1 /** 2 * Scaffolding file used to store all the setups needed to run 3 * tests automatically generated by EvoSuite 4 * Fri Jan 12 14:42:41 GMT 2018 5 */ 6 7 package uk.ac.sanger.artemis.io; 8 9 import org.evosuite.runtime.annotation.EvoSuiteClassExclude; 10 import org.junit.BeforeClass; 11 import org.junit.Before; 12 import org.junit.After; 13 import org.junit.AfterClass; 14 import org.evosuite.runtime.sandbox.Sandbox; 15 import org.evosuite.runtime.sandbox.Sandbox.SandboxMode; 16 17 @EvoSuiteClassExclude 18 public class EmblStreamFeature_ESTest_scaffolding { 19 20 @org.junit.Rule 21 public org.evosuite.runtime.vnet.NonFunctionalRequirementRule nfr = new org.evosuite.runtime.vnet.NonFunctionalRequirementRule(); 22 23 private static final java.util.Properties defaultProperties = (java.util.Properties) java.lang.System.getProperties().clone(); 24 25 private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000); 26 27 28 @BeforeClass initEvoSuiteFramework()29 public static void initEvoSuiteFramework() { 30 org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.io.EmblStreamFeature"; 31 org.evosuite.runtime.GuiSupport.initialize(); 32 org.evosuite.runtime.RuntimeSettings.maxNumberOfThreads = 100; 33 org.evosuite.runtime.RuntimeSettings.maxNumberOfIterationsPerLoop = 10000; 34 org.evosuite.runtime.RuntimeSettings.mockSystemIn = true; 35 org.evosuite.runtime.RuntimeSettings.sandboxMode = org.evosuite.runtime.sandbox.Sandbox.SandboxMode.RECOMMENDED; 36 org.evosuite.runtime.sandbox.Sandbox.initializeSecurityManagerForSUT(); 37 org.evosuite.runtime.classhandling.JDKClassResetter.init(); 38 setSystemProperties(); 39 initializeClasses(); 40 org.evosuite.runtime.Runtime.getInstance().resetRuntime(); 41 } 42 43 @AfterClass clearEvoSuiteFramework()44 public static void clearEvoSuiteFramework(){ 45 Sandbox.resetDefaultSecurityManager(); 46 java.lang.System.setProperties((java.util.Properties) defaultProperties.clone()); 47 } 48 49 @Before initTestCase()50 public void initTestCase(){ 51 threadStopper.storeCurrentThreads(); 52 threadStopper.startRecordingTime(); 53 org.evosuite.runtime.jvm.ShutdownHookHandler.getInstance().initHandler(); 54 org.evosuite.runtime.sandbox.Sandbox.goingToExecuteSUTCode(); 55 setSystemProperties(); 56 org.evosuite.runtime.GuiSupport.setHeadless(); 57 org.evosuite.runtime.Runtime.getInstance().resetRuntime(); 58 org.evosuite.runtime.agent.InstrumentingAgent.activate(); 59 } 60 61 @After doneWithTestCase()62 public void doneWithTestCase(){ 63 threadStopper.killAndJoinClientThreads(); 64 org.evosuite.runtime.jvm.ShutdownHookHandler.getInstance().safeExecuteAddedHooks(); 65 org.evosuite.runtime.classhandling.JDKClassResetter.reset(); 66 resetClasses(); 67 org.evosuite.runtime.sandbox.Sandbox.doneWithExecutingSUTCode(); 68 org.evosuite.runtime.agent.InstrumentingAgent.deactivate(); 69 org.evosuite.runtime.GuiSupport.restoreHeadlessMode(); 70 } 71 setSystemProperties()72 public static void setSystemProperties() { 73 74 java.lang.System.setProperties((java.util.Properties) defaultProperties.clone()); 75 java.lang.System.setProperty("file.encoding", "UTF-8"); 76 java.lang.System.setProperty("java.awt.headless", "true"); 77 java.lang.System.setProperty("user.country", "GB"); 78 java.lang.System.setProperty("user.language", "en"); 79 java.lang.System.setProperty("user.timezone", "Europe/London"); 80 java.lang.System.setProperty("log4j.configuration", "SUT.log4j.properties"); 81 } 82 initializeClasses()83 private static void initializeClasses() { 84 org.evosuite.runtime.classhandling.ClassStateSupport.initializeClasses(EmblStreamFeature_ESTest_scaffolding.class.getClassLoader() , 85 "uk.ac.sanger.artemis.components.LogViewer$1", 86 "org.biojava.bio.seq.AcceptNoneFilter", 87 "net.sf.cglib.core.EmitUtils$ArrayDelimiters", 88 "com.ibatis.common.jdbc.SimpleDataSource$SimplePooledConnection", 89 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.ConditionalTagHandler", 90 "org.biojava.bio.seq.io.SymbolTokenization$TokenType", 91 "org.biojava.bio.seq.ByHierarchy", 92 "org.biojava.bio.seq.ComponentFeature$Template", 93 "org.apache.log4j.AppenderSkeleton", 94 "com.ibatis.sqlmap.client.extensions.ParameterSetter", 95 "com.sshtools.j2ssh.connection.SshMsgRequestFailure", 96 "org.biojava.utils.stax.SAX2StAXAdaptor", 97 "uk.ac.sanger.artemis.io.SimpleDocumentFeature", 98 "uk.ac.sanger.artemis.sequence.BasePatternFormatException", 99 "com.sshtools.j2ssh.sftp.SshFxpRmdir", 100 "com.sshtools.j2ssh.authentication.PasswordAuthenticationClient", 101 "net.sf.cglib.core.KeyFactory$Generator", 102 "com.sshtools.j2ssh.SshClient", 103 "uk.ac.sanger.artemis.EntryChangeListener", 104 "org.biojava.ontology.Term", 105 "org.biojava.utils.ListTools$Triplet", 106 "org.biojava.bio.symbol.DoubleAlphabet$SubDoubleAlphabet", 107 "uk.ac.sanger.artemis.sequence.AminoAcidSequence", 108 "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$AlphabetHandler$1", 109 "uk.ac.sanger.artemis.Selectable", 110 "org.biojava.bio.seq.io.NameTokenization", 111 "net.sf.cglib.core.CodeEmitter$State", 112 "uk.ac.sanger.artemis.io.FeatureTable", 113 "uk.ac.sanger.artemis.io.RangeVector", 114 "org.biojava.bio.seq.FramedFeature$ReadingFrame", 115 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateTagHandler", 116 "org.biojava.bio.seq.io.CharacterTokenization", 117 "org.biojava.bio.seq.homol.SimilarityPairFeature$EmptyPairwiseAlignment", 118 "uk.ac.sanger.artemis.io.PublicDBDocumentEntry", 119 "uk.ac.sanger.artemis.util.StringVector", 120 "net.sf.cglib.core.Constants", 121 "net.sf.cglib.core.AbstractClassGenerator", 122 "org.biojava.bio.seq.Feature$Template", 123 "com.ibatis.common.beans.BaseProbe", 124 "com.sshtools.j2ssh.transport.AsyncService", 125 "com.ibatis.sqlmap.engine.mapping.statement.SelectKeyStatement", 126 "org.gmod.schema.sequence.Synonym", 127 "org.biojava.bio.symbol.SimpleAlphabet", 128 "org.biojava.bio.seq.io.SequenceBuilderFactory", 129 "org.gmod.schema.sequence.FeatureCvTermProp", 130 "org.apache.log4j.Hierarchy", 131 "htsjdk.samtools.seekablestream.SeekableFileStream", 132 "uk.ac.sanger.artemis.sequence.MarkerRange", 133 "org.biojava.utils.Changeable", 134 "org.biojava.bio.symbol.EmptyLocation", 135 "net.sf.cglib.asm.MethodWriter", 136 "com.ibatis.common.util.PaginatedList", 137 "uk.ac.sanger.artemis.io.QualifierInfoHash", 138 "com.sshtools.j2ssh.connection.Channel", 139 "net.sf.cglib.core.ClassNameReader$EarlyExitException", 140 "com.ibatis.sqlmap.engine.cache.CacheModel", 141 "org.apache.log4j.spi.OptionHandler", 142 "org.biojava.bio.symbol.SimpleManyToOneTranslationTable", 143 "org.biojava.utils.stax.DelegationManager", 144 "org.biojava.bio.seq.StrandedFeature", 145 "org.biojava.utils.lsid.LifeScienceIdentifier", 146 "net.sf.cglib.core.ReflectUtils", 147 "org.biojava.utils.ChangeVetoException", 148 "org.biojava.bio.symbol.IllegalAlphabetException", 149 "org.biojava.bio.symbol.DoubleAlphabet$DoubleRange", 150 "htsjdk.samtools.seekablestream.SeekableStream", 151 "uk.ac.sanger.artemis.sequence.MarkerInternal", 152 "com.sshtools.j2ssh.connection.ChannelEventListener", 153 "net.sf.cglib.core.AbstractClassGenerator$1", 154 "org.biojava.bio.symbol.AbstractTranslationTable", 155 "uk.ac.sanger.artemis.components.Splash$2", 156 "org.gmod.schema.dao.GeneralDaoI", 157 "com.ibatis.sqlmap.engine.exchange.DataExchangeFactory", 158 "net.sf.cglib.core.LocalVariablesSorter", 159 "org.apache.log4j.helpers.OptionConverter", 160 "org.gmod.schema.dao.BaseDaoI", 161 "com.ibatis.sqlmap.client.SqlMapExecutor", 162 "org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl", 163 "org.biojava.bio.symbol.Edit", 164 "com.ibatis.sqlmap.client.SqlMapException", 165 "uk.ac.sanger.artemis.io.MiscLineGroup", 166 "uk.ac.sanger.artemis.io.LazyQualifierValue", 167 "com.ibatis.sqlmap.engine.type.SqlTimeTypeHandler", 168 "org.postgresql.largeobject.BlobOutputStream", 169 "org.biojava.bio.symbol.AbstractSymbol", 170 "org.biojava.utils.bytecode.CodeGenerator", 171 "org.gmod.schema.cv.CvTerm", 172 "uk.ac.sanger.artemis.sequence.SequenceChangeListener", 173 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsGreaterThanTagHandler", 174 "com.sshtools.j2ssh.subsystem.SubsystemMessage", 175 "uk.ac.sanger.artemis.io.InvalidRelationException", 176 "org.biojava.utils.bytecode.CodeMethod", 177 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEqualTagHandler", 178 "org.biojava.bio.seq.impl.FeatureImpl$1", 179 "org.biojava.bio.seq.io.SimpleSequenceBuilder", 180 "com.sshtools.j2ssh.transport.InvalidMessageException", 181 "org.biojava.bio.Annotation", 182 "org.biojava.bio.symbol.IntegerAlphabet$IntegerSymbol", 183 "org.biojava.utils.lsid.LifeScienceIdentifierParseException", 184 "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler", 185 "com.sshtools.j2ssh.authentication.AuthenticationProtocolClient", 186 "org.apache.log4j.Category", 187 "uk.ac.sanger.artemis.io.LocationParseException", 188 "org.biojava.utils.ListTools$Mapper", 189 "htsjdk.samtools.SAMException", 190 "org.biojava.bio.seq.io.StreamParser", 191 "uk.ac.sanger.artemis.util.FastVector", 192 "org.biojava.bio.symbol.SimpleSymbol", 193 "com.ibatis.common.beans.ComplexBeanProbe", 194 "org.apache.log4j.helpers.ThreadLocalMap", 195 "net.sf.cglib.core.KeyFactory$2", 196 "org.biojava.bio.symbol.AbstractSimpleBasisSymbol", 197 "net.sf.cglib.core.KeyFactory$1", 198 "com.sshtools.j2ssh.transport.TransportProtocolEventHandler", 199 "org.gmod.schema.sequence.FeatureDbXRef", 200 "net.sf.cglib.core.ClassInfo", 201 "org.biojava.utils.ChangeEvent", 202 "uk.ac.sanger.artemis.components.variant.AbstractVCFReader", 203 "org.gmod.schema.pub.Pub", 204 "uk.ac.sanger.artemis.io.ChadoCanonicalGene", 205 "net.sf.cglib.core.ClassEmitter$3", 206 "net.sf.cglib.core.EmitUtils$9", 207 "net.sf.cglib.core.ClassEmitter$1", 208 "org.biojava.utils.stax.SAX2StAXAdaptor$S2SDelegationManager", 209 "net.sf.cglib.core.EmitUtils$8", 210 "net.sf.cglib.core.EmitUtils$7", 211 "net.sf.cglib.core.Predicate", 212 "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry$IndexContig", 213 "org.biojava.bio.symbol.SimpleCrossProductAlphabet", 214 "net.sf.cglib.core.ClassEmitter", 215 "org.biojava.bio.seq.DNATools", 216 "org.gmod.schema.sequence.FeatureCvTermDbXRef", 217 "org.biojava.bio.seq.FramedFeature$1", 218 "com.sshtools.j2ssh.transport.TransportProtocolState", 219 "org.biojava.bio.symbol.AbstractManyToOneTranslationTable", 220 "uk.ac.sanger.artemis.io.GenbankStreamSequence", 221 "net.sf.cglib.core.ClassNameReader", 222 "com.sshtools.j2ssh.connection.ChannelInputStream", 223 "com.ibatis.sqlmap.engine.cache.CacheController", 224 "net.sf.cglib.core.ClassNameReader$1", 225 "com.ibatis.sqlmap.engine.accessplan.BaseAccessPlan", 226 "htsjdk.samtools.util.RuntimeIOException", 227 "org.biojava.bio.BioRuntimeException", 228 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.BaseTagHandler", 229 "org.biojava.bio.seq.AcceptAllFilter", 230 "org.biojava.bio.seq.io.ChunkedSymbolListFactory", 231 "net.sf.cglib.core.Local", 232 "org.biojava.bio.symbol.IntegerAlphabet$SubIntegerAlphabet", 233 "org.biojava.bio.seq.homol.SimilarityPairFeature", 234 "org.gmod.schema.utils.propinterface.PropertyI", 235 "org.apache.log4j.spi.AppenderAttachable", 236 "com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate", 237 "com.sshtools.j2ssh.SshException", 238 "uk.ac.sanger.artemis.j2ssh.FTProgress", 239 "uk.ac.sanger.artemis.io.GFF3AttributeAggregator", 240 "net.sf.cglib.beans.BulkBean$Generator", 241 "org.gmod.schema.cv.Cv", 242 "uk.ac.sanger.artemis.util.InputStreamProgressListenerVector", 243 "com.sshtools.j2ssh.sftp.SshFxpRename", 244 "net.sf.cglib.core.DefaultNamingPolicy", 245 "uk.ac.sanger.artemis.util.PushBackException", 246 "com.ibatis.sqlmap.engine.exchange.DataExchange", 247 "com.ibatis.sqlmap.engine.mapping.sql.SqlChild", 248 "org.biojava.utils.ParseErrorListener", 249 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.DynamicTagHandler", 250 "com.sshtools.j2ssh.connection.IOChannel", 251 "org.biojava.utils.SingletonList", 252 "org.biojava.bio.symbol.SymbolList", 253 "org.biojava.bio.BioException", 254 "net.sf.cglib.asm.AnnotationVisitor", 255 "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange", 256 "com.ibatis.sqlmap.engine.type.TypeHandlerFactory$1", 257 "com.ibatis.sqlmap.engine.builder.xml.XMLSqlSource", 258 "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMapping", 259 "net.sf.cglib.asm.FieldVisitor", 260 "org.biojava.bio.seq.FramedFeature$Template", 261 "com.ibatis.sqlmap.engine.exchange.BaseDataExchange", 262 "net.sf.cglib.asm.MethodVisitor", 263 "net.sf.cglib.asm.ClassVisitor", 264 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595 "org.biojava.bio.symbol.AlphabetManager$SizeQueen", 596 "uk.ac.sanger.artemis.Entry", 597 "org.biojava.bio.symbol.HashedAlphabetIndex", 598 "org.biojava.utils.ClassTools", 599 "net.sf.cglib.core.Customizer", 600 "uk.ac.sanger.artemis.io.EmblStreamFeature", 601 "uk.ac.sanger.artemis.io.QualifierParseException", 602 "org.biojava.utils.cache.WeakValueHashMap", 603 "org.biojava.bio.symbol.IllegalSymbolException", 604 "uk.ac.sanger.artemis.ExternalProgramVector", 605 "com.ibatis.sqlmap.engine.type.TypeHandler", 606 "com.ibatis.sqlmap.engine.mapping.parameter.InlineParameterMapParser", 607 "org.apache.log4j.CategoryKey", 608 "uk.ac.sanger.artemis.io.Qualifier", 609 "uk.ac.sanger.artemis.util.InputStreamProgressListener", 610 "com.sshtools.j2ssh.sftp.SshFxpRemove", 611 "uk.ac.sanger.artemis.io.LocationLexer$TokenEnumeration", 612 "com.sshtools.j2ssh.connection.SshMsgChannelExtendedData", 613 "org.biojava.bio.seq.RemoteFeature", 614 "com.ibatis.sqlmap.engine.type.JdbcTypeRegistry", 615 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"com.ibatis.common.jdbc.exception.NestedSQLException", 713 "com.ibatis.sqlmap.engine.builder.xml.SqlMapClasspathEntityResolver", 714 "com.ibatis.sqlmap.engine.accessplan.AccessPlan", 715 "org.biojava.bio.seq.io.SequenceBuilder", 716 "net.sf.cglib.asm.Attribute", 717 "net.sf.cglib.asm.ClassAdapter", 718 "uk.ac.sanger.artemis.io.FeatureVector", 719 "org.biojava.bio.symbol.LinearAlphabetIndex", 720 "net.sf.cglib.asm.MethodAdapter", 721 "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler$1", 722 "com.ibatis.sqlmap.client.extensions.TypeHandlerCallback", 723 "org.apache.commons.logging.impl.Log4JLogger", 724 "org.biojava.bio.symbol.Location", 725 "org.gmod.schema.organism.Organism", 726 "org.gmod.schema.general.Db", 727 "com.ibatis.sqlmap.engine.config.CacheModelConfig", 728 "com.ibatis.sqlmap.engine.impl.SqlMapSessionImpl", 729 "org.apache.log4j.Appender", 730 "org.biojava.bio.symbol.SimpleReversibleTranslationTable", 731 "org.biojava.bio.symbol.Alphabet", 732 "org.biojava.bio.symbol.AbstractSymbolList$EditScreener", 733 "com.ibatis.sqlmap.engine.config.ParameterMapConfig", 734 "org.biojava.bio.seq.io.EmblFileFormer", 735 "org.biojava.utils.ListTools$5", 736 "net.sf.cglib.core.CodeGenerationException", 737 "org.biojava.bio.seq.Frame", 738 "uk.ac.sanger.artemis.chado.ChadoTransaction", 739 "com.sshtools.j2ssh.transport.SshMsgServiceAccept", 740 "org.biojava.utils.AssertionFailure", 741 "uk.ac.sanger.artemis.FeaturePredicate", 742 "com.sshtools.j2ssh.authentication.AuthenticationProtocolException", 743 "uk.ac.sanger.artemis.Logger", 744 "org.biojava.bio.seq.IsTopLevel", 745 "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl", 746 "com.ibatis.sqlmap.client.SqlMapSession", 747 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotEmptyTagHandler", 748 "org.gmod.schema.sequence.FeatureSynonym", 749 "org.apache.log4j.spi.LoggingEvent", 750 "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol", 751 "com.ibatis.sqlmap.engine.mapping.statement.CachingStatement", 752 "uk.ac.sanger.artemis.io.QualifierLazyLoading", 753 "uk.ac.sanger.artemis.util.DatabaseDocument", 754 "uk.ac.sanger.artemis.FeatureEnumeration", 755 "org.biojava.bio.symbol.AbstractSymbolList", 756 "net.sf.cglib.asm.Label", 757 "uk.ac.sanger.artemis.io.StreamFeatureTable", 758 "org.gmod.schema.dao.PubDaoI", 759 "org.biojava.bio.symbol.RangeLocation" 760 ); 761 } 762 resetClasses()763 private static void resetClasses() { 764 org.evosuite.runtime.classhandling.ClassResetter.getInstance().setClassLoader(EmblStreamFeature_ESTest_scaffolding.class.getClassLoader()); 765 766 org.evosuite.runtime.classhandling.ClassStateSupport.resetClasses( 767 "uk.ac.sanger.artemis.io.LineGroup", 768 "uk.ac.sanger.artemis.io.SimpleDocumentFeature", 769 "uk.ac.sanger.artemis.io.PublicDBStreamFeature", 770 "uk.ac.sanger.artemis.io.Key", 771 "uk.ac.sanger.artemis.io.LocationParseNodeVector", 772 "uk.ac.sanger.artemis.io.LocationParseNode", 773 "uk.ac.sanger.artemis.io.QualifierVector", 774 "uk.ac.sanger.artemis.components.filetree.RemoteFileNode", 775 "uk.ac.sanger.artemis.util.FastVector", 776 "org.biojava.bio.AbstractAnnotation", 777 "org.biojava.bio.SimpleAnnotation", 778 "org.biojava.bio.seq.SimpleFeatureRealizer", 779 "org.biojava.bio.seq.impl.FeatureImpl$1", 780 "org.biojava.bio.seq.impl.FeatureImpl", 781 "org.biojava.bio.symbol.AlphabetManager$GapSymbol", 782 "org.biojava.bio.symbol.AlphabetManager$SizeQueen", 783 "org.biojava.bio.symbol.IntegerAlphabet", 784 "org.biojava.bio.symbol.DoubleAlphabet", 785 "org.biojava.bio.symbol.SimpleSymbol", 786 "org.biojava.bio.symbol.AbstractSimpleBasisSymbol", 787 "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol", 788 "org.biojava.utils.ChangeType", 789 "org.biojava.bio.EmptyAnnotation", 790 "org.biojava.bio.Annotation", 791 "org.biojava.bio.symbol.EmptyAlphabet", 792 "org.biojava.bio.symbol.Alphabet", 793 "org.biojava.utils.ListTools", 794 "org.biojava.utils.SingletonList", 795 "org.biojava.bio.SmallAnnotation", 796 "org.biojava.utils.lsid.LifeScienceIdentifier", 797 "org.biojava.utils.SmallMap", 798 "org.biojava.bio.symbol.AlphabetManager$WellKnownBasisSymbol", 799 "org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol", 800 "org.biojava.bio.symbol.FundamentalAtomicSymbol", 801 "org.biojava.utils.ChangeListener", 802 "org.biojava.utils.ChangeSupport", 803 "org.biojava.bio.Annotatable", 804 "org.biojava.bio.symbol.AbstractAlphabet", 805 "org.biojava.bio.symbol.SingletonAlphabet", 806 "org.biojava.bio.symbol.SimpleAlphabet", 807 "org.biojava.bio.symbol.AlphabetManager$WellKnownAlphabet", 808 "org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper", 809 "org.biojava.bio.seq.io.CharacterTokenization", 810 "org.biojava.bio.symbol.SimpleBasisSymbol", 811 "org.biojava.bio.seq.io.AlternateTokenization", 812 "org.biojava.bio.symbol.AlphabetManager", 813 "org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper", 814 "org.biojava.bio.symbol.SimpleSymbolList", 815 "org.biojava.bio.seq.io.SymbolTokenization", 816 "org.biojava.bio.symbol.SimpleReversibleTranslationTable", 817 "org.biojava.bio.symbol.SimpleCrossProductAlphabet", 818 "org.biojava.utils.ListTools$Triplet", 819 "org.biojava.bio.symbol.SimpleAtomicSymbol", 820 "org.biojava.bio.seq.io.WordTokenization", 821 "org.biojava.bio.seq.io.NameTokenization", 822 "org.biojava.bio.symbol.SimpleManyToOneTranslationTable", 823 "org.biojava.bio.symbol.SimpleGeneticCodeTable", 824 "org.biojava.bio.symbol.AbstractSymbolList$ListView", 825 "org.biojava.bio.BioException", 826 "org.biojava.bio.symbol.IllegalSymbolException", 827 "org.biojava.bio.BioError", 828 "org.biojava.bio.seq.RNATools", 829 "org.biojava.bio.seq.DNATools", 830 "uk.ac.sanger.artemis.io.PublicDBDocumentEntry", 831 "org.apache.log4j.Category", 832 "org.apache.log4j.Logger", 833 "org.apache.log4j.Priority", 834 "org.apache.log4j.Level", 835 "org.apache.log4j.or.RendererMap", 836 "org.apache.log4j.helpers.OptionConverter", 837 "org.apache.log4j.helpers.Loader", 838 "org.apache.log4j.helpers.LogLog", 839 "org.apache.log4j.PropertyConfigurator", 840 "org.apache.log4j.LogManager", 841 "org.apache.log4j.CategoryKey", 842 "org.apache.log4j.ProvisionNode", 843 "uk.ac.sanger.artemis.util.DatabaseDocument", 844 "uk.ac.sanger.artemis.util.StringVector", 845 "uk.ac.sanger.artemis.components.Splash", 846 "uk.ac.sanger.artemis.io.KeyVector", 847 "uk.ac.sanger.artemis.io.QualifierInfo", 848 "uk.ac.sanger.artemis.ExternalProgram", 849 "uk.ac.sanger.artemis.Options", 850 "uk.ac.sanger.artemis.io.RangeVector", 851 "org.biojava.bio.seq.io.SequenceBuilderBase", 852 "org.biojava.bio.seq.io.SimpleSequenceBuilder$SSBFactory", 853 "org.biojava.bio.seq.io.SimpleSequenceBuilder", 854 "org.biojava.bio.seq.io.ChunkedSymbolListFactory", 855 "org.biojava.bio.symbol.EmptySymbolList", 856 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