1 /** 2 * Scaffolding file used to store all the setups needed to run 3 * tests automatically generated by EvoSuite 4 * Fri Jan 12 15:31:41 GMT 2018 5 */ 6 7 package uk.ac.sanger.artemis.io; 8 9 import org.evosuite.runtime.annotation.EvoSuiteClassExclude; 10 import org.junit.BeforeClass; 11 import org.junit.Before; 12 import org.junit.After; 13 import org.junit.AfterClass; 14 import org.evosuite.runtime.sandbox.Sandbox; 15 import org.evosuite.runtime.sandbox.Sandbox.SandboxMode; 16 17 @EvoSuiteClassExclude 18 public class Sequence_ESTest_scaffolding { 19 20 @org.junit.Rule 21 public org.evosuite.runtime.vnet.NonFunctionalRequirementRule nfr = new org.evosuite.runtime.vnet.NonFunctionalRequirementRule(); 22 23 private static final java.util.Properties defaultProperties = (java.util.Properties) java.lang.System.getProperties().clone(); 24 25 private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000); 26 27 28 @BeforeClass initEvoSuiteFramework()29 public static void initEvoSuiteFramework() { 30 org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.io.Sequence"; 31 org.evosuite.runtime.GuiSupport.initialize(); 32 org.evosuite.runtime.RuntimeSettings.maxNumberOfThreads = 100; 33 org.evosuite.runtime.RuntimeSettings.maxNumberOfIterationsPerLoop = 10000; 34 org.evosuite.runtime.RuntimeSettings.mockSystemIn = true; 35 org.evosuite.runtime.RuntimeSettings.sandboxMode = org.evosuite.runtime.sandbox.Sandbox.SandboxMode.RECOMMENDED; 36 org.evosuite.runtime.sandbox.Sandbox.initializeSecurityManagerForSUT(); 37 org.evosuite.runtime.classhandling.JDKClassResetter.init(); 38 setSystemProperties(); 39 initializeClasses(); 40 org.evosuite.runtime.Runtime.getInstance().resetRuntime(); 41 } 42 43 @AfterClass clearEvoSuiteFramework()44 public static void clearEvoSuiteFramework(){ 45 Sandbox.resetDefaultSecurityManager(); 46 java.lang.System.setProperties((java.util.Properties) defaultProperties.clone()); 47 } 48 49 @Before initTestCase()50 public void initTestCase(){ 51 threadStopper.storeCurrentThreads(); 52 threadStopper.startRecordingTime(); 53 org.evosuite.runtime.jvm.ShutdownHookHandler.getInstance().initHandler(); 54 org.evosuite.runtime.sandbox.Sandbox.goingToExecuteSUTCode(); 55 setSystemProperties(); 56 org.evosuite.runtime.GuiSupport.setHeadless(); 57 org.evosuite.runtime.Runtime.getInstance().resetRuntime(); 58 org.evosuite.runtime.agent.InstrumentingAgent.activate(); 59 } 60 61 @After doneWithTestCase()62 public void doneWithTestCase(){ 63 threadStopper.killAndJoinClientThreads(); 64 org.evosuite.runtime.jvm.ShutdownHookHandler.getInstance().safeExecuteAddedHooks(); 65 org.evosuite.runtime.classhandling.JDKClassResetter.reset(); 66 resetClasses(); 67 org.evosuite.runtime.sandbox.Sandbox.doneWithExecutingSUTCode(); 68 org.evosuite.runtime.agent.InstrumentingAgent.deactivate(); 69 org.evosuite.runtime.GuiSupport.restoreHeadlessMode(); 70 } 71 setSystemProperties()72 public static void setSystemProperties() { 73 74 java.lang.System.setProperties((java.util.Properties) defaultProperties.clone()); 75 java.lang.System.setProperty("file.encoding", "UTF-8"); 76 java.lang.System.setProperty("java.awt.headless", "true"); 77 java.lang.System.setProperty("user.country", "GB"); 78 java.lang.System.setProperty("user.language", "en"); 79 java.lang.System.setProperty("user.timezone", "Europe/London"); 80 java.lang.System.setProperty("log4j.configuration", "SUT.log4j.properties"); 81 } 82 initializeClasses()83 private static void initializeClasses() { 84 org.evosuite.runtime.classhandling.ClassStateSupport.initializeClasses(Sequence_ESTest_scaffolding.class.getClassLoader() , 85 "org.biojava.bio.seq.AcceptNoneFilter", 86 "uk.ac.sanger.artemis.components.LogViewer$1", 87 "net.sf.cglib.core.EmitUtils$ArrayDelimiters", 88 "org.biojava.bio.symbol.FuzzyLocation$1", 89 "com.ibatis.common.jdbc.SimpleDataSource$SimplePooledConnection", 90 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.ConditionalTagHandler", 91 "org.biojava.bio.seq.io.SymbolTokenization$TokenType", 92 "org.biojava.bio.seq.db.IDMaker$ByURN", 93 "org.biojava.bio.seq.ByHierarchy", 94 "org.biojava.bio.seq.ComponentFeature$Template", 95 "org.apache.log4j.AppenderSkeleton", 96 "com.ibatis.sqlmap.client.extensions.ParameterSetter", 97 "org.biojava.utils.stax.SAX2StAXAdaptor", 98 "uk.ac.sanger.artemis.io.SimpleDocumentFeature", 99 "uk.ac.sanger.artemis.sequence.BasePatternFormatException", 100 "com.sshtools.j2ssh.authentication.PasswordAuthenticationClient", 101 "net.sf.cglib.core.KeyFactory$Generator", 102 "com.sshtools.j2ssh.SshClient", 103 "uk.ac.sanger.artemis.EntryChangeListener", 104 "org.biojava.bio.seq.FeatureFilter$OverlapsLocation", 105 "org.biojava.bio.symbol.DoubleAlphabet$SubDoubleAlphabet", 106 "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$AlphabetHandler$1", 107 "uk.ac.sanger.artemis.Selectable", 108 "net.sf.cglib.core.CodeEmitter$State", 109 "org.biojava.bio.seq.io.NameTokenization", 110 "org.biojava.bio.seq.MergeFeatureHolder", 111 "uk.ac.sanger.artemis.io.RangeVector", 112 "uk.ac.sanger.artemis.io.FeatureTable", 113 "org.biojava.bio.seq.FramedFeature$ReadingFrame", 114 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateTagHandler", 115 "org.biojava.bio.seq.io.CharacterTokenization", 116 "org.biojava.bio.seq.homol.SimilarityPairFeature$EmptyPairwiseAlignment", 117 "uk.ac.sanger.artemis.io.PublicDBDocumentEntry", 118 "net.sf.cglib.core.Constants", 119 "uk.ac.sanger.artemis.util.StringVector", 120 "net.sf.cglib.core.AbstractClassGenerator", 121 "org.biojava.bio.seq.Feature$Template", 122 "com.ibatis.common.beans.BaseProbe", 123 "com.sshtools.j2ssh.transport.AsyncService", 124 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"com.sshtools.j2ssh.transport.InvalidMessageException", 184 "org.biojava.bio.Annotation", 185 "org.biojava.bio.symbol.IntegerAlphabet$IntegerSymbol", 186 "org.biojava.utils.lsid.LifeScienceIdentifierParseException", 187 "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler", 188 "com.sshtools.j2ssh.authentication.AuthenticationProtocolClient", 189 "org.apache.log4j.Category", 190 "uk.ac.sanger.artemis.io.LocationParseException", 191 "org.biojava.utils.ListTools$Mapper", 192 "org.biojava.bio.seq.io.StreamParser", 193 "org.biojava.bio.seq.Up", 194 "org.biojava.bio.seq.FeatureFilter$ByAncestor", 195 "uk.ac.sanger.artemis.util.FastVector", 196 "org.biojava.bio.symbol.SimpleSymbol", 197 "com.ibatis.common.beans.ComplexBeanProbe", 198 "org.apache.log4j.helpers.ThreadLocalMap", 199 "net.sf.cglib.core.KeyFactory$2", 200 "org.biojava.bio.symbol.AbstractSimpleBasisSymbol", 201 "net.sf.cglib.core.KeyFactory$1", 202 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"uk.ac.sanger.artemis.io.GFF3AttributeAggregator", 243 "net.sf.cglib.beans.BulkBean$Generator", 244 "org.gmod.schema.cv.Cv", 245 "uk.ac.sanger.artemis.util.InputStreamProgressListenerVector", 246 "net.sf.cglib.core.DefaultNamingPolicy", 247 "uk.ac.sanger.artemis.util.PushBackException", 248 "com.ibatis.sqlmap.engine.exchange.DataExchange", 249 "com.ibatis.sqlmap.engine.mapping.sql.SqlChild", 250 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.DynamicTagHandler", 251 "com.sshtools.j2ssh.connection.IOChannel", 252 "org.biojava.utils.SingletonList", 253 "org.biojava.bio.symbol.FuzzyLocation$OuterRangeResolver", 254 "org.biojava.bio.symbol.SymbolList", 255 "org.biojava.bio.BioException", 256 "net.sf.cglib.asm.AnnotationVisitor", 257 "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange", 258 "com.ibatis.sqlmap.engine.type.TypeHandlerFactory$1", 259 "com.ibatis.sqlmap.engine.builder.xml.XMLSqlSource", 260 "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMapping", 261 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"uk.ac.sanger.artemis.io.EMBLObject", 476 "org.postgresql.largeobject.LargeObject", 477 "uk.ac.sanger.artemis.chado.GmodDAO", 478 "net.sf.cglib.core.ClassGenerator", 479 "net.sf.cglib.core.ReflectUtils$4", 480 "org.apache.log4j.spi.DefaultRepositorySelector", 481 "uk.ac.sanger.artemis.OptionChangeListener", 482 "com.sshtools.j2ssh.connection.ChannelOutputStream", 483 "net.sf.cglib.core.ReflectUtils$1", 484 "net.sf.cglib.core.ReflectUtils$2", 485 "net.sf.cglib.core.ReflectUtils$3", 486 "uk.ac.sanger.artemis.io.Sequence", 487 "org.biojava.bio.symbol.LocationComparator", 488 "uk.ac.sanger.artemis.components.variant.BCFReader", 489 "uk.ac.sanger.artemis.util.LargeObjectDocument", 490 "uk.ac.sanger.artemis.io.GenbankMisc", 491 "uk.ac.sanger.artemis.chado.JdbcDAO", 492 "net.sf.cglib.core.ObjectSwitchCallback", 493 "org.biojava.utils.bytecode.GeneratedClassLoader", 494 "org.biojava.bio.dist.DistributionFactory", 495 "com.ibatis.sqlmap.engine.cache.CacheKey", 496 "uk.ac.sanger.artemis.io.Location", 497 "org.biojava.utils.stax.StAXContentHandler", 498 "uk.ac.sanger.artemis.io.PublicDBStreamFeature", 499 "net.sf.cglib.core.DefaultGeneratorStrategy", 500 "org.biojava.bio.seq.SequenceAnnotator", 501 "org.apache.log4j.or.ObjectRenderer", 502 "uk.ac.sanger.artemis.util.DatabaseLocationParser", 503 "org.biojava.bio.seq.FeatureFilter$ShadowOverlapsLocation", 504 "net.sf.cglib.core.DebuggingClassWriter$1", 505 "uk.ac.sanger.artemis.io.FastaStreamSequence", 506 "uk.ac.sanger.artemis.io.FeatureEnumeration", 507 "org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper", 508 "com.ibatis.sqlmap.engine.type.DateTypeHandler", 509 "org.biojava.utils.ChangeForwarder", 510 "uk.ac.sanger.artemis.io.StreamFeature", 511 "com.ibatis.common.io.ReaderInputStream", 512 "uk.ac.sanger.artemis.util.ReadOnlyException", 513 "org.biojava.bio.symbol.GappedSymbolList", 514 "org.biojava.bio.seq.FeatureFilter$Or", 515 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535 "org.biojava.bio.symbol.DoubleAlphabet$DoubleSymbol", 536 "org.apache.log4j.spi.Configurator", 537 "org.biojava.bio.PropertyConstraint", 538 "uk.ac.sanger.artemis.io.MSPcrunchStreamFeature", 539 "org.biojava.bio.seq.impl.SimpleFramedFeature", 540 "net.sf.cglib.core.CodeEmitter", 541 "org.gmod.schema.sequence.Feature", 542 "org.biojava.bio.symbol.FiniteAlphabet", 543 "org.biojava.bio.seq.FeatureFilter$OnlyChildren", 544 "org.biojava.bio.seq.homol.SimilarityPairFeature$Template", 545 "org.apache.log4j.PropertyWatchdog", 546 "uk.ac.sanger.artemis.io.KeyVector", 547 "org.biojava.bio.seq.Down", 548 "org.gmod.schema.sequence.FeatureCvTermPub", 549 "org.biojava.bio.Annotatable", 550 "org.gmod.schema.utils.Rankable", 551 "com.ibatis.sqlmap.engine.accessplan.ComplexAccessPlan", 552 "net.sf.cglib.core.ProcessSwitchCallback", 553 "com.ibatis.sqlmap.engine.mapping.sql.Sql", 554 "uk.ac.sanger.artemis.components.FileViewer$2", 555 "com.ibatis.common.beans.ProbeFactory", 556 "com.ibatis.common.beans.ClassInfo", 557 "uk.ac.sanger.artemis.FeatureVector", 558 "org.biojava.bio.seq.io.SequenceBuilderBase", 559 "uk.ac.sanger.artemis.io.EmblStreamSequence", 560 "org.biojava.utils.stax.StringElementHandlerBase", 561 "com.ibatis.sqlmap.engine.scope.ErrorContext", 562 "org.biojava.bio.seq.io.CrossProductTokenization", 563 "org.biojava.utils.walker.Visitor", 564 "org.biojava.bio.symbol.IntegerAlphabet$IntegerArray", 565 "org.biojava.bio.seq.FeatureFilter$StrandFilter", 566 "com.ibatis.sqlmap.engine.config.SqlSource", 567 "org.biojava.bio.symbol.FundamentalAtomicSymbol", 568 "org.biojava.bio.seq.FeatureHolder", 569 "net.sf.cglib.asm.Edge", 570 "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler$MappingHandler", 571 "org.biojava.utils.ChangeForwarder$Retyper", 572 "org.gmod.schema.dao.OrganismDaoI", 573 "com.ibatis.sqlmap.engine.mapping.sql.stat.StaticSql", 574 "net.sf.cglib.asm.ClassWriter", 575 "org.biojava.bio.seq.io.SymbolTokenization", 576 "com.sshtools.j2ssh.session.SessionChannelClient", 577 "htsjdk.samtools.util.LocationAware", 578 "uk.ac.sanger.artemis.io.QualifierInfo", 579 "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry$1", 580 "com.ibatis.common.resources.Resources", 581 "org.biojava.utils.Unchangeable", 582 "org.apache.log4j.Priority", 583 "org.biojava.bio.symbol.FuzzyLocation", 584 "org.biojava.bio.CardinalityConstraint", 585 "net.sf.cglib.core.AbstractClassGenerator$Source", 586 "org.biojava.bio.dp.SimpleDotState", 587 "org.apache.log4j.LogManager", 588 "org.gmod.schema.sequence.FeatureLoc", 589 "org.biojava.bio.symbol.AlphabetIndex", 590 "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler", 591 "org.biojava.bio.seq.FeatureHolder$EmptyFeatureHolder", 592 "com.ibatis.common.logging.jakarta.JakartaCommonsLoggingImpl", 593 "org.biojava.bio.seq.FeatureFilter$OnlyDescendants", 594 "uk.ac.sanger.artemis.io.DocumentEntry", 595 "org.biojava.bio.seq.FeatureFilter$ByFeature", 596 "org.biojava.bio.symbol.EmptySymbolList", 597 "uk.ac.sanger.artemis.io.BlastStreamFeature", 598 "org.apache.log4j.DefaultCategoryFactory", 599 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagHandlerFactory", 600 "org.postgresql.core.Logger", 601 "org.apache.log4j.or.RendererMap", 602 "com.ibatis.sqlmap.engine.mapping.sql.simple.SimpleDynamicSql", 603 "uk.ac.sanger.artemis.io.OutOfDateException", 604 "uk.ac.sanger.artemis.ExternalProgram", 605 "com.sshtools.j2ssh.transport.Service", 606 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateContext", 607 "uk.ac.sanger.artemis.io.EmblMisc", 608 "org.gmod.schema.pub.PubDbXRef", 609 "com.ibatis.sqlmap.engine.type.SqlDateTypeHandler", 610 "org.biojava.bio.symbol.AbstractAlphabet", 611 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsPropertyAvailableTagHandler", 612 "org.biojava.bio.seq.FeatureFilter$ByClass", 613 "org.gmod.schema.general.DbXRef", 614 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"uk.ac.sanger.artemis.io.Qualifier", 635 "uk.ac.sanger.artemis.util.InputStreamProgressListener", 636 "org.biojava.bio.AnnotationType$Impl", 637 "org.biojava.bio.seq.RemoteFeature", 638 "com.ibatis.sqlmap.engine.type.JdbcTypeRegistry", 639 "org.apache.log4j.helpers.OnlyOnceErrorHandler", 640 "org.biojava.bio.symbol.TranslationTable", 641 "uk.ac.sanger.artemis.sequence.MarkerRangeVector", 642 "uk.ac.sanger.artemis.io.DocumentEntryAutosaveThread", 643 "org.biojava.bio.symbol.CrossProductAlphabetIndex", 644 "com.ibatis.sqlmap.engine.execution.BatchException", 645 "com.sshtools.j2ssh.sftp.FileAttributes", 646 "org.biojava.bio.seq.impl.SimpleStrandedFeature", 647 "uk.ac.sanger.artemis.sequence.Marker", 648 "org.biojava.bio.seq.Feature$ByLocationComparator", 649 "org.biojava.bio.symbol.DoubleAlphabet", 650 "org.postgresql.largeobject.BlobInputStream", 651 "org.apache.log4j.ProvisionNode", 652 "com.sshtools.j2ssh.authentication.SshAuthenticationClient", 653 "uk.ac.sanger.artemis.io.GFFDocumentEntry", 654 "org.biojava.bio.symbol.AbstractSymbolList$EditTranslater", 655 "com.ibatis.sqlmap.engine.mapping.result.ResultObjectFactory", 656 "uk.ac.sanger.artemis.io.GFFStreamFeature", 657 "org.biojava.bio.seq.impl.SimpleSequence", 658 "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler", 659 "org.biojava.bio.symbol.AtomicSymbol", 660 "com.sshtools.j2ssh.transport.MessageStoreEOFException", 661 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsGreaterEqualTagHandler", 662 "org.biojava.bio.dist.Distribution", 663 "org.biojava.bio.seq.FeatureFilter$BySequenceName", 664 "org.apache.log4j.spi.RootLogger", 665 "org.biojava.bio.BioError", 666 "com.ibatis.common.beans.Invoker", 667 "net.sf.cglib.asm.Type", 668 "org.biojava.bio.seq.FilterUtils$FilterTransformer", 669 "org.apache.log4j.spi.ErrorHandler", 670 "com.ibatis.sqlmap.engine.accessplan.EnhancedPropertyAccessPlan", 671 "org.biojava.bio.seq.db.ViewingSequenceDB", 672 "net.sf.cglib.core.MethodInfo", 673 "uk.ac.sanger.artemis.ExternalProgramException", 674 "uk.ac.sanger.artemis.io.QualifierVector", 675 "org.apache.log4j.spi.RendererSupport", 676 "org.biojava.bio.symbol.SymbolListFactory", 677 "org.biojava.bio.seq.OptimizableFilter", 678 "uk.ac.sanger.artemis.components.variant.TabixReader$Iterator", 679 "com.ibatis.sqlmap.engine.execution.SqlExecutor", 680 "uk.ac.sanger.artemis.FeatureChangeListener", 681 "uk.ac.sanger.artemis.util.FileDocument", 682 "uk.ac.sanger.artemis.FeatureChangeEvent", 683 "net.sf.cglib.core.Block", 684 "org.biojava.bio.symbol.AlphabetManager$GapSymbol", 685 "com.ibatis.sqlmap.engine.mapping.sql.SqlText", 686 "net.sf.cglib.asm.Opcodes", 687 "uk.ac.sanger.artemis.io.LocationParseNodeVector", 688 "uk.ac.sanger.artemis.io.LineGroup", 689 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagContext", 690 "com.ibatis.sqlmap.engine.type.TimeOnlyTypeHandler", 691 "org.biojava.bio.symbol.AbstractLocation", 692 "org.biojava.bio.CollectionConstraint$AllValuesIn", 693 "com.ibatis.sqlmap.engine.mapping.statement.RowHandlerCallback", 694 "org.postgresql.Driver", 695 "org.biojava.utils.ChangeSupport", 696 "org.biojava.bio.NonePropertyConstraint", 697 "org.biojava.bio.seq.io.AlternateTokenization", 698 "com.ibatis.sqlmap.engine.accessplan.AccessPlanFactory", 699 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.DynamicParent", 700 "org.biojava.bio.molbio.RestrictionSite", 701 "org.biojava.bio.seq.StrandedFeature$Strand", 702 "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry", 703 "org.biojava.bio.symbol.AlphabetManager$1", 704 "org.apache.log4j.Logger", 705 "org.biojava.bio.dp.ScoreType$NullModel", 706 "org.biojava.bio.symbol.IntegerAlphabet$1", 707 "com.ibatis.sqlmap.engine.mapping.statement.ExecuteListener", 708 "org.biojava.bio.seq.homol.HomologyFeature", 709 "uk.ac.sanger.artemis.EntryGroup", 710 "uk.ac.sanger.artemis.io.Feature", 711 "com.ibatis.sqlmap.engine.mapping.statement.SelectStatement", 712 "org.biojava.bio.AbstractAnnotation", 713 "org.biojava.bio.symbol.ManyToOneTranslationTable", 714 "com.ibatis.sqlmap.engine.transaction.TransactionException", 715 "com.sshtools.j2ssh.authentication.AuthenticationProtocolListener", 716 "org.apache.log4j.helpers.LogLog", 717 "uk.ac.sanger.artemis.io.QualifierInfoVector", 718 "org.biojava.bio.seq.SequenceIterator", 719 "com.ibatis.common.logging.LogFactory", 720 "org.biojava.bio.seq.io.SimpleSequenceBuilder$SSBFactory", 721 "com.ibatis.sqlmap.engine.type.BaseTypeHandler", 722 "org.biojava.bio.seq.db.SequenceDBLite", 723 "org.apache.log4j.spi.RepositorySelector", 724 "org.biojava.utils.ListTools$SeriesList", 725 "org.biojava.bio.symbol.SimpleSymbolList", 726 "uk.ac.sanger.artemis.io.GFF3AttributeBuilder$1", 727 "com.ibatis.common.beans.DomProbe", 728 "com.ibatis.sqlmap.engine.type.CustomTypeHandler", 729 "org.biojava.utils.ChangeListener$LoggingListener", 730 "org.biojava.bio.seq.db.HashSequenceDB", 731 "net.sf.cglib.core.NamingPolicy", 732 "org.biojava.bio.symbol.SingletonAlphabet", 733 "org.biojava.bio.SmallAnnotation", 734 "org.biojava.bio.seq.io.SimpleSequenceBuilder$1", 735 "org.biojava.bio.symbol.ReversibleTranslationTable", 736 "uk.ac.sanger.artemis.io.Entry", 737 "net.sf.cglib.asm.Item", 738 "uk.ac.sanger.artemis.util.LinePushBackReader", 739 "org.apache.log4j.or.DefaultRenderer", 740 "uk.ac.sanger.artemis.util.ProgressInputStream", 741 "com.ibatis.common.jdbc.exception.NestedSQLException", 742 "com.ibatis.sqlmap.engine.builder.xml.SqlMapClasspathEntityResolver", 743 "com.ibatis.sqlmap.engine.accessplan.AccessPlan", 744 "org.biojava.bio.seq.FeatureFilter$ByChild", 745 "org.biojava.bio.seq.io.SequenceBuilder", 746 "net.sf.cglib.asm.Attribute", 747 "net.sf.cglib.asm.ClassAdapter", 748 "uk.ac.sanger.artemis.io.FeatureVector", 749 "net.sf.cglib.asm.MethodAdapter", 750 "org.biojava.bio.symbol.LinearAlphabetIndex", 751 "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler$1", 752 "com.ibatis.sqlmap.client.extensions.TypeHandlerCallback", 753 "org.apache.commons.logging.impl.Log4JLogger", 754 "org.biojava.bio.symbol.Location", 755 "org.gmod.schema.organism.Organism", 756 "org.gmod.schema.general.Db", 757 "com.ibatis.sqlmap.engine.config.CacheModelConfig", 758 "com.ibatis.sqlmap.engine.impl.SqlMapSessionImpl", 759 "org.apache.log4j.Appender", 760 "org.biojava.bio.symbol.SimpleReversibleTranslationTable", 761 "org.biojava.bio.symbol.Alphabet", 762 "com.ibatis.sqlmap.engine.config.ParameterMapConfig", 763 "org.biojava.bio.symbol.AbstractSymbolList$EditScreener", 764 "org.biojava.utils.ListTools$5", 765 "net.sf.cglib.core.CodeGenerationException", 766 "org.biojava.bio.seq.Frame", 767 "uk.ac.sanger.artemis.chado.ChadoTransaction", 768 "com.sshtools.j2ssh.transport.SshMsgServiceAccept", 769 "org.biojava.utils.AssertionFailure", 770 "uk.ac.sanger.artemis.FeaturePredicate", 771 "com.sshtools.j2ssh.authentication.AuthenticationProtocolException", 772 "uk.ac.sanger.artemis.Logger", 773 "org.biojava.bio.seq.IsTopLevel", 774 "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl", 775 "com.ibatis.sqlmap.client.SqlMapSession", 776 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotEmptyTagHandler", 777 "org.gmod.schema.sequence.FeatureSynonym", 778 "org.apache.log4j.spi.LoggingEvent", 779 "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol", 780 "com.ibatis.sqlmap.engine.mapping.statement.CachingStatement", 781 "uk.ac.sanger.artemis.io.QualifierLazyLoading", 782 "org.biojava.bio.symbol.FuzzyLocation$AverageRangeResolver", 783 "uk.ac.sanger.artemis.util.DatabaseDocument", 784 "uk.ac.sanger.artemis.FeatureEnumeration", 785 "net.sf.cglib.asm.Label", 786 "org.biojava.bio.symbol.AbstractSymbolList", 787 "uk.ac.sanger.artemis.io.StreamFeatureTable", 788 "org.gmod.schema.dao.PubDaoI", 789 "org.biojava.bio.symbol.RangeLocation" 790 ); 791 } 792 resetClasses()793 private static void resetClasses() { 794 org.evosuite.runtime.classhandling.ClassResetter.getInstance().setClassLoader(Sequence_ESTest_scaffolding.class.getClassLoader()); 795 796 org.evosuite.runtime.classhandling.ClassStateSupport.resetClasses( 797 "uk.ac.sanger.artemis.io.LineGroup", 798 "uk.ac.sanger.artemis.io.Packing", 799 "org.apache.log4j.Category", 800 "org.apache.log4j.Logger", 801 "org.apache.log4j.Priority", 802 "org.apache.log4j.Level", 803 "org.apache.log4j.or.RendererMap", 804 "org.apache.log4j.helpers.OptionConverter", 805 "org.apache.log4j.helpers.Loader", 806 "org.apache.log4j.helpers.LogLog", 807 "org.apache.log4j.PropertyConfigurator", 808 "org.apache.log4j.LogManager", 809 "org.apache.log4j.CategoryKey", 810 "org.apache.log4j.ProvisionNode", 811 "uk.ac.sanger.artemis.util.DatabaseDocument", 812 "uk.ac.sanger.artemis.util.DatabaseLocationParser", 813 "org.apache.log4j.MDC", 814 "uk.ac.sanger.artemis.chado.GmodDAO", 815 "uk.ac.sanger.artemis.chado.IBatisDAO", 816 "uk.ac.sanger.artemis.chado.SqlMapClientWrapper", 817 "com.ibatis.common.resources.Resources", 818 "com.ibatis.common.beans.ComplexBeanProbe", 819 "com.ibatis.common.beans.GenericProbe", 820 "com.ibatis.common.beans.ProbeFactory", 821 "com.ibatis.sqlmap.engine.config.SqlMapConfiguration", 822 "com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate", 823 "com.ibatis.sqlmap.engine.execution.SqlExecutor", 824 "com.ibatis.sqlmap.engine.type.TypeHandlerFactory$1", 825 "com.ibatis.sqlmap.engine.type.TypeHandlerFactory", 826 "com.ibatis.sqlmap.engine.type.UnknownTypeHandler", 827 "com.ibatis.sqlmap.engine.type.DateTypeHandler", 828 "com.ibatis.sqlmap.engine.type.DateOnlyTypeHandler", 829 "com.ibatis.sqlmap.engine.type.TimeOnlyTypeHandler", 830 "com.ibatis.sqlmap.engine.type.SqlDateTypeHandler", 831 "com.ibatis.sqlmap.engine.type.SqlTimeTypeHandler", 832 "com.ibatis.sqlmap.engine.type.SqlTimestampTypeHandler", 833 "com.ibatis.sqlmap.engine.exchange.ComplexDataExchange", 834 "com.ibatis.common.logging.LogFactory", 835 "org.apache.commons.logging.impl.Log4JLogger", 836 "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl", 837 "com.ibatis.sqlmap.engine.builder.xml.SqlMapClasspathEntityResolver", 838 "com.ibatis.common.beans.ClassInfo", 839 "com.ibatis.sqlmap.engine.accessplan.AccessPlanFactory", 840 "com.ibatis.common.jdbc.SimpleDataSource", 841 "org.postgresql.Driver", 842 "com.ibatis.sqlmap.engine.mapping.result.ResultMap", 843 "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange", 844 "net.sf.cglib.core.TypeUtils", 845 "net.sf.cglib.asm.Type", 846 "net.sf.cglib.core.KeyFactory", 847 "net.sf.cglib.core.AbstractClassGenerator", 848 "net.sf.cglib.core.KeyFactory$Generator", 849 "net.sf.cglib.core.DefaultGeneratorStrategy", 850 "net.sf.cglib.core.DefaultNamingPolicy", 851 "net.sf.cglib.asm.ClassWriter", 852 "net.sf.cglib.core.DebuggingClassWriter", 853 "net.sf.cglib.core.ClassEmitter", 854 "net.sf.cglib.core.ReflectUtils", 855 "net.sf.cglib.core.EmitUtils", 856 "net.sf.cglib.core.Constants", 857 "net.sf.cglib.core.CodeEmitter", 858 "net.sf.cglib.asm.Frame", 859 "net.sf.cglib.asm.ClassReader", 860 "net.sf.cglib.core.ClassNameReader$EarlyExitException", 861 "net.sf.cglib.core.ClassNameReader", 862 "net.sf.cglib.beans.BulkBean", 863 "org.biojava.bio.symbol.DoubleAlphabet", 864 "org.biojava.bio.symbol.AlphabetManager$GapSymbol", 865 "org.biojava.bio.symbol.AlphabetManager$SizeQueen", 866 "org.biojava.bio.symbol.IntegerAlphabet", 867 "org.biojava.bio.symbol.SimpleSymbol", 868 "org.biojava.bio.symbol.AbstractSimpleBasisSymbol", 869 "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol", 870 "org.biojava.utils.ChangeType", 871 "org.biojava.bio.EmptyAnnotation", 872 "org.biojava.bio.Annotation", 873 "org.biojava.bio.symbol.EmptyAlphabet", 874 "org.biojava.bio.symbol.Alphabet", 875 "org.biojava.bio.AbstractAnnotation", 876 "org.biojava.bio.SimpleAnnotation", 877 "org.biojava.utils.ListTools", 878 "org.biojava.utils.SingletonList", 879 "org.biojava.bio.SmallAnnotation", 880 "org.biojava.utils.lsid.LifeScienceIdentifier", 881 "org.biojava.utils.SmallMap", 882 "org.biojava.bio.symbol.AlphabetManager$WellKnownBasisSymbol", 883 "org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol", 884 "org.biojava.bio.symbol.FundamentalAtomicSymbol", 885 "org.biojava.utils.ChangeListener", 886 "org.biojava.utils.ChangeSupport", 887 "org.biojava.bio.Annotatable", 888 "org.biojava.bio.symbol.AbstractAlphabet", 889 "org.biojava.bio.symbol.SingletonAlphabet", 890 "org.biojava.bio.symbol.SimpleAlphabet", 891 "org.biojava.bio.symbol.AlphabetManager$WellKnownAlphabet", 892 "org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper", 893 "org.biojava.bio.seq.io.CharacterTokenization", 894 "org.biojava.bio.symbol.SimpleBasisSymbol", 895 "org.biojava.bio.seq.io.AlternateTokenization", 896 "org.biojava.bio.symbol.AlphabetManager", 897 "org.biojava.bio.dist.DistributionFactory$DefaultDistributionFactory", 898 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