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Coverage Report

Test testStructurePAE

Test
testStructurePAE 3FAIL 1 Apr 13:15:12 0.68
No PAE for second chain. expected:<1> but was:<0>
java.lang.AssertionError: No PAE for second chain. expected:<1> but was:<0>
at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364)
at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80)
at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:245)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
at org.testng.TestRunner.privateRun(TestRunner.java:771)
at org.testng.TestRunner.run(TestRunner.java:621)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
at org.testng.SuiteRunner.run(SuiteRunner.java:259)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
at org.testng.TestNG.run(TestNG.java:1009)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:141)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:90)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
at com.sun.proxy.$Proxy2.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:133)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
 
testStructurePAE
com.stevesoft.pat.patInf   com.stevesoft.pat.patInf 1.0100%
com.stevesoft.pat.Rthings   com.stevesoft.pat.Rthings 0.8461538684.6%
mc_view.Residue   mc_view.Residue 0.8461538684.6%
com.stevesoft.pat.oneChar   com.stevesoft.pat.oneChar 0.6285714562.9%
com.stevesoft.pat.OrMark   com.stevesoft.pat.OrMark 0.62562.5%
jalview.util.MapUtils   jalview.util.MapUtils 0.608695660.9%
com.stevesoft.pat.SubMark   com.stevesoft.pat.SubMark 0.660%
jalview.ext.jmol.JmolParser   jalview.ext.jmol.JmolParser 0.5532467455.3%
com.stevesoft.pat.StrPos   com.stevesoft.pat.StrPos 0.523255852.3%
com.stevesoft.pat.Multi_stage2   com.stevesoft.pat.Multi_stage2 0.5111111451.1%
com.stevesoft.pat.Multi   com.stevesoft.pat.Multi 0.550%
com.stevesoft.pat.Bracket   com.stevesoft.pat.Bracket 0.550%
mc_view.Bond   mc_view.Bond 0.550%
com.stevesoft.pat.wrap.StringWrap   com.stevesoft.pat.wrap.StringWrap 0.550%
com.stevesoft.pat.Range   com.stevesoft.pat.Range 0.4772727247.7%
com.stevesoft.pat.Pattern   com.stevesoft.pat.Pattern 0.437543.8%
com.stevesoft.pat.FastMulti   com.stevesoft.pat.FastMulti 0.435185243.5%
jalview.datamodel.HiddenCursorPosition   jalview.datamodel.HiddenCursorPosition 0.4285714342.9%
org.json.simple.parser.Yylex   org.json.simple.parser.Yylex 0.4012738840.1%
jalview.io.StructureFile   jalview.io.StructureFile 0.386046538.6%
jalview.datamodel.FloatContactMatrix   jalview.datamodel.FloatContactMatrix 0.3838%
com.stevesoft.pat.patInt   com.stevesoft.pat.patInt 0.3535%
jalview.datamodel.ContactMapHolder   jalview.datamodel.ContactMapHolder 0.3461538634.6%
jalview.ws.datamodel.alphafold.PAEContactMatrix   jalview.ws.datamodel.alphafold.PAEContactMatrix 0.3274336232.7%
jalview.util.Comparison   jalview.util.Comparison 0.3188976331.9%
org.json.simple.parser.JSONParser   org.json.simple.parser.JSONParser 0.3143564531.4%
com.stevesoft.pat.Or   com.stevesoft.pat.Or 0.294871829.5%
com.stevesoft.pat.Regex   com.stevesoft.pat.Regex 0.2927272629.3%
jalview.structure.StructureImportSettings   jalview.structure.StructureImportSettings 0.285714328.6%
mc_view.Atom   mc_view.Atom 0.282051328.2%
jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder   jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder 0.2608695626.1%
mc_view.PDBChain   mc_view.PDBChain 0.2592592525.9%
jalview.datamodel.SequenceCursor   jalview.datamodel.SequenceCursor 0.2333333323.3%
jalview.util.Format   jalview.util.Format 0.2236024922.4%
jalview.io.AlignFile   jalview.io.AlignFile 0.2191780821.9%
jalview.gui.PromptUserConfig   jalview.gui.PromptUserConfig 0.215909121.6%
jalview.datamodel.Sequence   jalview.datamodel.Sequence 0.2041166420.4%
jalview.datamodel.features.FeatureStore   jalview.datamodel.features.FeatureStore 0.1842900418.4%
com.stevesoft.pat.RegOpt   com.stevesoft.pat.RegOpt 0.1726618717.3%
jalview.io.FileParse   jalview.io.FileParse 0.1689750716.9%
jalview.datamodel.AlignmentAnnotation   jalview.datamodel.AlignmentAnnotation 0.1642512116.4%
jalview.ws.dbsources.EBIAlfaFold   jalview.ws.dbsources.EBIAlfaFold 0.1507692315.1%
jalview.datamodel.Annotation   jalview.datamodel.Annotation 0.1428571514.3%
jalview.gui.SplashScreen   jalview.gui.SplashScreen 0.1233766212.3%
jalview.datamodel.annotations.AnnotationRowBuilder   jalview.datamodel.annotations.AnnotationRowBuilder 0.10256410410.3%
com.stevesoft.pat.parsePerl   com.stevesoft.pat.parsePerl 0.098639469.9%
org.json.simple.parser.Yytoken   org.json.simple.parser.Yytoken 0.096774199.7%
jalview.util.CaseInsensitiveString   jalview.util.CaseInsensitiveString 0.086956528.7%
jalview.datamodel.SequenceFeature   jalview.datamodel.SequenceFeature 0.0863309358.6%
jalview.gui.Console   jalview.gui.Console 0.082568818.3%
jalview.datamodel.PDBEntry   jalview.datamodel.PDBEntry 0.0818505368.2%
jalview.ws.datamodel.alphafold.MappableContactMatrix   jalview.ws.datamodel.alphafold.MappableContactMatrix 0.079497917.9%
jalview.util.Platform   jalview.util.Platform 0.0707547147.1%
jalview.datamodel.features.SequenceFeatures   jalview.datamodel.features.SequenceFeatures 0.0700636957%
jalview.log.JLogger   jalview.log.JLogger 0.065934076.6%
jalview.datamodel.DBRefEntry   jalview.datamodel.DBRefEntry 0.0616438356.2%
jalview.util.MapList   jalview.util.MapList 0.0538461545.4%
jalview.bin.Console   jalview.bin.Console 0.0492610824.9%
org.json.simple.JSONObject   org.json.simple.JSONObject 0.037735853.8%
jalview.datamodel.Alignment   jalview.datamodel.Alignment 0.0330882373.3%
com.stevesoft.pat.RegRes   com.stevesoft.pat.RegRes 0.0289855082.9%
jalview.ws.seqfetcher.DbSourceProxyImpl   jalview.ws.seqfetcher.DbSourceProxyImpl 0.0270270282.7%
jalview.bin.Cache   jalview.bin.Cache 0.0220385682.2%
jalview.datamodel.HiddenColumnsCursor   jalview.datamodel.HiddenColumnsCursor 0.0156251.6%
jalview.datamodel.HiddenSequences   jalview.datamodel.HiddenSequences 0.009132420.9%
jalview.datamodel.GroupSet   jalview.datamodel.GroupSet 0.008620690.9%
org.json.simple.JSONArray   org.json.simple.JSONArray 0.0080645160.8%
jalview.gui.Desktop   jalview.gui.Desktop 0.00568181840.6%
jalview.ext.jmol.JalviewJmolBinding   jalview.ext.jmol.JalviewJmolBinding 0.0040160640.4%
com.stevesoft.pat.CaseMgr   com.stevesoft.pat.CaseMgr 0.00278551530.3%
jalview.datamodel.HiddenColumns   jalview.datamodel.HiddenColumns 0.00235849060.2%
jalview.bin.Jalview   jalview.bin.Jalview 0.00179856120.2%
jalview.schemes.ResidueProperties   jalview.schemes.ResidueProperties 0.00105042020.1%