/**
 * Scaffolding file used to store all the setups needed to run 
 * tests automatically generated by EvoSuite
 * Wed Sep 19 21:05:08 GMT 2018
 */

package uk.ac.sanger.artemis;

import org.evosuite.runtime.annotation.EvoSuiteClassExclude;
import org.junit.BeforeClass;
import org.junit.Before;
import org.junit.After;
import org.junit.AfterClass;
import org.evosuite.runtime.sandbox.Sandbox;
import org.evosuite.runtime.sandbox.Sandbox.SandboxMode;

@EvoSuiteClassExclude
public class ExternalProgram_ESTest_scaffolding {

  @org.junit.Rule 
  public org.evosuite.runtime.vnet.NonFunctionalRequirementRule nfr = new org.evosuite.runtime.vnet.NonFunctionalRequirementRule();

  private static final java.util.Properties defaultProperties = (java.util.Properties) java.lang.System.getProperties().clone(); 

  private org.evosuite.runtime.thread.ThreadStopper threadStopper =  new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);


  @BeforeClass 
  public static void initEvoSuiteFramework() { 
    org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.ExternalProgram"; 
    org.evosuite.runtime.GuiSupport.initialize(); 
    org.evosuite.runtime.RuntimeSettings.maxNumberOfThreads = 100; 
    org.evosuite.runtime.RuntimeSettings.maxNumberOfIterationsPerLoop = 10000; 
    org.evosuite.runtime.RuntimeSettings.mockSystemIn = true; 
    org.evosuite.runtime.RuntimeSettings.sandboxMode = org.evosuite.runtime.sandbox.Sandbox.SandboxMode.RECOMMENDED; 
    org.evosuite.runtime.sandbox.Sandbox.initializeSecurityManagerForSUT(); 
    org.evosuite.runtime.classhandling.JDKClassResetter.init();
    setSystemProperties();
    initializeClasses();
    org.evosuite.runtime.Runtime.getInstance().resetRuntime(); 
  } 

  @AfterClass 
  public static void clearEvoSuiteFramework(){ 
    Sandbox.resetDefaultSecurityManager(); 
    java.lang.System.setProperties((java.util.Properties) defaultProperties.clone()); 
  } 

  @Before 
  public void initTestCase(){ 
    threadStopper.storeCurrentThreads();
    threadStopper.startRecordingTime();
    org.evosuite.runtime.jvm.ShutdownHookHandler.getInstance().initHandler(); 
    org.evosuite.runtime.sandbox.Sandbox.goingToExecuteSUTCode(); 
    setSystemProperties(); 
    org.evosuite.runtime.GuiSupport.setHeadless(); 
    org.evosuite.runtime.Runtime.getInstance().resetRuntime(); 
    org.evosuite.runtime.agent.InstrumentingAgent.activate(); 
  } 

  @After 
  public void doneWithTestCase(){ 
    threadStopper.killAndJoinClientThreads();
    org.evosuite.runtime.jvm.ShutdownHookHandler.getInstance().safeExecuteAddedHooks(); 
    org.evosuite.runtime.classhandling.JDKClassResetter.reset(); 
    resetClasses(); 
    org.evosuite.runtime.sandbox.Sandbox.doneWithExecutingSUTCode(); 
    org.evosuite.runtime.agent.InstrumentingAgent.deactivate(); 
    org.evosuite.runtime.GuiSupport.restoreHeadlessMode(); 
  } 

  public static void setSystemProperties() {
 
    java.lang.System.setProperties((java.util.Properties) defaultProperties.clone()); 
    java.lang.System.setProperty("file.encoding", "UTF-8"); 
    java.lang.System.setProperty("java.awt.headless", "true"); 
    java.lang.System.setProperty("java.io.tmpdir", "/var/folders/r3/l648tx8s7hn8ppds6z2bk5cc000h2n/T/"); 
    java.lang.System.setProperty("user.country", "GB"); 
    java.lang.System.setProperty("user.dir", "/Users/kp11/workspace/applications/Artemis-build-ci/Artemis"); 
    java.lang.System.setProperty("user.home", "/Users/kp11"); 
    java.lang.System.setProperty("user.language", "en"); 
    java.lang.System.setProperty("user.name", "kp11"); 
    java.lang.System.setProperty("user.timezone", ""); 
    java.lang.System.setProperty("log4j.configuration", "SUT.log4j.properties"); 
  }

  private static void initializeClasses() {
    org.evosuite.runtime.classhandling.ClassStateSupport.initializeClasses(ExternalProgram_ESTest_scaffolding.class.getClassLoader() ,
      "org.biojava.bio.seq.AcceptNoneFilter",
      "com.ibatis.common.jdbc.SimpleDataSource$SimplePooledConnection",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.ConditionalTagHandler",
      "org.biojava.bio.seq.io.SymbolTokenization$TokenType",
      "org.apache.log4j.helpers.PatternConverter",
      "org.biojava.bio.seq.ByHierarchy",
      "com.ibatis.sqlmap.client.extensions.ParameterSetter",
      "uk.ac.sanger.artemis.OptionChangeEvent",
      "uk.ac.sanger.artemis.components.genebuilder.JExtendedComboBox",
      "com.ibatis.common.xml.Nodelet",
      "uk.ac.sanger.artemis.components.BasePlotGroup",
      "com.sshtools.j2ssh.authentication.PasswordChangePrompt",
      "com.ibatis.sqlmap.engine.type.BlobTypeHandlerCallback",
      "com.sshtools.j2ssh.SshClient",
      "uk.ac.sanger.artemis.EntryChangeListener",
      "uk.ac.sanger.artemis.plot.CoilFeatureAlgorithm",
      "org.biojava.utils.ListTools$Triplet",
      "uk.ac.sanger.artemis.sequence.AminoAcidSequence",
      "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$AlphabetHandler$1",
      "uk.ac.sanger.artemis.Selectable",
      "com.sshtools.j2ssh.transport.ServiceState",
      "com.ibatis.common.xml.NodeletParser",
      "com.ibatis.sqlmap.engine.datasource.DataSourceFactory",
      "net.sf.cglib.core.LocalVariablesSorter$1",
      "org.apache.log4j.spi.Filter",
      "uk.ac.sanger.artemis.io.RangeVector",
      "org.biojava.bio.seq.io.CharacterTokenization",
      "uk.ac.sanger.artemis.plot.NcAlgorithm",
      "com.ibatis.sqlmap.engine.mapping.statement.UpdateStatement",
      "uk.ac.sanger.artemis.util.StringVector",
      "net.sf.cglib.core.AbstractClassGenerator",
      "uk.ac.sanger.artemis.io.GenbankDocumentEntry",
      "com.sshtools.j2ssh.transport.publickey.InvalidSshKeySignatureException",
      "com.sshtools.j2ssh.transport.AsyncService",
      "org.gmod.schema.sequence.Synonym",
      "com.ibatis.common.beans.SetFieldInvoker",
      "org.biojava.bio.symbol.PointLocation",
      "org.gmod.schema.sequence.FeatureCvTermProp",
      "org.biojava.bio.seq.io.SequenceBuilderFactory",
      "uk.ac.sanger.artemis.sequence.MarkerRange",
      "org.biojava.utils.Changeable",
      "org.biojava.bio.symbol.EmptyLocation",
      "uk.ac.sanger.artemis.FeaturePatternPredicate",
      "com.ibatis.common.util.PaginatedList",
      "org.biojava.utils.stax.DelegationManager",
      "org.biojava.bio.seq.StrandedFeature",
      "net.sf.cglib.core.ReflectUtils",
      "org.biojava.bio.symbol.IllegalAlphabetException",
      "com.sshtools.j2ssh.connection.SshMsgChannelRequest",
      "uk.ac.sanger.artemis.sequence.MarkerInternal",
      "com.sshtools.j2ssh.connection.ChannelEventListener",
      "org.biojava.bio.symbol.AbstractTranslationTable",
      "org.gmod.schema.dao.GeneralDaoI",
      "net.sf.cglib.core.LocalVariablesSorter",
      "org.apache.log4j.helpers.OptionConverter",
      "org.apache.log4j.helpers.FormattingInfo",
      "com.ibatis.sqlmap.client.SqlMapExecutor",
      "org.biojava.bio.symbol.Edit",
      "com.ibatis.sqlmap.client.SqlMapException",
      "uk.ac.sanger.artemis.io.MiscLineGroup",
      "org.apache.log4j.pattern.NameAbbreviator$MaxElementAbbreviator",
      "org.biojava.bio.seq.db.IllegalIDException",
      "org.hsqldb.lib.Iterator",
      "uk.ac.sanger.artemis.io.InvalidRelationException",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEqualTagHandler",
      "org.biojava.bio.seq.impl.FeatureImpl$1",
      "org.apache.log4j.helpers.PatternParser",
      "com.sshtools.j2ssh.transport.InvalidMessageException",
      "org.biojava.bio.Annotation",
      "org.biojava.bio.symbol.IntegerAlphabet$IntegerSymbol",
      "org.apache.log4j.Category",
      "uk.ac.sanger.artemis.io.LocationParseException",
      "org.biojava.bio.seq.io.StreamParser",
      "org.biojava.bio.symbol.SimpleSymbol",
      "com.sshtools.j2ssh.sftp.SftpFileOutputStream",
      "org.hsqldb.lib.FileAccess",
      "net.sf.cglib.core.ClassInfo",
      "uk.ac.sanger.artemis.util.URLDocument",
      "org.biojava.utils.ChangeEvent",
      "uk.ac.sanger.artemis.components.variant.AbstractVCFReader",
      "org.gmod.schema.pub.Pub",
      "uk.ac.sanger.artemis.io.ChadoCanonicalGene",
      "net.sf.cglib.core.EmitUtils$9",
      "net.sf.cglib.core.EmitUtils$8",
      "net.sf.cglib.core.EmitUtils$7",
      "org.biojava.bio.symbol.SimpleCrossProductAlphabet",
      "org.biojava.bio.seq.DNATools",
      "com.sshtools.j2ssh.transport.TransportProtocolState",
      "com.sshtools.j2ssh.forwarding.ForwardingListener",
      "com.sshtools.j2ssh.connection.ChannelInputStream",
      "org.biojava.bio.seq.RNATools$1",
      "org.apache.log4j.helpers.PatternParser$NamedPatternConverter",
      "uk.ac.sanger.artemis.plot.CodonUsageWeight",
      "net.sf.cglib.core.ClassNameReader$1",
      "org.biojava.bio.BioRuntimeException",
      "com.ibatis.sqlmap.engine.type.ByteTypeHandler",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.BaseTagHandler",
      "org.biojava.bio.seq.AcceptAllFilter",
      "org.biojava.bio.seq.homol.SimilarityPairFeature",
      "com.sshtools.j2ssh.forwarding.ForwardingClient",
      "org.gmod.schema.utils.propinterface.PropertyI",
      "uk.ac.sanger.artemis.components.DisplayAdjustmentEvent",
      "uk.ac.sanger.artemis.chado.FeatureForUpdatingResidues",
      "org.apache.log4j.spi.AppenderAttachable",
      "com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate",
      "uk.ac.sanger.artemis.io.GFF3AttributeAggregator",
      "com.sshtools.j2ssh.sftp.SshFxpRename",
      "org.postgresql.Driver$1",
      "uk.ac.sanger.artemis.util.PushBackException",
      "com.ibatis.sqlmap.engine.exchange.DataExchange",
      "com.ibatis.sqlmap.engine.mapping.sql.SqlChild",
      "org.biojava.utils.ParseErrorListener",
      "com.sshtools.j2ssh.connection.IOChannel",
      "org.apache.log4j.pattern.LoggingEventPatternConverter",
      "org.biojava.utils.SingletonList",
      "org.biojava.bio.seq.db.BioIndex$IndexFileAsList",
      "com.sshtools.j2ssh.DirectoryOperation",
      "org.biojava.bio.BioException",
      "uk.ac.sanger.artemis.SimpleEntryGroup$FeatureEnumerator",
      "com.ibatis.sqlmap.engine.builder.xml.XmlParserState",
      "net.sf.cglib.asm.AnnotationVisitor",
      "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange",
      "com.sshtools.j2ssh.sftp.SftpFileInputStream",
      "com.ibatis.sqlmap.engine.builder.xml.XMLSqlSource",
      "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMapping",
      "org.apache.log4j.pattern.ThreadPatternConverter",
      "org.biojava.bio.seq.FramedFeature$Template",
      "com.ibatis.sqlmap.engine.exchange.BaseDataExchange",
      "net.sf.cglib.asm.ClassVisitor",
      "com.sshtools.j2ssh.connection.SshMsgChannelData",
      "net.sf.cglib.core.ClassEmitter$FieldInfo",
      "uk.ac.sanger.artemis.util.WorkingGZIPInputStream",
      "com.ibatis.sqlmap.engine.mapping.statement.MappedStatement",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotPropertyAvailableTagHandler",
      "org.biojava.utils.ChangeType$1",
      "org.apache.log4j.pattern.MethodLocationPatternConverter",
      "org.biojava.bio.seq.io.AbstractGenEmblFileFormer",
      "com.sshtools.j2ssh.connection.SshMsgRequestSuccess",
      "org.postgresql.util.SharedTimer",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsLessThanTagHandler",
      "uk.ac.sanger.artemis.SelectionChangeEvent",
      "org.biojava.utils.ChangeAdapter",
      "uk.ac.sanger.artemis.plot.BaseAlgorithm",
      "org.biojava.bio.symbol.SoftMaskedAlphabet$1",
      "uk.ac.sanger.artemis.io.Key",
      "com.ibatis.sqlmap.engine.transaction.Transaction",
      "com.sshtools.j2ssh.connection.ChannelFactory",
      "uk.ac.sanger.artemis.io.FeatureHeader",
      "net.sf.cglib.beans.BulkBeanEmitter",
      "uk.ac.sanger.artemis.components.filetree.FileList",
      "com.sshtools.j2ssh.connection.ConnectionProtocol",
      "com.ibatis.common.xml.NodeletParser$1",
      "uk.ac.sanger.artemis.chado.Graph",
      "com.ibatis.sqlmap.engine.type.ClobTypeHandlerCallback",
      "org.apache.log4j.WriterAppender",
      "uk.ac.sanger.artemis.plot.ATDeviationAlgorithm",
      "org.biojava.bio.seq.io.WordTokenization",
      "org.apache.log4j.varia.DenyAllFilter",
      "uk.ac.sanger.artemis.ChangeListener",
      "com.ibatis.sqlmap.engine.transaction.jdbc.JdbcTransactionConfig",
      "uk.ac.sanger.artemis.io.FeatureTree",
      "net.sf.cglib.core.KeyFactory",
      "org.biojava.bio.seq.impl.SimpleFeature",
      "org.apache.log4j.pattern.PropertiesPatternConverter",
      "org.postgresql.util.ExpressionProperties",
      "com.ibatis.sqlmap.engine.datasource.SimpleDataSourceFactory",
      "org.biojava.bio.seq.GappedSequence",
      "net.sf.cglib.core.EmitUtils",
      "org.biojava.bio.symbol.Alignment",
      "org.apache.log4j.MDC",
      "org.biojava.bio.seq.impl.SimpleRestrictionSite",
      "net.sf.cglib.core.CollectionUtils",
      "net.sf.cglib.core.TypeUtils",
      "com.ibatis.sqlmap.engine.cache.lru.LruCacheController",
      "org.gmod.schema.dao.SequenceDaoI",
      "uk.ac.sanger.artemis.sequence.SequenceChangeEvent",
      "com.ibatis.sqlmap.engine.mapping.result.ResultMapping",
      "com.sshtools.j2ssh.forwarding.ForwardingClient$ClientForwardingListener",
      "com.sshtools.j2ssh.sftp.SshFxpReadDir",
      "org.biojava.bio.seq.StrandedFeature$Template",
      "org.biojava.bio.seq.impl.AssembledSymbolList",
      "org.biojava.bio.seq.db.emblcd.DivisionLkpReader",
      "com.sshtools.j2ssh.transport.HostKeyVerification",
      "org.biojava.bio.symbol.Symbol",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotParameterPresentTagHandler",
      "org.gmod.schema.sequence.FeatureCvTerm",
      "org.biojava.bio.seq.FramedFeature",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsParameterPresentTagHandler",
      "com.ibatis.sqlmap.engine.config.MappedStatementConfig",
      "org.biojava.utils.ListTools",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEmptyTagHandler",
      "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$AlphabetHandler",
      "uk.ac.sanger.artemis.io.DatabaseStreamFeature",
      "uk.ac.sanger.artemis.util.CacheHashMap",
      "com.ibatis.common.xml.NodeletException",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagHandler",
      "com.sshtools.j2ssh.forwarding.XDisplay",
      "net.sf.cglib.core.EmitUtils$ParameterTyper",
      "net.sf.cglib.asm.ByteVector",
      "org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper",
      "uk.ac.sanger.artemis.io.LocationLexer",
      "com.sshtools.j2ssh.connection.InvalidChannelException",
      "net.sf.cglib.beans.BulkBean$BulkBeanKey",
      "com.sshtools.j2ssh.transport.MessageNotAvailableException",
      "uk.ac.sanger.artemis.io.StreamSequence",
      "uk.ac.sanger.artemis.io.GFF3AttributeBuilder",
      "com.ibatis.sqlmap.engine.config.SqlMapConfiguration",
      "uk.ac.sanger.artemis.sequence.Bases",
      "uk.ac.sanger.artemis.components.LogViewer",
      "com.ibatis.common.beans.MethodInvoker",
      "com.sshtools.j2ssh.forwarding.ForwardingConfiguration",
      "org.biojava.bio.symbol.AbstractRangeLocation",
      "com.sshtools.j2ssh.transport.SshMessage",
      "uk.ac.sanger.artemis.j2ssh.SshLogin",
      "uk.ac.sanger.artemis.util.Document",
      "org.biojava.bio.seq.io.ParseException",
      "uk.ac.sanger.artemis.components.FileViewer",
      "org.biojava.bio.seq.FeatureRealizer",
      "uk.ac.sanger.artemis.FeaturePredicateVector",
      "org.biojava.bio.seq.io.SequenceFormat",
      "net.sf.cglib.core.ProcessArrayCallback",
      "uk.ac.sanger.artemis.plot.ICDIAlgorithm",
      "org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess",
      "net.sf.cglib.asm.ClassReader",
      "org.apache.log4j.spi.LoggerRepository",
      "com.sshtools.j2ssh.transport.TransportProtocolException",
      "com.ibatis.common.beans.ProbeException",
      "com.ibatis.sqlmap.engine.impl.ExtendedSqlMapClient",
      "com.ibatis.common.beans.Probe",
      "uk.ac.sanger.artemis.chado.DbSqlConfig",
      "com.sshtools.j2ssh.connection.SshMsgChannelSuccess",
      "uk.ac.sanger.artemis.io.GFFMisc",
      "com.ibatis.sqlmap.engine.scope.StatementScope",
      "uk.ac.sanger.artemis.chado.IBatisDAO",
      "org.biojava.bio.seq.db.BioIndex$Commitable",
      "uk.ac.sanger.artemis.plot.GCDeviationAlgorithm",
      "com.sshtools.j2ssh.sftp.SshFxpMkdir",
      "org.apache.log4j.pattern.DatePatternConverter$DefaultZoneDateFormat",
      "uk.ac.sanger.artemis.io.FuzzyRange",
      "org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol",
      "org.biojava.bio.symbol.AbstractReversibleTranslationTable",
      "org.biojava.bio.seq.io.SeqIOAdapter",
      "org.biojava.bio.symbol.SimpleGeneticCodeTable",
      "com.ibatis.sqlmap.engine.type.UnknownTypeHandler",
      "uk.ac.sanger.artemis.sequence.MarkerChangeListener",
      "org.apache.log4j.helpers.ISO8601DateFormat",
      "org.biojava.bio.seq.db.BioIndex",
      "net.sf.cglib.asm.FieldWriter",
      "com.sshtools.j2ssh.sftp.SftpSubsystemClient",
      "org.biojava.utils.ChangeListener",
      "org.apache.log4j.pattern.PatternParser",
      "uk.ac.sanger.artemis.util.TextDocument",
      "uk.ac.sanger.artemis.GotoEvent",
      "uk.ac.sanger.artemis.components.BasePlot",
      "org.biojava.utils.AbstractChangeable",
      "org.apache.log4j.pattern.FormattingInfo",
      "org.apache.log4j.Layout",
      "uk.ac.sanger.artemis.EntrySourceVector",
      "net.sf.cglib.core.LocalVariablesSorter$State",
      "com.sshtools.j2ssh.forwarding.ForwardingConfigurationException",
      "org.biojava.bio.seq.SimpleAssembly",
      "com.ibatis.sqlmap.engine.config.ResultMapConfig",
      "com.sshtools.j2ssh.sftp.SshFxpReadlink",
      "org.gmod.schema.dao.SchemaDaoI",
      "uk.ac.sanger.artemis.LastSegmentException",
      "org.apache.log4j.pattern.FullLocationPatternConverter",
      "uk.ac.sanger.artemis.ChangeEvent",
      "uk.ac.sanger.artemis.util.OutOfRangeException",
      "com.ibatis.sqlmap.engine.scope.SessionScope",
      "org.postgresql.util.PSQLException",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapConfigParser$10",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapConfigParser$11",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapConfigParser$12",
      "org.biojava.utils.lsid.Identifiable",
      "org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser",
      "net.sf.cglib.core.ClassGenerator",
      "org.apache.log4j.spi.DefaultRepositorySelector",
      "org.biojava.ontology.OntologyException",
      "com.sshtools.j2ssh.connection.ChannelOutputStream",
      "org.biojava.bio.seq.db.BioIndex$ListAsSet",
      "uk.ac.sanger.artemis.io.Sequence",
      "org.biojava.bio.symbol.SoftMaskedAlphabet$CaseSensitiveTokenization",
      "net.sf.cglib.core.ObjectSwitchCallback",
      "org.biojava.utils.bytecode.GeneratedClassLoader",
      "com.ibatis.sqlmap.engine.cache.CacheKey",
      "uk.ac.sanger.artemis.io.Location",
      "org.apache.log4j.pattern.SequenceNumberPatternConverter",
      "org.apache.log4j.or.ObjectRenderer",
      "uk.ac.sanger.artemis.util.DatabaseLocationParser",
      "net.sf.cglib.core.DebuggingClassWriter$1",
      "com.ibatis.sqlmap.engine.mapping.statement.DefaultRowHandler",
      "com.ibatis.sqlmap.engine.type.LongTypeHandler",
      "com.ibatis.sqlmap.engine.type.DateTypeHandler",
      "uk.ac.sanger.artemis.io.StreamFeature",
      "uk.ac.sanger.artemis.util.ReadOnlyException",
      "com.sshtools.j2ssh.transport.publickey.SshPublicKey",
      "com.ibatis.sqlmap.engine.accessplan.MapAccessPlan",
      "uk.ac.sanger.artemis.FilteredEntryGroup$3",
      "uk.ac.sanger.artemis.FilteredEntryGroup$2",
      "uk.ac.sanger.artemis.FilteredEntryGroup$1",
      "uk.ac.sanger.artemis.components.PlotMouseListener",
      "com.sshtools.j2ssh.SshEventAdapter",
      "org.apache.log4j.pattern.DatePatternConverter",
      "uk.ac.sanger.artemis.Feature",
      "uk.ac.sanger.artemis.plot.FeatureAlgorithm",
      "org.biojava.utils.cache.KeyedWeakReference",
      "org.biojava.bio.seq.homol.HomologyFeature$Template",
      "com.sshtools.j2ssh.subsystem.SubsystemChannel",
      "com.ibatis.sqlmap.client.extensions.ResultGetter",
      "com.sshtools.j2ssh.FileTransferProgress",
      "org.apache.log4j.helpers.RelativeTimeDateFormat",
      "com.ibatis.sqlmap.engine.transaction.TransactionManager",
      "org.apache.log4j.spi.LoggerFactory",
      "org.biojava.bio.symbol.DoubleAlphabet$DoubleSymbol",
      "org.biojava.bio.seq.impl.SimpleFramedFeature",
      "org.biojava.bio.seq.io.ReferenceAnnotation",
      "org.apache.log4j.spi.LocationInfo",
      "net.sf.cglib.core.CodeEmitter",
      "org.biojava.bio.seq.FeatureFilter$OnlyChildren",
      "org.biojava.bio.seq.homol.SimilarityPairFeature$Template",
      "uk.ac.sanger.artemis.io.KeyVector",
      "org.postgresql.util.HostSpec",
      "org.biojava.bio.seq.io.SubIntegerTokenization",
      "org.gmod.schema.sequence.FeatureCvTermPub",
      "org.biojava.bio.Annotatable",
      "com.ibatis.sqlmap.engine.mapping.statement.ProcedureStatement",
      "uk.ac.sanger.artemis.io.MSPcrunchEntryInformation",
      "org.biojava.utils.ParseErrorEvent",
      "com.ibatis.sqlmap.engine.mapping.sql.Sql",
      "uk.ac.sanger.artemis.components.FileViewer$2",
      "org.biojava.bio.seq.io.EmblLikeFormat",
      "uk.ac.sanger.artemis.io.UpperInteger",
      "com.sshtools.j2ssh.sftp.SshFxpRead",
      "com.ibatis.common.beans.ClassInfo",
      "org.biojava.bio.seq.SimpleFeatureRealizer$1",
      "org.biojava.utils.stax.StringElementHandlerBase",
      "uk.ac.sanger.artemis.io.FeatureComparator",
      "com.ibatis.sqlmap.engine.config.SqlSource",
      "org.biojava.bio.seq.io.GenpeptFileFormer",
      "org.hsqldb.lib.ObjectComparator",
      "org.biojava.utils.ChangeForwarder$Retyper",
      "com.ibatis.sqlmap.engine.mapping.sql.stat.StaticSql",
      "com.sshtools.j2ssh.session.SessionChannelClient",
      "org.biojava.bio.seq.io.SymbolTokenization",
      "net.sf.cglib.asm.ClassWriter",
      "com.sshtools.j2ssh.SftpClient",
      "com.sshtools.j2ssh.connection.SshMsgChannelWindowAdjust",
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      "org.biojava.bio.seq.impl.SimpleSimilarityPairFeature",
      "uk.ac.sanger.artemis.io.SimpleDocumentEntry$1",
      "com.sshtools.j2ssh.sftp.SshFxpStat",
      "org.biojava.bio.symbol.SimpleSymbolList$SSLIOListener",
      "org.biojava.bio.seq.RemoteFeature$Template",
      "org.apache.log4j.Level",
      "org.apache.log4j.helpers.DateTimeDateFormat",
      "com.sshtools.j2ssh.sftp.SshFxpOpen",
      "org.biojava.bio.symbol.SoftMaskedAlphabet",
      "com.sshtools.j2ssh.authentication.TerminatedStateException",
      "uk.ac.sanger.artemis.io.EntryInformation",
      "htsjdk.samtools.util.BlockCompressedInputStream",
      "org.biojava.bio.seq.io.SeqIOListener",
      "org.biojava.utils.ChangeType",
      "uk.ac.sanger.artemis.io.ReadFormatException",
      "com.sshtools.j2ssh.util.InvalidStateException",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotNullTagHandler",
      "com.sshtools.j2ssh.connection.SshMsgChannelEOF",
      "org.apache.log4j.helpers.PatternParser$BasicPatternConverter",
      "org.gmod.schema.sequence.FeaturePub",
      "com.sshtools.j2ssh.sftp.SshFxpSetStat",
      "com.sshtools.j2ssh.io.ByteArrayReader",
      "com.ibatis.sqlmap.client.SqlMapTransactionManager",
      "org.biojava.bio.symbol.EmptyAlphabet",
      "org.gmod.schema.analysis.AnalysisFeature",
      "org.hsqldb.types.TimestampData",
      "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMap",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTag",
      "org.postgresql.util.ServerErrorMessage",
      "org.gmod.schema.sequence.FeatureRelationship",
      "org.biojava.bio.seq.SimpleFeatureRealizer",
      "uk.ac.sanger.artemis.io.GenbankStreamFeature",
      "com.sshtools.j2ssh.connection.GlobalRequestHandler",
      "net.sf.cglib.beans.BulkBean",
      "org.hsqldb.map.ValuePoolHashMap",
      "org.apache.log4j.helpers.PatternParser$CategoryPatternConverter",
      "com.ibatis.common.logging.Log",
      "org.biojava.bio.symbol.SimpleBasisSymbol",
      "com.ibatis.sqlmap.engine.mapping.result.ResultMap",
      "org.biojava.bio.seq.io.ProteinRefSeqProcessor",
      "org.biojava.bio.seq.DNATools$DNAComplementTranslationTable",
      "uk.ac.sanger.artemis.io.EMBLObject",
      "uk.ac.sanger.artemis.ActionVector",
      "uk.ac.sanger.artemis.sequence.Strand",
      "uk.ac.sanger.artemis.chado.GmodDAO",
      "net.sf.cglib.core.ReflectUtils$4",
      "org.apache.log4j.helpers.NullEnumeration",
      "uk.ac.sanger.artemis.OptionChangeListener",
      "net.sf.cglib.core.ReflectUtils$1",
      "net.sf.cglib.core.ReflectUtils$2",
      "com.sshtools.j2ssh.sftp.SshFxpSymlink",
      "net.sf.cglib.core.ReflectUtils$3",
      "com.ibatis.sqlmap.engine.transaction.IsolationLevel",
      "org.biojava.bio.symbol.LocationComparator",
      "com.sshtools.j2ssh.sftp.SftpFile",
      "com.ibatis.sqlmap.engine.type.ShortTypeHandler",
      "uk.ac.sanger.artemis.util.LargeObjectDocument",
      "uk.ac.sanger.artemis.io.GenbankMisc",
      "uk.ac.sanger.artemis.chado.JdbcDAO",
      "org.biojava.utils.stax.StAXContentHandler",
      "uk.ac.sanger.artemis.util.RemoteFileDocument",
      "uk.ac.sanger.artemis.components.SwingWorker",
      "uk.ac.sanger.artemis.io.PublicDBStreamFeature",
      "net.sf.cglib.core.DefaultGeneratorStrategy",
      "com.ibatis.sqlmap.engine.mapping.statement.StatementType",
      "uk.ac.sanger.artemis.io.FastaStreamSequence",
      "uk.ac.sanger.artemis.io.FeatureEnumeration",
      "org.apache.log4j.helpers.PatternParser$ClassNamePatternConverter",
      "org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper",
      "org.biojava.utils.ChangeForwarder",
      "com.ibatis.common.io.ReaderInputStream",
      "org.biojava.bio.symbol.GappedSymbolList",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapConfigParser$9",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapConfigParser$8",
      "org.gmod.schema.analysis.Analysis",
      "com.ibatis.sqlmap.engine.type.BigDecimalTypeHandler",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapConfigParser$5",
      "com.ibatis.sqlmap.engine.transaction.TransactionConfig",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapConfigParser$4",
      "uk.ac.sanger.artemis.EntryChangeEvent",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapConfigParser$7",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapConfigParser$6",
      "org.biojava.bio.symbol.HashedAlphabetIndex$HashComparator",
      "org.biojava.bio.seq.FeatureFilter",
      "com.sshtools.j2ssh.sftp.SshFxpClose",
      "uk.ac.sanger.artemis.io.EmblDocumentEntry",
      "uk.ac.sanger.artemis.io.DocumentFeature",
      "org.biojava.bio.SimpleAnnotation",
      "org.biojava.bio.symbol.IntegerAlphabet",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotEqualTagHandler",
      "org.hsqldb.DatabaseURL",
      "uk.ac.sanger.artemis.plot.Algorithm",
      "com.ibatis.common.jdbc.SimpleDataSource",
      "org.biojava.bio.seq.impl.FeatureImpl",
      "org.apache.log4j.spi.Configurator",
      "uk.ac.sanger.artemis.io.MSPcrunchStreamFeature",
      "org.biojava.bio.seq.io.GenbankFileFormer",
      "org.gmod.schema.sequence.Feature",
      "org.biojava.bio.symbol.FiniteAlphabet",
      "org.gmod.schema.sequence.FeatureProp",
      "uk.ac.sanger.artemis.io.FeatureTree$FeatureEnumerator",
      "org.gmod.schema.utils.Rankable",
      "com.ibatis.sqlmap.engine.accessplan.ComplexAccessPlan",
      "net.sf.cglib.core.ProcessSwitchCallback",
      "com.ibatis.common.beans.ProbeFactory",
      "uk.ac.sanger.artemis.FeatureVector",
      "uk.ac.sanger.artemis.io.BioJavaSequence",
      "org.biojava.bio.seq.io.SequenceBuilderBase",
      "uk.ac.sanger.artemis.io.EmblStreamSequence",
      "uk.ac.sanger.artemis.SimpleGotoEventSource",
      "org.hsqldb.lib.FileAccess$FileSync",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapConfigParser$1",
      "org.biojava.bio.seq.io.CrossProductTokenization",
      "com.ibatis.sqlmap.engine.scope.ErrorContext",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapConfigParser$3",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapConfigParser$2",
      "org.biojava.bio.seq.io.SequenceBuilderFilter",
      "org.biojava.bio.seq.FeatureHolder",
      "org.biojava.bio.symbol.FundamentalAtomicSymbol",
      "net.sf.cglib.asm.Edge",
      "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler$MappingHandler",
      "org.gmod.schema.dao.OrganismDaoI",
      "com.sshtools.j2ssh.connection.ChannelState",
      "uk.ac.sanger.artemis.FeaturePredicateConjunction",
      "org.apache.log4j.helpers.PatternParser$MDCPatternConverter",
      "uk.ac.sanger.artemis.io.QualifierInfo",
      "org.biojava.utils.Unchangeable",
      "com.ibatis.common.resources.Resources",
      "org.biojava.bio.symbol.FuzzyLocation",
      "com.sshtools.j2ssh.connection.SocketChannel",
      "net.sf.cglib.core.AbstractClassGenerator$Source",
      "org.apache.log4j.LogManager",
      "org.gmod.schema.sequence.FeatureLoc",
      "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler",
      "org.biojava.bio.symbol.AlphabetIndex",
      "org.biojava.bio.seq.db.SimpleIndex",
      "com.ibatis.common.logging.jakarta.JakartaCommonsLoggingImpl",
      "uk.ac.sanger.artemis.j2ssh.SshFileManager",
      "org.biojava.bio.symbol.EmptySymbolList",
      "com.sshtools.j2ssh.subsystem.SubsystemMessageStore",
      "com.ibatis.sqlmap.engine.type.ByteArrayTypeHandler",
      "org.apache.log4j.or.RendererMap",
      "uk.ac.sanger.artemis.ExternalProgram",
      "com.ibatis.sqlmap.engine.exchange.ListDataExchange",
      "org.apache.log4j.pattern.BridgePatternParser",
      "org.biojava.bio.symbol.SoftMaskedAlphabet$MaskingDetector",
      "org.apache.log4j.pattern.ClassNamePatternConverter",
      "uk.ac.sanger.artemis.io.EmblMisc",
      "org.biojava.bio.seq.io.GenbankFormat",
      "com.ibatis.sqlmap.engine.type.SqlDateTypeHandler",
      "uk.ac.sanger.artemis.io.PartialSequence",
      "net.sf.cglib.asm.Handler",
      "uk.ac.sanger.artemis.plot.ScaledChiAlgorithm",
      "uk.ac.sanger.artemis.Entry",
      "org.biojava.bio.seq.io.SmartSequenceBuilder",
      "uk.ac.sanger.artemis.components.genebuilder.GeneUtils",
      "org.biojava.utils.ClassTools",
      "org.biojava.bio.seq.db.IndexStore",
      "net.sf.cglib.core.Customizer",
      "uk.ac.sanger.artemis.io.EmblStreamFeature",
      "org.biojava.utils.cache.WeakValueHashMap",
      "org.biojava.bio.symbol.IllegalSymbolException",
      "uk.ac.sanger.artemis.ExternalProgramVector",
      "com.ibatis.sqlmap.engine.type.TypeHandler",
      "org.apache.log4j.helpers.PatternParser$LocationPatternConverter",
      "com.ibatis.sqlmap.engine.mapping.parameter.InlineParameterMapParser",
      "uk.ac.sanger.artemis.util.InputStreamProgressListener",
      "uk.ac.sanger.artemis.io.LocationLexer$TokenEnumeration",
      "org.apache.log4j.helpers.OnlyOnceErrorHandler",
      "org.biojava.bio.symbol.TranslationTable",
      "org.biojava.bio.symbol.CrossProductAlphabetIndex",
      "org.biojava.bio.symbol.SimpleSymbolList$1",
      "com.sshtools.j2ssh.connection.ChannelDataWindow",
      "com.sshtools.j2ssh.sftp.FileAttributes",
      "com.ibatis.sqlmap.engine.execution.BatchException",
      "com.ibatis.sqlmap.engine.builder.xml.SqlStatementParser",
      "org.biojava.bio.seq.impl.SimpleStrandedFeature",
      "uk.ac.sanger.artemis.sequence.Marker",
      "org.biojava.bio.symbol.DoubleAlphabet",
      "uk.ac.sanger.artemis.plot.CSCSAlgorithm",
      "org.apache.log4j.ProvisionNode",
      "com.sshtools.j2ssh.TransferCancelledException",
      "uk.ac.sanger.artemis.io.GFFDocumentEntry",
      "uk.ac.sanger.artemis.io.GFFStreamFeature",
      "org.biojava.bio.symbol.AtomicSymbol",
      "org.apache.log4j.pattern.LineLocationPatternConverter",
      "com.sshtools.j2ssh.transport.MessageStoreEOFException",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsGreaterEqualTagHandler",
      "org.apache.log4j.helpers.PatternParser$LiteralPatternConverter",
      "com.ibatis.common.beans.Invoker",
      "net.sf.cglib.asm.Type",
      "com.ibatis.sqlmap.engine.accessplan.EnhancedPropertyAccessPlan",
      "uk.ac.sanger.artemis.ExternalProgramException",
      "net.sf.cglib.core.MethodInfo",
      "uk.ac.sanger.artemis.components.variant.TabixReader$Iterator",
      "org.biojava.bio.symbol.SymbolListFactory",
      "uk.ac.sanger.artemis.FeatureChangeEvent",
      "com.ibatis.sqlmap.engine.execution.SqlExecutor",
      "com.ibatis.sqlmap.engine.mapping.sql.raw.RawSql",
      "org.apache.log4j.pattern.NameAbbreviator$PatternAbbreviator",
      "uk.ac.sanger.artemis.plot.CodonWeight",
      "uk.ac.sanger.artemis.io.LineGroup",
      "uk.ac.sanger.artemis.Entry$FeatureEnumerator",
      "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagContext",
      "com.ibatis.sqlmap.engine.type.BooleanTypeHandler",
      "uk.ac.sanger.artemis.util.InputStreamProgressEvent",
      "org.postgresql.Driver",
      "com.ibatis.sqlmap.engine.mapping.statement.RowHandlerCallback",
      "uk.ac.sanger.artemis.GotoEventSource",
      "org.biojava.utils.ChangeSupport",
      "org.biojava.bio.seq.io.AlternateTokenization",
      "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry",
      "com.ibatis.sqlmap.engine.transaction.BaseTransactionConfig",
      "org.apache.log4j.helpers.AbsoluteTimeDateFormat",
      "org.biojava.bio.symbol.AlphabetManager$1",
      "org.apache.log4j.Logger",
      "uk.ac.sanger.artemis.FeatureSegment",
      "com.ibatis.sqlmap.engine.mapping.statement.ExecuteListener",
      "com.ibatis.sqlmap.engine.type.IntegerTypeHandler",
      "org.biojava.bio.seq.homol.HomologyFeature",
      "uk.ac.sanger.artemis.EntryGroup",
      "uk.ac.sanger.artemis.io.Feature",
      "org.biojava.bio.AbstractAnnotation",
      "org.biojava.bio.symbol.ManyToOneTranslationTable",
      "com.ibatis.sqlmap.engine.mapping.statement.SelectStatement",
      "com.ibatis.common.xml.NodeletUtils",
      "com.sshtools.j2ssh.authentication.AuthenticationProtocolListener",
      "com.ibatis.sqlmap.engine.transaction.TransactionException",
      "com.ibatis.common.beans.GetFieldInvoker",
      "uk.ac.sanger.artemis.io.QualifierInfoVector",
      "org.biojava.bio.seq.io.SwissprotFileFormer",
      "com.ibatis.common.logging.LogFactory",
      "com.ibatis.sqlmap.engine.type.ObjectTypeHandler",
      "com.ibatis.sqlmap.engine.type.BaseTypeHandler",
      "org.apache.log4j.spi.RepositorySelector",
      "org.biojava.bio.seq.io.ProteinRefSeqProcessor$Factory",
      "org.biojava.utils.ListTools$SeriesList",
      "com.ibatis.sqlmap.engine.type.CustomTypeHandler",
      "org.biojava.utils.ChangeListener$LoggingListener",
      "org.apache.log4j.pattern.NameAbbreviator$PatternAbbreviatorFragment",
      "uk.ac.sanger.artemis.io.ReadEvent",
      "uk.ac.sanger.artemis.io.Entry",
      "uk.ac.sanger.artemis.util.LinePushBackReader",
      "org.biojava.utils.ParseErrorSource",
      "uk.ac.sanger.artemis.util.ProgressInputStream",
      "com.ibatis.sqlmap.engine.builder.xml.SqlMapClasspathEntityResolver",
      "com.ibatis.sqlmap.engine.accessplan.AccessPlan",
      "net.sf.cglib.asm.Attribute",
      "net.sf.cglib.asm.ClassAdapter",
      "uk.ac.sanger.artemis.io.FeatureVector",
      "uk.ac.sanger.artemis.chado.ChadoTransactionManager",
      "org.biojava.bio.symbol.LinearAlphabetIndex",
      "com.ibatis.sqlmap.client.extensions.TypeHandlerCallback",
      "com.sshtools.j2ssh.authentication.SshAuthenticationPrompt",
      "org.biojava.bio.symbol.Location",
      "org.gmod.schema.organism.Organism",
      "org.hsqldb.map.BaseHashMap",
      "org.biojava.bio.symbol.Alphabet",
      "org.biojava.bio.seq.io.EmblFileFormer",
      "com.ibatis.sqlmap.engine.config.ParameterMapConfig",
      "org.biojava.utils.ListTools$5",
      "net.sf.cglib.core.CodeGenerationException",
      "org.apache.log4j.pattern.NameAbbreviator$DropElementAbbreviator",
      "uk.ac.sanger.artemis.chado.ChadoTransaction",
      "com.sshtools.j2ssh.transport.SshMsgServiceAccept",
      "org.apache.log4j.spi.HierarchyEventListener",
      "org.apache.log4j.pattern.NamePatternConverter",
      "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl",
      "org.gmod.schema.sequence.FeatureSynonym",
      "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol",
      "uk.ac.sanger.artemis.io.QualifierLazyLoading",
      "uk.ac.sanger.artemis.util.DatabaseDocument",
      "com.sshtools.j2ssh.sftp.SshFxpRealPath",
      "org.biojava.bio.seq.io.GAMEFormat",
      "org.biojava.bio.seq.db.Index",
      "uk.ac.sanger.artemis.SelectionChangeListener",
      "org.biojava.bio.dist.DistributionTrainerContext"
    );
  } 

  private static void resetClasses() {
    org.evosuite.runtime.classhandling.ClassResetter.getInstance().setClassLoader(ExternalProgram_ESTest_scaffolding.class.getClassLoader()); 

    org.evosuite.runtime.classhandling.ClassStateSupport.resetClasses(
      "org.apache.log4j.Category",
      "org.apache.log4j.Logger",
      "org.apache.log4j.Hierarchy",
      "org.apache.log4j.spi.RootLogger",
      "org.apache.log4j.Priority",
      "org.apache.log4j.Level",
      "org.apache.log4j.or.DefaultRenderer",
      "org.apache.log4j.or.RendererMap",
      "org.apache.log4j.DefaultCategoryFactory",
      "org.apache.log4j.spi.DefaultRepositorySelector",
      "org.apache.log4j.helpers.OptionConverter",
      "org.apache.log4j.helpers.Loader",
      "org.apache.log4j.helpers.LogLog",
      "org.apache.log4j.PropertyConfigurator",
      "org.apache.log4j.LogManager",
      "org.apache.log4j.CategoryKey",
      "org.apache.log4j.ProvisionNode",
      "uk.ac.sanger.artemis.ExternalProgram",
      "uk.ac.sanger.artemis.util.Document",
      "uk.ac.sanger.artemis.util.DatabaseDocument",
      "uk.ac.sanger.artemis.util.StringVector",
      "uk.ac.sanger.artemis.util.FileDocument",
      "uk.ac.sanger.artemis.util.InputStreamProgressListenerVector",
      "org.apache.log4j.AppenderSkeleton",
      "uk.ac.sanger.artemis.components.LogViewer",
      "org.apache.log4j.helpers.OnlyOnceErrorHandler",
      "uk.ac.sanger.artemis.components.Splash",
      "uk.ac.sanger.artemis.io.QualifierInfoVector",
      "uk.ac.sanger.artemis.util.FastVector",
      "uk.ac.sanger.artemis.io.KeyVector",
      "uk.ac.sanger.artemis.io.Key",
      "uk.ac.sanger.artemis.io.QualifierInfo",
      "uk.ac.sanger.artemis.io.SimpleEntryInformation",
      "uk.ac.sanger.artemis.io.QualifierInfoHash",
      "uk.ac.sanger.artemis.ExternalProgramVector",
      "uk.ac.sanger.artemis.Options",
      "uk.ac.sanger.artemis.components.genebuilder.GeneUtils",
      "uk.ac.sanger.artemis.components.filetree.FileList",
      "uk.ac.sanger.artemis.j2ssh.SshFileManager",
      "uk.ac.sanger.artemis.j2ssh.SshLogin",
      "uk.ac.sanger.artemis.components.filetree.RemoteFileNode",
      "uk.ac.sanger.artemis.io.EMBLObject",
      "uk.ac.sanger.artemis.io.LineGroup",
      "uk.ac.sanger.artemis.io.StreamSequence",
      "uk.ac.sanger.artemis.io.EmblStreamSequence",
      "uk.ac.sanger.artemis.util.URLDocument",
      "uk.ac.sanger.artemis.io.RawStreamSequence",
      "uk.ac.sanger.artemis.io.FastaStreamSequence",
      "uk.ac.sanger.artemis.Selection",
      "uk.ac.sanger.artemis.FeatureVector",
      "uk.ac.sanger.artemis.FeatureSegmentVector",
      "uk.ac.sanger.artemis.EntryVector",
      "uk.ac.sanger.artemis.SimpleEntryGroup",
      "uk.ac.sanger.artemis.ActionController",
      "uk.ac.sanger.artemis.ActionVector",
      "uk.ac.sanger.artemis.FeatureKeyQualifierPredicate",
      "uk.ac.sanger.artemis.FilteredEntryGroup",
      "uk.ac.sanger.artemis.FilteredEntryGroup$1",
      "uk.ac.sanger.artemis.FilteredEntryGroup$2",
      "uk.ac.sanger.artemis.FilteredEntryGroup$3",
      "uk.ac.sanger.artemis.Entry",
      "uk.ac.sanger.artemis.io.SimpleDocumentEntry",
      "uk.ac.sanger.artemis.io.PublicDBDocumentEntry",
      "uk.ac.sanger.artemis.io.EmblDocumentEntry",
      "uk.ac.sanger.artemis.io.FeatureVector",
      "uk.ac.sanger.artemis.io.SimpleDocumentEntry$1",
      "uk.ac.sanger.artemis.Entry$FeatureEnumerator",
      "uk.ac.sanger.artemis.ChangeEvent",
      "uk.ac.sanger.artemis.EntryGroupChangeEvent",
      "uk.ac.sanger.artemis.EntryChangeEvent",
      "uk.ac.sanger.artemis.io.Range",
      "org.biojava.utils.AbstractChangeable",
      "org.biojava.bio.seq.SimpleAssembly",
      "org.biojava.bio.AbstractAnnotation",
      "org.biojava.bio.SimpleAnnotation",
      "org.biojava.bio.seq.SimpleFeatureRealizer",
      "org.biojava.bio.seq.impl.FeatureImpl$1",
      "org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl",
      "org.biojava.bio.seq.impl.FeatureImpl",
      "org.biojava.bio.symbol.AbstractSymbolList",
      "org.biojava.bio.seq.impl.AssembledSymbolList",
      "org.biojava.utils.Unchangeable",
      "org.biojava.bio.symbol.AlphabetManager$GapSymbol",
      "org.biojava.bio.symbol.AlphabetManager$SizeQueen",
      "org.biojava.bio.symbol.IntegerAlphabet",
      "org.biojava.utils.cache.WeakValueHashMap",
      "org.biojava.bio.symbol.DoubleAlphabet",
      "org.biojava.bio.symbol.AbstractSymbol",
      "org.biojava.bio.symbol.SimpleSymbol",
      "org.biojava.bio.symbol.AbstractSimpleBasisSymbol",
      "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol",
      "org.biojava.utils.ChangeType",
      "org.biojava.bio.EmptyAnnotation",
      "org.biojava.bio.Annotation",
      "org.biojava.bio.symbol.EmptyAlphabet",
      "org.biojava.bio.symbol.Alphabet",
      "org.biojava.utils.ListTools$5",
      "org.biojava.utils.ListTools",
      "org.biojava.utils.SingletonList",
      "org.biojava.utils.ClassTools",
      "org.biojava.utils.stax.SAX2StAXAdaptor",
      "org.biojava.utils.stax.StAXContentHandlerBase",
      "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler",
      "org.biojava.utils.stax.SAX2StAXAdaptor$HandlerBinding",
      "org.biojava.utils.stax.SAX2StAXAdaptor$S2SDelegationManager",
      "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler",
      "org.biojava.bio.SmallAnnotation",
      "org.biojava.utils.lsid.LifeScienceIdentifier",
      "org.biojava.utils.stax.StringElementHandlerBase",
      "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler$1",
      "org.biojava.utils.SmallMap",
      "org.biojava.bio.symbol.AlphabetManager$WellKnownBasisSymbol",
      "org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol",
      "org.biojava.bio.symbol.FundamentalAtomicSymbol",
      "org.biojava.utils.ChangeListener$AlwaysVetoListener",
      "org.biojava.utils.ChangeListener$LoggingListener",
      "org.biojava.utils.ChangeListener",
      "org.biojava.utils.ChangeSupport",
      "org.biojava.bio.Annotatable",
      "org.biojava.utils.ChangeType$1",
      "org.biojava.utils.ChangeForwarder",
      "org.biojava.utils.ChangeForwarder$Retyper",
      "org.biojava.bio.symbol.AbstractAlphabet",
      "org.biojava.bio.symbol.SingletonAlphabet",
      "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$AlphabetHandler",
      "org.biojava.bio.symbol.SimpleAlphabet",
      "org.biojava.bio.symbol.AlphabetManager$WellKnownAlphabet",
      "org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper",
      "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$AlphabetHandler$1",
      "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler",
      "org.biojava.bio.seq.io.CharacterTokenization",
      "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler$MappingHandler",
      "org.biojava.bio.symbol.SimpleBasisSymbol",
      "org.biojava.bio.seq.io.AlternateTokenization",
      "org.biojava.bio.symbol.AlphabetManager",
      "org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper",
      "org.biojava.bio.symbol.SimpleSymbolList",
      "org.biojava.bio.seq.io.SymbolTokenization$TokenType",
      "org.biojava.bio.seq.io.SymbolTokenization",
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      "uk.ac.sanger.artemis.io.BlastEntryInformation",
      "com.ibatis.common.xml.NodeletException",
      "uk.ac.sanger.artemis.io.DocumentEntryAutosaveThread",
      "uk.ac.sanger.artemis.util.CacheHashMap",
      "org.biojava.bio.symbol.DoubleAlphabet$SubDoubleAlphabet",
      "org.apache.log4j.helpers.PatternParser$BasicPatternConverter",
      "uk.ac.sanger.artemis.SelectionChangeEvent",
      "uk.ac.sanger.artemis.util.ZipFileDocument",
      "org.apache.log4j.helpers.DateLayout",
      "org.apache.log4j.TTCCLayout"
    );
  }
}
