527       "com.ibatis.sqlmap.engine.accessplan.ComplexAccessPlan",
528       "net.sf.cglib.core.ProcessSwitchCallback",
529       "com.ibatis.sqlmap.engine.mapping.sql.Sql",
530       "org.biojava.utils.ParseErrorEvent",
531       "uk.ac.sanger.artemis.components.FileViewer$2",
532       "org.biojava.bio.seq.io.EmblLikeFormat",
533       "com.ibatis.common.beans.ProbeFactory",
534       "com.ibatis.common.beans.ClassInfo",
535       "uk.ac.sanger.artemis.FeatureVector",
536       "org.biojava.bio.seq.io.SequenceBuilderBase",
537       "uk.ac.sanger.artemis.io.EmblStreamSequence",
538       "org.biojava.utils.stax.StringElementHandlerBase",
539       "com.ibatis.sqlmap.engine.scope.ErrorContext",
540       "org.biojava.bio.seq.io.CrossProductTokenization",
541       "org.biojava.bio.seq.io.SequenceBuilderFilter",
542       "com.ibatis.sqlmap.engine.config.SqlSource",
543       "org.biojava.bio.seq.FeatureHolder",
544       "org.biojava.bio.symbol.FundamentalAtomicSymbol",
545       "org.biojava.bio.seq.io.GenpeptFileFormer",
546       "net.sf.cglib.asm.Edge",
547       "htsjdk.samtools.util.LineReader",
548       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler$MappingHandler",
549       "org.biojava.utils.ChangeForwarder$Retyper",
550       "org.gmod.schema.dao.OrganismDaoI",
551       "com.ibatis.sqlmap.engine.mapping.sql.stat.StaticSql",
552       "net.sf.cglib.asm.ClassWriter",
553       "org.biojava.bio.seq.io.SymbolTokenization",
554       "htsjdk.samtools.util.LocationAware",
555       "uk.ac.sanger.artemis.io.QualifierInfo",
556       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry$1",
557       "com.ibatis.common.resources.Resources",
558       "org.biojava.utils.Unchangeable",
559       "org.apache.log4j.Priority",
560       "org.biojava.bio.symbol.FuzzyLocation",
561       "net.sf.cglib.core.AbstractClassGenerator$Source",
562       "org.biojava.bio.seq.RNATools$RNAComplementTranslationTable",
563       "org.apache.log4j.LogManager",
564       "org.gmod.schema.sequence.FeatureLoc",
565       "org.biojava.bio.symbol.AlphabetIndex",
566       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler",
567       "org.biojava.bio.seq.FeatureHolder$EmptyFeatureHolder",
568       "com.ibatis.common.logging.jakarta.JakartaCommonsLoggingImpl",
569       "uk.ac.sanger.artemis.io.DocumentEntry",
570       "org.biojava.bio.symbol.SimpleAtomicSymbol",
571       "org.biojava.bio.symbol.EmptySymbolList",
572       "uk.ac.sanger.artemis.io.BlastStreamFeature",
573       "org.apache.log4j.DefaultCategoryFactory",
574       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagHandlerFactory",
575       "org.postgresql.core.Logger",
576       "org.apache.log4j.or.RendererMap",
577       "com.ibatis.sqlmap.engine.mapping.sql.simple.SimpleDynamicSql",
578       "uk.ac.sanger.artemis.io.OutOfDateException",
579       "uk.ac.sanger.artemis.ExternalProgram",
580       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateContext",
581       "uk.ac.sanger.artemis.io.EmblMisc",
582       "org.biojava.bio.seq.io.GenbankFormat",
583       "org.gmod.schema.pub.PubDbXRef",
584       "com.ibatis.sqlmap.engine.type.SqlDateTypeHandler",
585       "org.biojava.bio.symbol.AbstractAlphabet",
586       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsPropertyAvailableTagHandler",
587       "org.biojava.bio.seq.io.SimpleAssemblyBuilder$SSBFactory",
588       "org.gmod.schema.general.DbXRef",
589       "uk.ac.sanger.artemis.io.PartialSequence",
590       "org.biojava.utils.ChangeListener$AlwaysVetoListener",
591       "uk.ac.sanger.artemis.EntryGroupChangeEvent",
592       "org.biojava.bio.seq.io.GenbankXmlFormat$GenbankXmlSequence",
593       "uk.ac.sanger.artemis.chado.SqlMapClientWrapper",
594       "uk.ac.sanger.artemis.Entry",
595       "org.biojava.bio.symbol.AlphabetManager$SizeQueen",
596       "org.biojava.bio.symbol.HashedAlphabetIndex",
597       "org.biojava.utils.ClassTools",
598       "org.biojava.bio.seq.db.IndexStore",
599       "net.sf.cglib.core.Customizer",
600       "org.biojava.bio.seq.io.GenpeptFormat",
601       "uk.ac.sanger.artemis.io.EmblStreamFeature",
602       "uk.ac.sanger.artemis.io.QualifierParseException",
603       "org.biojava.utils.cache.WeakValueHashMap",
604       "org.biojava.bio.symbol.IllegalSymbolException",
605       "uk.ac.sanger.artemis.ExternalProgramVector",
606       "com.ibatis.sqlmap.engine.type.TypeHandler",
607       "com.ibatis.sqlmap.engine.mapping.parameter.InlineParameterMapParser",
608       "org.apache.log4j.CategoryKey",
609       "uk.ac.sanger.artemis.io.Qualifier",
610       "uk.ac.sanger.artemis.util.InputStreamProgressListener",
611       "org.biojava.bio.seq.RemoteFeature",
612       "com.ibatis.sqlmap.engine.type.JdbcTypeRegistry",
613       "org.apache.log4j.helpers.OnlyOnceErrorHandler",
614       "org.biojava.bio.symbol.TranslationTable",
615       "uk.ac.sanger.artemis.io.DocumentEntryAutosaveThread",
616       "org.biojava.bio.symbol.CrossProductAlphabetIndex",
617       "com.ibatis.sqlmap.engine.execution.BatchException",
618       "org.biojava.bio.seq.impl.SimpleStrandedFeature",
619       "com.sshtools.j2ssh.sftp.FileAttributes",
620       "uk.ac.sanger.artemis.sequence.Marker",
621       "org.biojava.bio.seq.Feature$ByLocationComparator",
622       "org.postgresql.largeobject.BlobInputStream",
623       "org.biojava.bio.symbol.DoubleAlphabet",
624       "org.apache.log4j.ProvisionNode",
625       "uk.ac.sanger.artemis.io.GFFDocumentEntry",
626       "org.biojava.bio.symbol.AbstractSymbolList$EditTranslater",
627       "com.ibatis.sqlmap.engine.mapping.result.ResultObjectFactory",
628       "uk.ac.sanger.artemis.io.GFFStreamFeature",
629       "org.biojava.bio.seq.impl.SimpleSequence",
630       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler",
631       "org.biojava.bio.symbol.AtomicSymbol",
632       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsGreaterEqualTagHandler",
633       "org.biojava.bio.dist.Distribution",
634       "org.apache.log4j.spi.RootLogger",
635       "org.biojava.bio.BioError",
636       "com.ibatis.common.beans.Invoker",
637       "net.sf.cglib.asm.Type",
638       "org.apache.log4j.spi.ErrorHandler",
639       "com.ibatis.sqlmap.engine.accessplan.EnhancedPropertyAccessPlan",
640       "uk.ac.sanger.artemis.ExternalProgramException",
641       "net.sf.cglib.core.MethodInfo",
642       "uk.ac.sanger.artemis.io.QualifierVector",
643       "org.apache.log4j.spi.RendererSupport",
644       "uk.ac.sanger.artemis.components.variant.TabixReader$Iterator",
645       "org.biojava.bio.symbol.SymbolListFactory",
646       "org.biojava.bio.seq.OptimizableFilter",
647       "uk.ac.sanger.artemis.util.FileDocument",
648       "uk.ac.sanger.artemis.FeatureChangeListener",
649       "com.ibatis.sqlmap.engine.execution.SqlExecutor",
650       "uk.ac.sanger.artemis.FeatureChangeEvent",
651       "net.sf.cglib.core.Block",
652       "com.ibatis.sqlmap.engine.mapping.sql.SqlText",
653       "org.biojava.bio.symbol.AlphabetManager$GapSymbol",
654       "net.sf.cglib.asm.Opcodes",
655       "uk.ac.sanger.artemis.io.LocationParseNodeVector",
656       "uk.ac.sanger.artemis.io.LineGroup",
657       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagContext",
658       "com.ibatis.sqlmap.engine.type.TimeOnlyTypeHandler",
659       "org.biojava.bio.symbol.AbstractLocation",
660       "com.ibatis.sqlmap.engine.mapping.statement.RowHandlerCallback",
661       "org.postgresql.Driver",
662       "uk.ac.sanger.artemis.io.BioJavaFeature",
663       "org.biojava.utils.ChangeSupport",
664       "org.biojava.bio.seq.io.AlternateTokenization",
665       "com.ibatis.sqlmap.engine.accessplan.AccessPlanFactory",
666       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.DynamicParent",
667       "org.biojava.bio.molbio.RestrictionSite",
668       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry",
669       "org.biojava.bio.seq.StrandedFeature$Strand",
670       "org.biojava.bio.seq.io.SeqFileFormer",
671       "org.biojava.bio.symbol.AlphabetManager$1",
672       "org.apache.log4j.Logger",
673       "com.ibatis.sqlmap.engine.mapping.statement.ExecuteListener",
674       "org.biojava.bio.seq.homol.HomologyFeature",
675       "uk.ac.sanger.artemis.EntryGroup",
676       "uk.ac.sanger.artemis.io.Feature",
677       "com.ibatis.sqlmap.engine.mapping.statement.SelectStatement",
678       "org.biojava.bio.AbstractAnnotation",
679       "org.biojava.bio.symbol.ManyToOneTranslationTable",
680       "com.ibatis.sqlmap.engine.transaction.TransactionException",
681       "org.apache.log4j.helpers.LogLog",
682       "uk.ac.sanger.artemis.io.QualifierInfoVector",
683       "org.biojava.bio.seq.SequenceIterator",
684       "uk.ac.sanger.artemis.io.BlastEntryInformation",
685       "org.biojava.bio.seq.io.SwissprotFileFormer",
686       "com.ibatis.common.logging.LogFactory",
687       "org.biojava.bio.seq.io.SimpleSequenceBuilder$SSBFactory",
688       "com.ibatis.sqlmap.engine.type.BaseTypeHandler",
689       "org.biojava.bio.symbol.FuzzyPointLocation$MinPointResolver",
690       "org.biojava.bio.seq.db.SequenceDBLite",
691       "org.apache.log4j.spi.RepositorySelector",
692       "org.biojava.utils.ListTools$SeriesList",
693       "org.biojava.bio.symbol.SimpleSymbolList",
694       "uk.ac.sanger.artemis.io.GFF3AttributeBuilder$1",
695       "com.ibatis.common.beans.DomProbe",
696       "com.ibatis.sqlmap.engine.type.CustomTypeHandler",
697       "org.biojava.utils.ChangeListener$LoggingListener",
698       "org.biojava.bio.seq.db.HashSequenceDB",
699       "net.sf.cglib.core.NamingPolicy",
700       "org.biojava.bio.symbol.SingletonAlphabet",
701       "htsjdk.samtools.reference.IndexedFastaSequenceFile",
702       "org.biojava.bio.symbol.AbstractLocationDecorator",
703       "org.biojava.bio.SmallAnnotation",
704       "org.biojava.bio.seq.io.SimpleSequenceBuilder$1",
705       "org.biojava.bio.symbol.ReversibleTranslationTable",
706       "uk.ac.sanger.artemis.io.Entry",
707       "htsjdk.samtools.reference.ReferenceSequence",
708       "net.sf.cglib.asm.Item",
709       "uk.ac.sanger.artemis.util.LinePushBackReader",
710       "org.biojava.utils.ParseErrorSource",
711       "org.apache.log4j.or.DefaultRenderer",
712       "uk.ac.sanger.artemis.util.ProgressInputStream",
713       "com.ibatis.common.jdbc.exception.NestedSQLException",
714       "com.ibatis.sqlmap.engine.builder.xml.SqlMapClasspathEntityResolver",
715       "com.ibatis.sqlmap.engine.accessplan.AccessPlan",
716       "org.biojava.bio.seq.db.BioIndex$FileAsList",
717       "org.biojava.bio.seq.io.SequenceBuilder",
718       "net.sf.cglib.asm.Attribute",
719       "net.sf.cglib.asm.ClassAdapter",
720       "uk.ac.sanger.artemis.io.FeatureVector",
721       "net.sf.cglib.asm.MethodAdapter",
722       "org.biojava.bio.symbol.LinearAlphabetIndex",
723       "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler$1",
724       "com.ibatis.sqlmap.client.extensions.TypeHandlerCallback",
725       "uk.ac.sanger.artemis.io.IndexFastaStream",
726       "org.apache.commons.logging.impl.Log4JLogger",
727       "org.biojava.bio.symbol.Location",
728       "org.gmod.schema.organism.Organism",
729       "org.gmod.schema.general.Db",
730       "com.ibatis.sqlmap.engine.config.CacheModelConfig",
731       "com.ibatis.sqlmap.engine.impl.SqlMapSessionImpl",
732       "org.apache.log4j.Appender",
733       "org.biojava.bio.symbol.SimpleReversibleTranslationTable",
734       "org.biojava.bio.symbol.Alphabet",
735       "org.biojava.bio.symbol.FuzzyPointLocation$PointResolver",
736       "com.ibatis.sqlmap.engine.config.ParameterMapConfig",
737       "org.biojava.bio.symbol.AbstractSymbolList$EditScreener",
738       "org.biojava.bio.seq.io.EmblFileFormer",
739       "org.biojava.utils.ListTools$5",
740       "net.sf.cglib.core.CodeGenerationException",
741       "org.biojava.bio.seq.Frame",
742       "uk.ac.sanger.artemis.chado.ChadoTransaction",
743       "org.biojava.utils.AssertionFailure",
744       "uk.ac.sanger.artemis.FeaturePredicate",
745       "uk.ac.sanger.artemis.Logger",
746       "org.biojava.bio.seq.IsTopLevel",
747       "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl",
748       "com.ibatis.sqlmap.client.SqlMapSession",
749       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotEmptyTagHandler",
750       "org.gmod.schema.sequence.FeatureSynonym",
751       "org.apache.log4j.spi.LoggingEvent",
752       "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol",
753       "com.ibatis.sqlmap.engine.mapping.statement.CachingStatement",
754       "uk.ac.sanger.artemis.io.QualifierLazyLoading",
755       "org.biojava.bio.symbol.FuzzyLocation$AverageRangeResolver",
756       "uk.ac.sanger.artemis.util.DatabaseDocument",
757       "org.biojava.bio.seq.io.GAMEFormat",
758       "uk.ac.sanger.artemis.FeatureEnumeration",
759       "net.sf.cglib.asm.Label",
760       "org.biojava.bio.symbol.AbstractSymbolList",
761       "uk.ac.sanger.artemis.io.StreamFeatureTable",
762       "org.biojava.bio.seq.db.Index",
763       "htsjdk.samtools.reference.FastaSequenceIndex",
764       "org.gmod.schema.dao.PubDaoI",
765       "org.biojava.bio.symbol.RangeLocation"
766     );
767   }
768 
resetClasses()769   private static void resetClasses() {
770     org.evosuite.runtime.classhandling.ClassResetter.getInstance().setClassLoader(IndexFastaStream_ESTest_scaffolding.class.getClassLoader());
771 
772     org.evosuite.runtime.classhandling.ClassStateSupport.resetClasses(
773       "uk.ac.sanger.artemis.io.LineGroup",
774       "htsjdk.samtools.reference.ReferenceSequenceFileFactory$1",
775       "htsjdk.samtools.reference.ReferenceSequenceFileFactory",
776       "org.apache.log4j.Category",
777       "org.apache.log4j.Logger",
778       "org.apache.log4j.Priority",
779       "org.apache.log4j.Level",
780       "org.apache.log4j.or.RendererMap",
781       "org.apache.log4j.helpers.OptionConverter",
782       "org.apache.log4j.helpers.Loader",
783       "org.apache.log4j.helpers.LogLog",
784       "org.apache.log4j.PropertyConfigurator",
785       "org.apache.log4j.LogManager",
786       "org.apache.log4j.CategoryKey",
787       "org.apache.log4j.ProvisionNode",
788       "uk.ac.sanger.artemis.util.DatabaseDocument",
789       "uk.ac.sanger.artemis.util.StringVector",
790       "uk.ac.sanger.artemis.components.Splash",
791       "uk.ac.sanger.artemis.util.FastVector",
792       "uk.ac.sanger.artemis.io.KeyVector",
793       "uk.ac.sanger.artemis.io.Key",
794       "uk.ac.sanger.artemis.io.QualifierInfo",
795       "uk.ac.sanger.artemis.ExternalProgram",
796       "uk.ac.sanger.artemis.Options",
797       "uk.ac.sanger.artemis.io.PublicDBDocumentEntry",
798       "uk.ac.sanger.artemis.io.FeatureVector",
799       "uk.ac.sanger.artemis.util.DatabaseLocationParser",
800       "org.apache.log4j.MDC",
801       "uk.ac.sanger.artemis.chado.GmodDAO",
802       "uk.ac.sanger.artemis.chado.IBatisDAO",
803       "uk.ac.sanger.artemis.chado.SqlMapClientWrapper",
804       "com.ibatis.common.resources.Resources",
805       "com.ibatis.common.beans.ComplexBeanProbe",
806       "com.ibatis.common.beans.GenericProbe",
807       "com.ibatis.common.beans.ProbeFactory",
808       "com.ibatis.sqlmap.engine.config.SqlMapConfiguration",
809       "com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate",
810       "com.ibatis.sqlmap.engine.execution.SqlExecutor",
811       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory$1",
812       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory",
813       "com.ibatis.sqlmap.engine.type.UnknownTypeHandler",
814       "com.ibatis.sqlmap.engine.type.DateTypeHandler",
815       "com.ibatis.sqlmap.engine.type.DateOnlyTypeHandler",
816       "com.ibatis.sqlmap.engine.type.TimeOnlyTypeHandler",
817       "com.ibatis.sqlmap.engine.type.SqlDateTypeHandler",
818       "com.ibatis.sqlmap.engine.type.SqlTimeTypeHandler",
819       "com.ibatis.sqlmap.engine.type.SqlTimestampTypeHandler",
820       "com.ibatis.sqlmap.engine.exchange.ComplexDataExchange",
821       "com.ibatis.common.logging.LogFactory",
822       "org.apache.commons.logging.impl.Log4JLogger",
823       "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl",
824       "com.ibatis.sqlmap.engine.builder.xml.SqlMapClasspathEntityResolver",
825       "uk.ac.sanger.artemis.io.BioJavaFeature",
826       "org.postgresql.largeobject.LargeObject",
827       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry",
828       "uk.ac.sanger.artemis.util.CacheHashMap",
829       "uk.ac.sanger.artemis.util.ByteBuffer",
830       "com.ibatis.common.beans.ClassInfo",
831       "com.ibatis.sqlmap.engine.accessplan.AccessPlanFactory",
832       "com.ibatis.common.jdbc.SimpleDataSource",
833       "org.postgresql.Driver",
834       "com.ibatis.sqlmap.engine.mapping.result.ResultMap",
835       "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange",
836       "net.sf.cglib.core.TypeUtils",
837       "net.sf.cglib.asm.Type",
838       "net.sf.cglib.core.KeyFactory",
839       "net.sf.cglib.core.AbstractClassGenerator",
840       "net.sf.cglib.core.KeyFactory$Generator",
841       "net.sf.cglib.core.DefaultGeneratorStrategy",
842       "net.sf.cglib.core.DefaultNamingPolicy",
843       "net.sf.cglib.asm.ClassWriter",
844       "net.sf.cglib.core.DebuggingClassWriter",
845       "net.sf.cglib.core.ClassEmitter",
846       "net.sf.cglib.core.ReflectUtils",
847       "net.sf.cglib.core.EmitUtils",
848       "net.sf.cglib.core.Constants",
849       "net.sf.cglib.core.CodeEmitter",
850       "net.sf.cglib.asm.Frame",
851       "net.sf.cglib.asm.ClassReader",
852       "net.sf.cglib.core.ClassNameReader$EarlyExitException",
853       "net.sf.cglib.core.ClassNameReader",
854       "net.sf.cglib.beans.BulkBean",
855       "net.sf.cglib.beans.BulkBean$Generator",
856       "net.sf.cglib.beans.BulkBeanEmitter",
857       "com.ibatis.sqlmap.engine.type.JdbcTypeRegistry",
858       "com.ibatis.sqlmap.engine.mapping.parameter.InlineParameterMapParser",
859       "com.ibatis.sqlmap.engine.builder.xml.XMLSqlSource",
860       "com.ibatis.sqlmap.engine.config.MappedStatementConfig",
861       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.DynamicSql",
862       "com.ibatis.sqlmap.engine.mapping.sql.simple.SimpleDynamicSql",
863       "com.ibatis.sqlmap.engine.cache.CacheKey",
864       "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMapping",
865       "com.ibatis.sqlmap.engine.cache.CacheModel",
866       "com.ibatis.sqlmap.engine.accessplan.ComplexAccessPlan",
867       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.ConditionalTagHandler",
868       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEmptyTagHandler",
869       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNullTagHandler",
870       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsPropertyAvailableTagHandler",
871       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateTagHandler",
872       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagHandlerFactory",
873       "com.ibatis.sqlmap.engine.config.ParameterMapConfig",
874       "com.ibatis.common.beans.ProbeException",
875       "com.ibatis.sqlmap.engine.accessplan.PropertyAccessPlan",
876       "net.sf.cglib.beans.BulkBeanException",
877       "uk.ac.sanger.artemis.ChangeEvent",
878       "uk.ac.sanger.artemis.EntryGroupChangeEvent",
879       "uk.ac.sanger.artemis.io.SimpleDocumentFeature",
880       "uk.ac.sanger.artemis.io.PublicDBStreamFeature",
881       "uk.ac.sanger.artemis.io.LocationParseNodeVector",
882       "uk.ac.sanger.artemis.io.LocationParseNode",
883       "uk.ac.sanger.artemis.io.QualifierVector",
884       "org.biojava.bio.seq.io.FastaFormat",
885       "uk.ac.sanger.artemis.io.FeatureTree",
886       "com.ibatis.common.xml.NodeletException",
887       "org.biojava.bio.AbstractAnnotation",
888       "org.biojava.bio.SimpleAnnotation",
889       "org.biojava.bio.seq.SimpleFeatureRealizer",
890       "org.biojava.bio.seq.impl.FeatureImpl$1",
891       "org.biojava.bio.seq.impl.FeatureImpl",
892       "org.biojava.bio.symbol.AlphabetManager$GapSymbol",
893       "org.biojava.bio.symbol.AlphabetManager$SizeQueen",
894       "org.biojava.bio.symbol.IntegerAlphabet",
895       "org.biojava.bio.symbol.DoubleAlphabet",
896       "org.biojava.bio.symbol.SimpleSymbol",
897       "org.biojava.bio.symbol.AbstractSimpleBasisSymbol",
898       "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol",
899       "org.biojava.utils.ChangeType",
900       "org.biojava.bio.EmptyAnnotation",
901       "org.biojava.bio.Annotation",
902       "org.biojava.bio.symbol.EmptyAlphabet",
903       "org.biojava.bio.symbol.Alphabet",
904       "org.biojava.utils.ListTools",
905       "org.biojava.utils.SingletonList",
906       "org.biojava.bio.SmallAnnotation",
907       "org.biojava.utils.lsid.LifeScienceIdentifier",
908       "org.biojava.utils.SmallMap",
909       "org.biojava.bio.symbol.AlphabetManager$WellKnownBasisSymbol",
910       "org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol",
911       "org.biojava.bio.symbol.FundamentalAtomicSymbol",
912       "org.biojava.utils.ChangeListener",
913       "org.biojava.utils.ChangeSupport",
914       "org.biojava.bio.Annotatable",
915       "org.biojava.bio.symbol.AbstractAlphabet",
916       "org.biojava.bio.symbol.SingletonAlphabet",
917       "org.biojava.bio.symbol.SimpleAlphabet",
918       "org.biojava.bio.symbol.AlphabetManager$WellKnownAlphabet",
919       "org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper",
920       "org.biojava.bio.seq.io.CharacterTokenization",
921       "org.biojava.bio.symbol.SimpleBasisSymbol",
922       "org.biojava.bio.seq.io.AlternateTokenization",
923       "org.biojava.bio.symbol.AlphabetManager",
924       "org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper",
925       "org.biojava.bio.symbol.SimpleSymbolList",
926       "org.biojava.bio.seq.io.SymbolTokenization",
927       "org.biojava.bio.symbol.SimpleReversibleTranslationTable",
928       "org.biojava.bio.symbol.SimpleCrossProductAlphabet",
929       "org.biojava.utils.ListTools$Triplet",
930       "org.biojava.bio.symbol.SimpleAtomicSymbol",
931       "org.biojava.bio.seq.io.WordTokenization",
932       "org.biojava.bio.seq.io.NameTokenization",
933       "org.biojava.bio.symbol.SimpleManyToOneTranslationTable",
934       "org.biojava.bio.symbol.SimpleGeneticCodeTable",
935       "org.biojava.bio.symbol.AbstractSymbolList$ListView",
936       "org.biojava.bio.BioException",
937       "org.biojava.bio.symbol.IllegalSymbolException",
938       "org.biojava.bio.BioError",
939       "org.biojava.bio.seq.RNATools",
940       "org.biojava.bio.seq.DNATools",
941       "uk.ac.sanger.artemis.io.Packing",
942       "uk.ac.sanger.artemis.sequence.Bases",
943       "uk.ac.sanger.artemis.sequence.Strand",
944       "org.biojava.bio.seq.Feature$Template",
945       "org.biojava.bio.seq.StrandedFeature$Template",
946       "org.biojava.bio.molbio.RestrictionSite$Template",
947       "org.biojava.bio.seq.impl.SimpleFeature",
948       "org.biojava.bio.seq.impl.SimpleStrandedFeature",
949       "org.biojava.bio.seq.impl.SimpleRestrictionSite",
950       "org.biojava.bio.seq.io.GAMEFormat",
951       "org.biojava.bio.seq.db.IDMaker$ByURN",
952       "org.biojava.bio.seq.db.IDMaker$ByName",
953       "org.biojava.bio.seq.db.IDMaker",
954       "org.biojava.bio.seq.db.BioIndex",
955       "org.biojava.bio.program.phred.PhredFormat",
956       "uk.ac.sanger.artemis.util.OutOfRangeException",
957       "org.biojava.bio.seq.io.SequenceBuilderBase",
958       "org.biojava.bio.seq.io.SimpleSequenceBuilder$SSBFactory",
959       "org.biojava.bio.seq.io.SimpleSequenceBuilder",
960       "org.biojava.bio.seq.io.ChunkedSymbolListFactory",
961       "org.biojava.bio.symbol.EmptySymbolList",
962       "org.biojava.bio.seq.impl.SimpleSequence",
963       "uk.ac.sanger.artemis.components.filetree.RemoteFileNode",
964       "org.biojava.bio.seq.io.GenbankFormat",
965       "org.biojava.bio.seq.io.GenpeptFormat",
966       "org.biojava.bio.seq.io.SimpleAssemblyBuilder$SSBFactory",
967       "org.biojava.bio.seq.io.SimpleAssemblyBuilder",
968       "uk.ac.sanger.artemis.io.GFFStreamFeature",
969       "uk.ac.sanger.artemis.io.ReadFormatException",
970       "uk.ac.sanger.artemis.io.LocationParseException",
971       "org.biojava.bio.seq.MergeFeatureHolder",
972       "org.biojava.utils.ChangeVetoException",
973       "uk.ac.sanger.artemis.io.EntryInformationException",
974       "uk.ac.sanger.artemis.components.filetree.FileList",
975       "com.sshtools.j2ssh.sftp.FileAttributes",
976       "uk.ac.sanger.artemis.io.RangeVector",
977       "org.biojava.bio.seq.io.GenbankXmlFormat",
978       "org.biojava.bio.seq.io.EmblProcessor",
979       "org.biojava.bio.seq.io.FeatureTableParser",
980       "org.biojava.bio.seq.StrandedFeature$Strand",
981       "org.biojava.bio.seq.StrandedFeature",
982       "org.biojava.bio.seq.io.EmblLikeFormat",
983       "org.biojava.bio.seq.ComponentFeature$Template",
984       "org.biojava.bio.seq.io.AbstractGenEmblFileFormer",
985       "org.biojava.bio.seq.db.HashSequenceDB",
986       "org.biojava.bio.seq.db.IllegalIDException"
987     );
988   }
989 }
990