1 /** 2 * Scaffolding file used to store all the setups needed to run 3 * tests automatically generated by EvoSuite 4 * Fri Jan 12 15:03:09 GMT 2018 5 */ 6 7 package uk.ac.sanger.artemis.io; 8 9 import org.evosuite.runtime.annotation.EvoSuiteClassExclude; 10 import org.junit.BeforeClass; 11 import org.junit.Before; 12 import org.junit.After; 13 import org.junit.AfterClass; 14 import org.evosuite.runtime.sandbox.Sandbox; 15 import org.evosuite.runtime.sandbox.Sandbox.SandboxMode; 16 17 @EvoSuiteClassExclude 18 public class IndexFastaStream_ESTest_scaffolding { 19 20 @org.junit.Rule 21 public org.evosuite.runtime.vnet.NonFunctionalRequirementRule nfr = new org.evosuite.runtime.vnet.NonFunctionalRequirementRule(); 22 23 private static final java.util.Properties defaultProperties = (java.util.Properties) java.lang.System.getProperties().clone(); 24 25 private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000); 26 27 28 @BeforeClass initEvoSuiteFramework()29 public static void initEvoSuiteFramework() { 30 org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.io.IndexFastaStream"; 31 org.evosuite.runtime.GuiSupport.initialize(); 32 org.evosuite.runtime.RuntimeSettings.maxNumberOfThreads = 100; 33 org.evosuite.runtime.RuntimeSettings.maxNumberOfIterationsPerLoop = 10000; 34 org.evosuite.runtime.RuntimeSettings.mockSystemIn = true; 35 org.evosuite.runtime.RuntimeSettings.sandboxMode = org.evosuite.runtime.sandbox.Sandbox.SandboxMode.RECOMMENDED; 36 org.evosuite.runtime.sandbox.Sandbox.initializeSecurityManagerForSUT(); 37 org.evosuite.runtime.classhandling.JDKClassResetter.init(); 38 setSystemProperties(); 39 initializeClasses(); 40 org.evosuite.runtime.Runtime.getInstance().resetRuntime(); 41 } 42 43 @AfterClass clearEvoSuiteFramework()44 public static void clearEvoSuiteFramework(){ 45 Sandbox.resetDefaultSecurityManager(); 46 java.lang.System.setProperties((java.util.Properties) defaultProperties.clone()); 47 } 48 49 @Before initTestCase()50 public void initTestCase(){ 51 threadStopper.storeCurrentThreads(); 52 threadStopper.startRecordingTime(); 53 org.evosuite.runtime.jvm.ShutdownHookHandler.getInstance().initHandler(); 54 org.evosuite.runtime.sandbox.Sandbox.goingToExecuteSUTCode(); 55 setSystemProperties(); 56 org.evosuite.runtime.GuiSupport.setHeadless(); 57 org.evosuite.runtime.Runtime.getInstance().resetRuntime(); 58 org.evosuite.runtime.agent.InstrumentingAgent.activate(); 59 } 60 61 @After doneWithTestCase()62 public void doneWithTestCase(){ 63 threadStopper.killAndJoinClientThreads(); 64 org.evosuite.runtime.jvm.ShutdownHookHandler.getInstance().safeExecuteAddedHooks(); 65 org.evosuite.runtime.classhandling.JDKClassResetter.reset(); 66 resetClasses(); 67 org.evosuite.runtime.sandbox.Sandbox.doneWithExecutingSUTCode(); 68 org.evosuite.runtime.agent.InstrumentingAgent.deactivate(); 69 org.evosuite.runtime.GuiSupport.restoreHeadlessMode(); 70 } 71 setSystemProperties()72 public static void setSystemProperties() { 73 74 java.lang.System.setProperties((java.util.Properties) defaultProperties.clone()); 75 java.lang.System.setProperty("file.encoding", "UTF-8"); 76 java.lang.System.setProperty("java.awt.headless", "true"); 77 java.lang.System.setProperty("user.country", "GB"); 78 java.lang.System.setProperty("user.language", "en"); 79 java.lang.System.setProperty("user.timezone", "Europe/London"); 80 java.lang.System.setProperty("log4j.configuration", "SUT.log4j.properties"); 81 } 82 initializeClasses()83 private static void initializeClasses() { 84 org.evosuite.runtime.classhandling.ClassStateSupport.initializeClasses(IndexFastaStream_ESTest_scaffolding.class.getClassLoader() , 85 "uk.ac.sanger.artemis.components.LogViewer$1", 86 "org.biojava.bio.seq.AcceptNoneFilter", 87 "net.sf.cglib.core.EmitUtils$ArrayDelimiters", 88 "com.ibatis.common.jdbc.SimpleDataSource$SimplePooledConnection", 89 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.ConditionalTagHandler", 90 "org.biojava.bio.seq.io.SymbolTokenization$TokenType", 91 "org.biojava.bio.seq.db.IDMaker$ByURN", 92 "org.biojava.bio.seq.ByHierarchy", 93 "org.biojava.bio.seq.ComponentFeature$Template", 94 "org.apache.log4j.AppenderSkeleton", 95 "com.ibatis.sqlmap.client.extensions.ParameterSetter", 96 "org.biojava.utils.stax.SAX2StAXAdaptor", 97 "uk.ac.sanger.artemis.io.SimpleDocumentFeature", 98 "uk.ac.sanger.artemis.sequence.BasePatternFormatException", 99 "net.sf.cglib.core.KeyFactory$Generator", 100 "uk.ac.sanger.artemis.io.MSPcrunchDocumentEntry", 101 "uk.ac.sanger.artemis.EntryChangeListener", 102 "org.biojava.ontology.Term", 103 "org.biojava.utils.ListTools$Triplet", 104 "org.biojava.bio.symbol.DoubleAlphabet$SubDoubleAlphabet", 105 "uk.ac.sanger.artemis.sequence.AminoAcidSequence", 106 "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$AlphabetHandler$1", 107 "uk.ac.sanger.artemis.Selectable", 108 "net.sf.cglib.core.CodeEmitter$State", 109 "org.biojava.bio.seq.io.NameTokenization", 110 "org.biojava.bio.seq.MergeFeatureHolder", 111 "uk.ac.sanger.artemis.io.FeatureTable", 112 "htsjdk.samtools.reference.ReferenceSequenceFileFactory", 113 "uk.ac.sanger.artemis.io.RangeVector", 114 "org.biojava.bio.seq.FramedFeature$ReadingFrame", 115 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateTagHandler", 116 "org.biojava.bio.seq.io.CharacterTokenization", 117 "org.biojava.bio.seq.homol.SimilarityPairFeature$EmptyPairwiseAlignment", 118 "uk.ac.sanger.artemis.io.PublicDBDocumentEntry", 119 "htsjdk.samtools.reference.ReferenceSequenceFileFactory$1", 120 "uk.ac.sanger.artemis.util.StringVector", 121 "net.sf.cglib.core.Constants", 122 "net.sf.cglib.core.AbstractClassGenerator", 123 "org.biojava.bio.seq.Feature$Template", 124 "com.ibatis.common.beans.BaseProbe", 125 "com.ibatis.sqlmap.engine.mapping.statement.SelectKeyStatement", 126 "org.gmod.schema.sequence.Synonym", 127 "org.biojava.bio.symbol.PointLocation", 128 "org.biojava.bio.symbol.SimpleAlphabet", 129 "org.gmod.schema.sequence.FeatureCvTermProp", 130 "org.biojava.bio.seq.io.SequenceBuilderFactory", 131 "org.apache.log4j.Hierarchy", 132 "uk.ac.sanger.artemis.sequence.MarkerRange", 133 "org.biojava.utils.Changeable", 134 "org.biojava.bio.symbol.EmptyLocation", 135 "net.sf.cglib.asm.MethodWriter", 136 "com.ibatis.common.util.PaginatedList", 137 "uk.ac.sanger.artemis.io.QualifierInfoHash", 138 "net.sf.cglib.core.ClassNameReader$EarlyExitException", 139 "com.ibatis.sqlmap.engine.cache.CacheModel", 140 "org.apache.log4j.spi.OptionHandler", 141 "org.biojava.bio.symbol.SimpleManyToOneTranslationTable", 142 "org.biojava.utils.stax.DelegationManager", 143 "org.biojava.bio.seq.StrandedFeature", 144 "org.biojava.utils.lsid.LifeScienceIdentifier", 145 "net.sf.cglib.core.ReflectUtils", 146 "org.biojava.bio.symbol.FuzzyLocation$InnerRangeResolver", 147 "org.biojava.utils.ChangeVetoException", 148 "org.biojava.bio.symbol.IllegalAlphabetException", 149 "org.biojava.bio.seq.db.SequenceDB", 150 "htsjdk.samtools.reference.AbstractFastaSequenceFile", 151 "org.biojava.bio.symbol.DoubleAlphabet$DoubleRange", 152 "htsjdk.samtools.seekablestream.SeekableStream", 153 "org.biojava.bio.symbol.BetweenLocation", 154 "net.sf.cglib.core.AbstractClassGenerator$1", 155 "uk.ac.sanger.artemis.components.Splash$2", 156 "org.biojava.bio.symbol.AbstractTranslationTable", 157 "org.gmod.schema.dao.GeneralDaoI", 158 "com.ibatis.sqlmap.engine.exchange.DataExchangeFactory", 159 "net.sf.cglib.core.LocalVariablesSorter", 160 "org.apache.log4j.helpers.OptionConverter", 161 "org.gmod.schema.dao.BaseDaoI", 162 "com.ibatis.sqlmap.client.SqlMapExecutor", 163 "org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl", 164 "org.biojava.bio.symbol.Edit", 165 "com.ibatis.sqlmap.client.SqlMapException", 166 "uk.ac.sanger.artemis.io.MiscLineGroup", 167 "uk.ac.sanger.artemis.io.LazyQualifierValue", 168 "com.ibatis.sqlmap.engine.type.SqlTimeTypeHandler", 169 "org.postgresql.largeobject.BlobOutputStream", 170 "org.biojava.bio.symbol.AbstractSymbol", 171 "org.biojava.utils.bytecode.CodeGenerator", 172 "org.gmod.schema.cv.CvTerm", 173 "org.biojava.bio.seq.db.IllegalIDException", 174 "uk.ac.sanger.artemis.sequence.SequenceChangeListener", 175 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsGreaterThanTagHandler", 176 "uk.ac.sanger.artemis.io.InvalidRelationException", 177 "org.biojava.utils.bytecode.CodeMethod", 178 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEqualTagHandler", 179 "org.biojava.bio.seq.impl.FeatureImpl$1", 180 "org.biojava.bio.seq.io.SimpleSequenceBuilder", 181 "org.biojava.bio.Annotation", 182 "org.biojava.bio.symbol.IntegerAlphabet$IntegerSymbol", 183 "org.biojava.utils.lsid.LifeScienceIdentifierParseException", 184 "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$CharacterTokenizationHandler", 185 "org.biojava.bio.seq.io.SimpleAssemblyBuilder$1", 186 "org.apache.log4j.Category", 187 "uk.ac.sanger.artemis.io.LocationParseException", 188 "org.biojava.utils.ListTools$Mapper", 189 "htsjdk.samtools.SAMException", 190 "org.biojava.bio.seq.io.StreamParser", 191 "uk.ac.sanger.artemis.util.FastVector", 192 "org.biojava.bio.symbol.SimpleSymbol", 193 "com.ibatis.common.beans.ComplexBeanProbe", 194 "org.apache.log4j.helpers.ThreadLocalMap", 195 "net.sf.cglib.core.KeyFactory$2", 196 "org.biojava.bio.symbol.AbstractSimpleBasisSymbol", 197 "net.sf.cglib.core.KeyFactory$1", 198 "org.gmod.schema.sequence.FeatureDbXRef", 199 "net.sf.cglib.core.ClassInfo", 200 "org.biojava.utils.ChangeEvent", 201 "uk.ac.sanger.artemis.components.variant.AbstractVCFReader", 202 "org.gmod.schema.pub.Pub", 203 "uk.ac.sanger.artemis.io.ChadoCanonicalGene", 204 "net.sf.cglib.core.ClassEmitter$3", 205 "net.sf.cglib.core.EmitUtils$9", 206 "net.sf.cglib.core.ClassEmitter$1", 207 "org.biojava.utils.stax.SAX2StAXAdaptor$S2SDelegationManager", 208 "net.sf.cglib.core.EmitUtils$8", 209 "net.sf.cglib.core.EmitUtils$7", 210 "net.sf.cglib.core.Predicate", 211 "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry$IndexContig", 212 "org.biojava.bio.symbol.SimpleCrossProductAlphabet", 213 "net.sf.cglib.core.ClassEmitter", 214 "org.biojava.bio.seq.DNATools", 215 "org.gmod.schema.sequence.FeatureCvTermDbXRef", 216 "org.biojava.bio.symbol.AbstractManyToOneTranslationTable", 217 "uk.ac.sanger.artemis.io.GenbankStreamSequence", 218 "net.sf.cglib.core.ClassNameReader", 219 "org.biojava.bio.seq.io.ProteinRefSeqFileFormer", 220 "org.biojava.bio.seq.io.SimpleAssemblyBuilder", 221 "com.ibatis.sqlmap.engine.cache.CacheController", 222 "com.sshtools.j2ssh.io.UnsignedInteger32", 223 "org.biojava.bio.molbio.RestrictionEnzyme", 224 "net.sf.cglib.core.ClassNameReader$1", 225 "com.ibatis.sqlmap.engine.accessplan.BaseAccessPlan", 226 "org.biojava.bio.BioRuntimeException", 227 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.BaseTagHandler", 228 "org.biojava.bio.seq.AcceptAllFilter", 229 "org.biojava.bio.seq.io.ChunkedSymbolListFactory", 230 "net.sf.cglib.core.Local", 231 "org.biojava.bio.symbol.IntegerAlphabet$SubIntegerAlphabet", 232 "org.biojava.bio.seq.homol.SimilarityPairFeature", 233 "org.biojava.bio.symbol.FuzzyLocation$RangeResolver", 234 "org.gmod.schema.utils.propinterface.PropertyI", 235 "org.apache.log4j.spi.AppenderAttachable", 236 "com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate", 237 "uk.ac.sanger.artemis.j2ssh.FTProgress", 238 "uk.ac.sanger.artemis.io.GFF3AttributeAggregator", 239 "net.sf.cglib.beans.BulkBean$Generator", 240 "org.gmod.schema.cv.Cv", 241 "uk.ac.sanger.artemis.util.InputStreamProgressListenerVector", 242 "net.sf.cglib.core.DefaultNamingPolicy", 243 "uk.ac.sanger.artemis.util.PushBackException", 244 "com.ibatis.sqlmap.engine.exchange.DataExchange", 245 "com.ibatis.sqlmap.engine.mapping.sql.SqlChild", 246 "org.biojava.utils.ParseErrorListener", 247 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.DynamicTagHandler", 248 "org.biojava.utils.SingletonList", 249 "org.biojava.bio.seq.db.BioIndex$IndexFileAsList", 250 "org.biojava.bio.symbol.FuzzyLocation$OuterRangeResolver", 251 "org.biojava.bio.symbol.SymbolList", 252 "org.biojava.bio.BioException", 253 "net.sf.cglib.asm.AnnotationVisitor", 254 "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange", 255 "com.ibatis.sqlmap.engine.type.TypeHandlerFactory$1", 256 "com.ibatis.sqlmap.engine.builder.xml.XMLSqlSource", 257 "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMapping", 258 "net.sf.cglib.asm.FieldVisitor", 259 "org.biojava.bio.seq.FramedFeature$Template", 260 "org.biojava.bio.symbol.FuzzyPointLocation$MaxPointResolver", 261 "com.ibatis.sqlmap.engine.exchange.BaseDataExchange", 262 "net.sf.cglib.asm.MethodVisitor", 263 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597 "org.biojava.utils.ClassTools", 598 "org.biojava.bio.seq.db.IndexStore", 599 "net.sf.cglib.core.Customizer", 600 "org.biojava.bio.seq.io.GenpeptFormat", 601 "uk.ac.sanger.artemis.io.EmblStreamFeature", 602 "uk.ac.sanger.artemis.io.QualifierParseException", 603 "org.biojava.utils.cache.WeakValueHashMap", 604 "org.biojava.bio.symbol.IllegalSymbolException", 605 "uk.ac.sanger.artemis.ExternalProgramVector", 606 "com.ibatis.sqlmap.engine.type.TypeHandler", 607 "com.ibatis.sqlmap.engine.mapping.parameter.InlineParameterMapParser", 608 "org.apache.log4j.CategoryKey", 609 "uk.ac.sanger.artemis.io.Qualifier", 610 "uk.ac.sanger.artemis.util.InputStreamProgressListener", 611 "org.biojava.bio.seq.RemoteFeature", 612 "com.ibatis.sqlmap.engine.type.JdbcTypeRegistry", 613 "org.apache.log4j.helpers.OnlyOnceErrorHandler", 614 "org.biojava.bio.symbol.TranslationTable", 615 "uk.ac.sanger.artemis.io.DocumentEntryAutosaveThread", 616 "org.biojava.bio.symbol.CrossProductAlphabetIndex", 617 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"com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagContext", 658 "com.ibatis.sqlmap.engine.type.TimeOnlyTypeHandler", 659 "org.biojava.bio.symbol.AbstractLocation", 660 "com.ibatis.sqlmap.engine.mapping.statement.RowHandlerCallback", 661 "org.postgresql.Driver", 662 "uk.ac.sanger.artemis.io.BioJavaFeature", 663 "org.biojava.utils.ChangeSupport", 664 "org.biojava.bio.seq.io.AlternateTokenization", 665 "com.ibatis.sqlmap.engine.accessplan.AccessPlanFactory", 666 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.DynamicParent", 667 "org.biojava.bio.molbio.RestrictionSite", 668 "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry", 669 "org.biojava.bio.seq.StrandedFeature$Strand", 670 "org.biojava.bio.seq.io.SeqFileFormer", 671 "org.biojava.bio.symbol.AlphabetManager$1", 672 "org.apache.log4j.Logger", 673 "com.ibatis.sqlmap.engine.mapping.statement.ExecuteListener", 674 "org.biojava.bio.seq.homol.HomologyFeature", 675 "uk.ac.sanger.artemis.EntryGroup", 676 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"com.ibatis.sqlmap.engine.accessplan.AccessPlan", 716 "org.biojava.bio.seq.db.BioIndex$FileAsList", 717 "org.biojava.bio.seq.io.SequenceBuilder", 718 "net.sf.cglib.asm.Attribute", 719 "net.sf.cglib.asm.ClassAdapter", 720 "uk.ac.sanger.artemis.io.FeatureVector", 721 "net.sf.cglib.asm.MethodAdapter", 722 "org.biojava.bio.symbol.LinearAlphabetIndex", 723 "org.biojava.bio.symbol.AlphabetManager$AlphabetManagerHandler$SymbolHandler$1", 724 "com.ibatis.sqlmap.client.extensions.TypeHandlerCallback", 725 "uk.ac.sanger.artemis.io.IndexFastaStream", 726 "org.apache.commons.logging.impl.Log4JLogger", 727 "org.biojava.bio.symbol.Location", 728 "org.gmod.schema.organism.Organism", 729 "org.gmod.schema.general.Db", 730 "com.ibatis.sqlmap.engine.config.CacheModelConfig", 731 "com.ibatis.sqlmap.engine.impl.SqlMapSessionImpl", 732 "org.apache.log4j.Appender", 733 "org.biojava.bio.symbol.SimpleReversibleTranslationTable", 734 "org.biojava.bio.symbol.Alphabet", 735 "org.biojava.bio.symbol.FuzzyPointLocation$PointResolver", 736 "com.ibatis.sqlmap.engine.config.ParameterMapConfig", 737 "org.biojava.bio.symbol.AbstractSymbolList$EditScreener", 738 "org.biojava.bio.seq.io.EmblFileFormer", 739 "org.biojava.utils.ListTools$5", 740 "net.sf.cglib.core.CodeGenerationException", 741 "org.biojava.bio.seq.Frame", 742 "uk.ac.sanger.artemis.chado.ChadoTransaction", 743 "org.biojava.utils.AssertionFailure", 744 "uk.ac.sanger.artemis.FeaturePredicate", 745 "uk.ac.sanger.artemis.Logger", 746 "org.biojava.bio.seq.IsTopLevel", 747 "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl", 748 "com.ibatis.sqlmap.client.SqlMapSession", 749 "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNotEmptyTagHandler", 750 "org.gmod.schema.sequence.FeatureSynonym", 751 "org.apache.log4j.spi.LoggingEvent", 752 "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol", 753 "com.ibatis.sqlmap.engine.mapping.statement.CachingStatement", 754 "uk.ac.sanger.artemis.io.QualifierLazyLoading", 755 "org.biojava.bio.symbol.FuzzyLocation$AverageRangeResolver", 756 "uk.ac.sanger.artemis.util.DatabaseDocument", 757 "org.biojava.bio.seq.io.GAMEFormat", 758 "uk.ac.sanger.artemis.FeatureEnumeration", 759 "net.sf.cglib.asm.Label", 760 "org.biojava.bio.symbol.AbstractSymbolList", 761 "uk.ac.sanger.artemis.io.StreamFeatureTable", 762 "org.biojava.bio.seq.db.Index", 763 "htsjdk.samtools.reference.FastaSequenceIndex", 764 "org.gmod.schema.dao.PubDaoI", 765 "org.biojava.bio.symbol.RangeLocation" 766 ); 767 } 768 resetClasses()769 private static void resetClasses() { 770 org.evosuite.runtime.classhandling.ClassResetter.getInstance().setClassLoader(IndexFastaStream_ESTest_scaffolding.class.getClassLoader()); 771 772 org.evosuite.runtime.classhandling.ClassStateSupport.resetClasses( 773 "uk.ac.sanger.artemis.io.LineGroup", 774 "htsjdk.samtools.reference.ReferenceSequenceFileFactory$1", 775 "htsjdk.samtools.reference.ReferenceSequenceFileFactory", 776 "org.apache.log4j.Category", 777 "org.apache.log4j.Logger", 778 "org.apache.log4j.Priority", 779 "org.apache.log4j.Level", 780 "org.apache.log4j.or.RendererMap", 781 "org.apache.log4j.helpers.OptionConverter", 782 "org.apache.log4j.helpers.Loader", 783 "org.apache.log4j.helpers.LogLog", 784 "org.apache.log4j.PropertyConfigurator", 785 "org.apache.log4j.LogManager", 786 "org.apache.log4j.CategoryKey", 787 "org.apache.log4j.ProvisionNode", 788 "uk.ac.sanger.artemis.util.DatabaseDocument", 789 "uk.ac.sanger.artemis.util.StringVector", 790 "uk.ac.sanger.artemis.components.Splash", 791 "uk.ac.sanger.artemis.util.FastVector", 792 "uk.ac.sanger.artemis.io.KeyVector", 793 "uk.ac.sanger.artemis.io.Key", 794 "uk.ac.sanger.artemis.io.QualifierInfo", 795 "uk.ac.sanger.artemis.ExternalProgram", 796 "uk.ac.sanger.artemis.Options", 797 "uk.ac.sanger.artemis.io.PublicDBDocumentEntry", 798 "uk.ac.sanger.artemis.io.FeatureVector", 799 "uk.ac.sanger.artemis.util.DatabaseLocationParser", 800 "org.apache.log4j.MDC", 801 "uk.ac.sanger.artemis.chado.GmodDAO", 802 "uk.ac.sanger.artemis.chado.IBatisDAO", 803 "uk.ac.sanger.artemis.chado.SqlMapClientWrapper", 804 "com.ibatis.common.resources.Resources", 805 "com.ibatis.common.beans.ComplexBeanProbe", 806 "com.ibatis.common.beans.GenericProbe", 807 "com.ibatis.common.beans.ProbeFactory", 808 "com.ibatis.sqlmap.engine.config.SqlMapConfiguration", 809 "com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate", 810 "com.ibatis.sqlmap.engine.execution.SqlExecutor", 811 "com.ibatis.sqlmap.engine.type.TypeHandlerFactory$1", 812 "com.ibatis.sqlmap.engine.type.TypeHandlerFactory", 813 "com.ibatis.sqlmap.engine.type.UnknownTypeHandler", 814 "com.ibatis.sqlmap.engine.type.DateTypeHandler", 815 "com.ibatis.sqlmap.engine.type.DateOnlyTypeHandler", 816 "com.ibatis.sqlmap.engine.type.TimeOnlyTypeHandler", 817 "com.ibatis.sqlmap.engine.type.SqlDateTypeHandler", 818 "com.ibatis.sqlmap.engine.type.SqlTimeTypeHandler", 819 "com.ibatis.sqlmap.engine.type.SqlTimestampTypeHandler", 820 "com.ibatis.sqlmap.engine.exchange.ComplexDataExchange", 821 "com.ibatis.common.logging.LogFactory", 822 "org.apache.commons.logging.impl.Log4JLogger", 823 "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl", 824 "com.ibatis.sqlmap.engine.builder.xml.SqlMapClasspathEntityResolver", 825 "uk.ac.sanger.artemis.io.BioJavaFeature", 826 "org.postgresql.largeobject.LargeObject", 827 "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry", 828 "uk.ac.sanger.artemis.util.CacheHashMap", 829 "uk.ac.sanger.artemis.util.ByteBuffer", 830 "com.ibatis.common.beans.ClassInfo", 831 "com.ibatis.sqlmap.engine.accessplan.AccessPlanFactory", 832 "com.ibatis.common.jdbc.SimpleDataSource", 833 "org.postgresql.Driver", 834 "com.ibatis.sqlmap.engine.mapping.result.ResultMap", 835 "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange", 836 "net.sf.cglib.core.TypeUtils", 837 "net.sf.cglib.asm.Type", 838 "net.sf.cglib.core.KeyFactory", 839 "net.sf.cglib.core.AbstractClassGenerator", 840 "net.sf.cglib.core.KeyFactory$Generator", 841 "net.sf.cglib.core.DefaultGeneratorStrategy", 842 "net.sf.cglib.core.DefaultNamingPolicy", 843 "net.sf.cglib.asm.ClassWriter", 844 "net.sf.cglib.core.DebuggingClassWriter", 845 "net.sf.cglib.core.ClassEmitter", 846 "net.sf.cglib.core.ReflectUtils", 847 "net.sf.cglib.core.EmitUtils", 848 "net.sf.cglib.core.Constants", 849 "net.sf.cglib.core.CodeEmitter", 850 "net.sf.cglib.asm.Frame", 851 "net.sf.cglib.asm.ClassReader", 852 "net.sf.cglib.core.ClassNameReader$EarlyExitException", 853 "net.sf.cglib.core.ClassNameReader", 854 "net.sf.cglib.beans.BulkBean", 855 "net.sf.cglib.beans.BulkBean$Generator", 856 "net.sf.cglib.beans.BulkBeanEmitter", 857 "com.ibatis.sqlmap.engine.type.JdbcTypeRegistry", 858 "com.ibatis.sqlmap.engine.mapping.parameter.InlineParameterMapParser", 859 "com.ibatis.sqlmap.engine.builder.xml.XMLSqlSource", 860 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"com.ibatis.common.beans.ProbeException", 875 "com.ibatis.sqlmap.engine.accessplan.PropertyAccessPlan", 876 "net.sf.cglib.beans.BulkBeanException", 877 "uk.ac.sanger.artemis.ChangeEvent", 878 "uk.ac.sanger.artemis.EntryGroupChangeEvent", 879 "uk.ac.sanger.artemis.io.SimpleDocumentFeature", 880 "uk.ac.sanger.artemis.io.PublicDBStreamFeature", 881 "uk.ac.sanger.artemis.io.LocationParseNodeVector", 882 "uk.ac.sanger.artemis.io.LocationParseNode", 883 "uk.ac.sanger.artemis.io.QualifierVector", 884 "org.biojava.bio.seq.io.FastaFormat", 885 "uk.ac.sanger.artemis.io.FeatureTree", 886 "com.ibatis.common.xml.NodeletException", 887 "org.biojava.bio.AbstractAnnotation", 888 "org.biojava.bio.SimpleAnnotation", 889 "org.biojava.bio.seq.SimpleFeatureRealizer", 890 "org.biojava.bio.seq.impl.FeatureImpl$1", 891 "org.biojava.bio.seq.impl.FeatureImpl", 892 "org.biojava.bio.symbol.AlphabetManager$GapSymbol", 893 "org.biojava.bio.symbol.AlphabetManager$SizeQueen", 894 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"org.biojava.bio.symbol.SimpleGeneticCodeTable", 935 "org.biojava.bio.symbol.AbstractSymbolList$ListView", 936 "org.biojava.bio.BioException", 937 "org.biojava.bio.symbol.IllegalSymbolException", 938 "org.biojava.bio.BioError", 939 "org.biojava.bio.seq.RNATools", 940 "org.biojava.bio.seq.DNATools", 941 "uk.ac.sanger.artemis.io.Packing", 942 "uk.ac.sanger.artemis.sequence.Bases", 943 "uk.ac.sanger.artemis.sequence.Strand", 944 "org.biojava.bio.seq.Feature$Template", 945 "org.biojava.bio.seq.StrandedFeature$Template", 946 "org.biojava.bio.molbio.RestrictionSite$Template", 947 "org.biojava.bio.seq.impl.SimpleFeature", 948 "org.biojava.bio.seq.impl.SimpleStrandedFeature", 949 "org.biojava.bio.seq.impl.SimpleRestrictionSite", 950 "org.biojava.bio.seq.io.GAMEFormat", 951 "org.biojava.bio.seq.db.IDMaker$ByURN", 952 "org.biojava.bio.seq.db.IDMaker$ByName", 953 "org.biojava.bio.seq.db.IDMaker", 954 "org.biojava.bio.seq.db.BioIndex", 955 "org.biojava.bio.program.phred.PhredFormat", 956 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