1 /**
2  * Scaffolding file used to store all the setups needed to run
3  * tests automatically generated by EvoSuite
4  * Fri Jan 12 16:32:16 GMT 2018
5  */
6 
7 package uk.ac.sanger.artemis.sequence;
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.evosuite.runtime.sandbox.Sandbox;
14 import org.evosuite.runtime.sandbox.Sandbox.SandboxMode;
15 
16 @EvoSuiteClassExclude
17 public class MarkerChangeListener_ESTest_scaffolding {
18 
19   @org.junit.Rule
20   public org.evosuite.runtime.vnet.NonFunctionalRequirementRule nfr = new org.evosuite.runtime.vnet.NonFunctionalRequirementRule();
21 
22   private org.evosuite.runtime.thread.ThreadStopper threadStopper =  new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);
23 
24 
25   @BeforeClass
initEvoSuiteFramework()26   public static void initEvoSuiteFramework() {
27     org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.sequence.MarkerChangeListener";
28     org.evosuite.runtime.GuiSupport.initialize();
29     org.evosuite.runtime.RuntimeSettings.maxNumberOfThreads = 100;
30     org.evosuite.runtime.RuntimeSettings.maxNumberOfIterationsPerLoop = 10000;
31     org.evosuite.runtime.RuntimeSettings.mockSystemIn = true;
32     org.evosuite.runtime.RuntimeSettings.sandboxMode = org.evosuite.runtime.sandbox.Sandbox.SandboxMode.RECOMMENDED;
33     org.evosuite.runtime.sandbox.Sandbox.initializeSecurityManagerForSUT();
34     org.evosuite.runtime.classhandling.JDKClassResetter.init();
35     setSystemProperties();
36     initializeClasses();
37     org.evosuite.runtime.Runtime.getInstance().resetRuntime();
38   }
39 
40   @Before
initTestCase()41   public void initTestCase(){
42     threadStopper.storeCurrentThreads();
43     threadStopper.startRecordingTime();
44     org.evosuite.runtime.jvm.ShutdownHookHandler.getInstance().initHandler();
45     org.evosuite.runtime.sandbox.Sandbox.goingToExecuteSUTCode();
46     org.evosuite.runtime.GuiSupport.setHeadless();
47     org.evosuite.runtime.Runtime.getInstance().resetRuntime();
48     org.evosuite.runtime.agent.InstrumentingAgent.activate();
49   }
50 
51   @After
doneWithTestCase()52   public void doneWithTestCase(){
53     threadStopper.killAndJoinClientThreads();
54     org.evosuite.runtime.jvm.ShutdownHookHandler.getInstance().safeExecuteAddedHooks();
55     org.evosuite.runtime.classhandling.JDKClassResetter.reset();
56     resetClasses();
57     org.evosuite.runtime.sandbox.Sandbox.doneWithExecutingSUTCode();
58     org.evosuite.runtime.agent.InstrumentingAgent.deactivate();
59     org.evosuite.runtime.GuiSupport.restoreHeadlessMode();
60   }
61 
setSystemProperties()62   public static void setSystemProperties() {
63 
64     /*No java.lang.System property to set*/
65   }
66 
initializeClasses()67   private static void initializeClasses() {
68     org.evosuite.runtime.classhandling.ClassStateSupport.initializeClasses(MarkerChangeListener_ESTest_scaffolding.class.getClassLoader() ,
69       "uk.ac.sanger.artemis.ChangeListener",
70       "uk.ac.sanger.artemis.sequence.MarkerChangeListener"
71     );
72   }
73 
resetClasses()74   private static void resetClasses() {
75     org.evosuite.runtime.classhandling.ClassResetter.getInstance().setClassLoader(MarkerChangeListener_ESTest_scaffolding.class.getClassLoader());
76 
77     org.evosuite.runtime.classhandling.ClassStateSupport.resetClasses(
78       "uk.ac.sanger.artemis.io.PublicDBDocumentEntry",
79       "org.apache.log4j.Category",
80       "org.apache.log4j.Logger",
81       "org.apache.log4j.Priority",
82       "org.apache.log4j.Level",
83       "org.apache.log4j.or.RendererMap",
84       "org.apache.log4j.helpers.OptionConverter",
85       "org.apache.log4j.helpers.Loader",
86       "org.apache.log4j.helpers.LogLog",
87       "org.apache.log4j.PropertyConfigurator",
88       "org.apache.log4j.LogManager",
89       "org.apache.log4j.CategoryKey",
90       "org.apache.log4j.ProvisionNode",
91       "uk.ac.sanger.artemis.util.DatabaseDocument",
92       "uk.ac.sanger.artemis.util.StringVector",
93       "uk.ac.sanger.artemis.components.Splash",
94       "uk.ac.sanger.artemis.util.FastVector",
95       "uk.ac.sanger.artemis.io.KeyVector",
96       "uk.ac.sanger.artemis.io.Key",
97       "uk.ac.sanger.artemis.io.QualifierInfo",
98       "uk.ac.sanger.artemis.ExternalProgram",
99       "uk.ac.sanger.artemis.Options",
100       "uk.ac.sanger.artemis.io.FeatureVector",
101       "uk.ac.sanger.artemis.ChangeEvent",
102       "uk.ac.sanger.artemis.EntryGroupChangeEvent",
103       "uk.ac.sanger.artemis.util.OutOfRangeException",
104       "uk.ac.sanger.artemis.io.QualifierVector",
105       "uk.ac.sanger.artemis.io.LineGroup",
106       "uk.ac.sanger.artemis.io.Packing",
107       "uk.ac.sanger.artemis.sequence.Bases",
108       "uk.ac.sanger.artemis.sequence.Strand",
109       "uk.ac.sanger.artemis.io.LocationParseNode",
110       "uk.ac.sanger.artemis.io.RangeVector",
111       "uk.ac.sanger.artemis.sequence.AminoAcidSequence",
112       "uk.ac.sanger.artemis.FeatureSegment",
113       "org.gmod.schema.sequence.FeatureLoc",
114       "uk.ac.sanger.artemis.components.genebuilder.GeneUtils",
115       "uk.ac.sanger.artemis.sequence.NoSequenceException",
116       "uk.ac.sanger.artemis.FeaturePredicateConjunction",
117       "uk.ac.sanger.artemis.EntryChangeEvent",
118       "org.biojava.bio.AbstractAnnotation",
119       "org.biojava.bio.SimpleAnnotation",
120       "org.biojava.bio.seq.SimpleFeatureRealizer",
121       "org.biojava.bio.seq.impl.FeatureImpl$1",
122       "org.biojava.bio.seq.impl.FeatureImpl",
123       "org.biojava.bio.symbol.AlphabetManager$GapSymbol",
124       "org.biojava.bio.symbol.AlphabetManager$SizeQueen",
125       "org.biojava.bio.symbol.IntegerAlphabet",
126       "org.biojava.bio.symbol.DoubleAlphabet",
127       "org.biojava.bio.symbol.SimpleSymbol",
128       "org.biojava.bio.symbol.AbstractSimpleBasisSymbol",
129       "org.biojava.bio.symbol.AlphabetManager$WellKnownGapSymbol",
130       "org.biojava.utils.ChangeType",
131       "org.biojava.bio.EmptyAnnotation",
132       "org.biojava.bio.Annotation",
133       "org.biojava.bio.symbol.EmptyAlphabet",
134       "org.biojava.bio.symbol.Alphabet",
135       "org.biojava.utils.ListTools",
136       "org.biojava.utils.SingletonList",
137       "org.biojava.bio.SmallAnnotation",
138       "org.biojava.utils.lsid.LifeScienceIdentifier",
139       "org.biojava.utils.SmallMap",
140       "org.biojava.bio.symbol.AlphabetManager$WellKnownBasisSymbol",
141       "org.biojava.bio.symbol.AlphabetManager$WellKnownAtomicSymbol",
142       "org.biojava.bio.symbol.FundamentalAtomicSymbol",
143       "org.biojava.utils.ChangeListener",
144       "org.biojava.utils.ChangeSupport",
145       "org.biojava.bio.Annotatable",
146       "org.biojava.bio.symbol.AbstractAlphabet",
147       "org.biojava.bio.symbol.SingletonAlphabet",
148       "org.biojava.bio.symbol.SimpleAlphabet",
149       "org.biojava.bio.symbol.AlphabetManager$WellKnownAlphabet",
150       "org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper",
151       "org.biojava.bio.seq.io.CharacterTokenization",
152       "org.biojava.bio.symbol.SimpleBasisSymbol",
153       "org.biojava.bio.seq.io.AlternateTokenization",
154       "org.biojava.bio.symbol.AlphabetManager",
155       "org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper",
156       "org.biojava.bio.symbol.SimpleSymbolList",
157       "org.biojava.bio.seq.io.SymbolTokenization",
158       "org.biojava.bio.symbol.SimpleReversibleTranslationTable",
159       "org.biojava.bio.symbol.SimpleCrossProductAlphabet",
160       "org.biojava.utils.ListTools$Triplet",
161       "org.biojava.bio.symbol.SimpleAtomicSymbol",
162       "org.biojava.bio.seq.io.WordTokenization",
163       "org.biojava.bio.seq.io.NameTokenization",
164       "org.biojava.bio.symbol.SimpleManyToOneTranslationTable",
165       "org.biojava.bio.symbol.SimpleGeneticCodeTable",
166       "org.biojava.bio.symbol.AbstractSymbolList$ListView",
167       "org.biojava.bio.BioException",
168       "org.biojava.bio.symbol.IllegalSymbolException",
169       "org.biojava.bio.BioError",
170       "org.biojava.bio.seq.RNATools",
171       "org.biojava.bio.seq.DNATools",
172       "uk.ac.sanger.artemis.components.BasePlotGroup",
173       "org.biojava.bio.seq.Feature",
174       "uk.ac.sanger.artemis.io.SimpleDocumentFeature",
175       "uk.ac.sanger.artemis.io.PublicDBStreamFeature",
176       "uk.ac.sanger.artemis.io.LocationParseNodeVector",
177       "uk.ac.sanger.artemis.io.ReadFormatException",
178       "uk.ac.sanger.artemis.io.LocationParseException",
179       "uk.ac.sanger.artemis.io.StreamSequenceFactory",
180       "uk.ac.sanger.artemis.sequence.BasePattern",
181       "uk.ac.sanger.artemis.util.DatabaseLocationParser",
182       "org.apache.log4j.MDC",
183       "uk.ac.sanger.artemis.chado.GmodDAO",
184       "uk.ac.sanger.artemis.chado.IBatisDAO",
185       "uk.ac.sanger.artemis.chado.SqlMapClientWrapper",
186       "com.ibatis.common.resources.Resources",
187       "com.ibatis.common.beans.ComplexBeanProbe",
188       "com.ibatis.common.beans.GenericProbe",
189       "com.ibatis.common.beans.ProbeFactory",
190       "com.ibatis.sqlmap.engine.config.SqlMapConfiguration",
191       "com.ibatis.sqlmap.engine.impl.SqlMapExecutorDelegate",
192       "com.ibatis.sqlmap.engine.execution.SqlExecutor",
193       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory$1",
194       "com.ibatis.sqlmap.engine.type.TypeHandlerFactory",
195       "com.ibatis.sqlmap.engine.type.UnknownTypeHandler",
196       "com.ibatis.sqlmap.engine.type.DateTypeHandler",
197       "com.ibatis.sqlmap.engine.type.DateOnlyTypeHandler",
198       "com.ibatis.sqlmap.engine.type.TimeOnlyTypeHandler",
199       "com.ibatis.sqlmap.engine.type.SqlDateTypeHandler",
200       "com.ibatis.sqlmap.engine.type.SqlTimeTypeHandler",
201       "com.ibatis.sqlmap.engine.type.SqlTimestampTypeHandler",
202       "com.ibatis.sqlmap.engine.exchange.ComplexDataExchange",
203       "com.ibatis.common.logging.LogFactory",
204       "org.apache.commons.logging.impl.Log4JLogger",
205       "com.ibatis.sqlmap.engine.impl.SqlMapClientImpl",
206       "com.ibatis.sqlmap.engine.builder.xml.SqlMapClasspathEntityResolver",
207       "com.ibatis.common.beans.ClassInfo",
208       "com.ibatis.sqlmap.engine.accessplan.AccessPlanFactory",
209       "com.ibatis.common.jdbc.SimpleDataSource",
210       "org.postgresql.Driver",
211       "com.ibatis.sqlmap.engine.mapping.result.ResultMap",
212       "com.ibatis.sqlmap.engine.exchange.JavaBeanDataExchange",
213       "net.sf.cglib.core.TypeUtils",
214       "net.sf.cglib.asm.Type",
215       "net.sf.cglib.core.KeyFactory",
216       "net.sf.cglib.core.AbstractClassGenerator",
217       "net.sf.cglib.core.KeyFactory$Generator",
218       "net.sf.cglib.core.DefaultGeneratorStrategy",
219       "net.sf.cglib.core.DefaultNamingPolicy",
220       "net.sf.cglib.asm.ClassWriter",
221       "net.sf.cglib.core.DebuggingClassWriter",
222       "net.sf.cglib.core.ClassEmitter",
223       "net.sf.cglib.core.ReflectUtils",
224       "net.sf.cglib.core.EmitUtils",
225       "net.sf.cglib.core.Constants",
226       "net.sf.cglib.core.CodeEmitter",
227       "net.sf.cglib.asm.Frame",
228       "net.sf.cglib.asm.ClassReader",
229       "net.sf.cglib.core.ClassNameReader$EarlyExitException",
230       "net.sf.cglib.core.ClassNameReader",
231       "net.sf.cglib.beans.BulkBean",
232       "net.sf.cglib.beans.BulkBean$Generator",
233       "net.sf.cglib.beans.BulkBeanEmitter",
234       "com.ibatis.sqlmap.engine.type.JdbcTypeRegistry",
235       "com.ibatis.sqlmap.engine.mapping.parameter.InlineParameterMapParser",
236       "com.ibatis.sqlmap.engine.builder.xml.XMLSqlSource",
237       "com.ibatis.sqlmap.engine.config.MappedStatementConfig",
238       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.DynamicSql",
239       "com.ibatis.sqlmap.engine.mapping.sql.simple.SimpleDynamicSql",
240       "com.ibatis.sqlmap.engine.cache.CacheKey",
241       "com.ibatis.sqlmap.engine.mapping.parameter.ParameterMapping",
242       "com.ibatis.sqlmap.engine.cache.CacheModel",
243       "com.ibatis.sqlmap.engine.accessplan.ComplexAccessPlan",
244       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.ConditionalTagHandler",
245       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsEmptyTagHandler",
246       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsNullTagHandler",
247       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IsPropertyAvailableTagHandler",
248       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.IterateTagHandler",
249       "com.ibatis.sqlmap.engine.mapping.sql.dynamic.elements.SqlTagHandlerFactory",
250       "com.ibatis.sqlmap.engine.config.ParameterMapConfig",
251       "com.ibatis.common.beans.ProbeException",
252       "com.ibatis.sqlmap.engine.accessplan.PropertyAccessPlan",
253       "net.sf.cglib.beans.BulkBeanException",
254       "uk.ac.sanger.artemis.io.GFFStreamFeature",
255       "uk.ac.sanger.artemis.components.CanvasPanel",
256       "uk.ac.sanger.artemis.components.EntryGroupPanel",
257       "uk.ac.sanger.artemis.components.FeatureDisplay",
258       "uk.ac.sanger.artemis.components.ZoomScrollBar",
259       "org.biojava.bio.seq.Feature$Template",
260       "org.biojava.bio.seq.StrandedFeature$Template",
261       "org.biojava.bio.seq.homol.SimilarityPairFeature$Template",
262       "uk.ac.sanger.artemis.sequence.Marker",
263       "uk.ac.sanger.artemis.io.ReadEvent",
264       "uk.ac.sanger.artemis.io.EntryInformationException",
265       "uk.ac.sanger.artemis.io.InvalidKeyException",
266       "org.biojava.bio.seq.impl.SimpleFeature",
267       "org.biojava.bio.seq.impl.SimpleStrandedFeature",
268       "org.biojava.bio.seq.impl.SimpleSimilarityPairFeature",
269       "uk.ac.sanger.artemis.io.MSPcrunchStreamFeature",
270       "org.gmod.schema.organism.Organism",
271       "uk.ac.sanger.artemis.io.FeatureTree",
272       "uk.ac.sanger.artemis.io.DocumentEntryAutosaveThread",
273       "uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry",
274       "uk.ac.sanger.artemis.util.CacheHashMap",
275       "uk.ac.sanger.artemis.components.FileViewer",
276       "uk.ac.sanger.artemis.sequence.SequenceChangeEvent",
277       "uk.ac.sanger.artemis.FeatureChangeEvent",
278       "org.postgresql.largeobject.LargeObject",
279       "uk.ac.sanger.artemis.io.BioJavaFeature",
280       "uk.ac.sanger.artemis.components.filetree.FileList",
281       "uk.ac.sanger.artemis.j2ssh.SshLogin"
282     );
283   }
284 }
285