Class jalview.gui.SeqPanelTest

all > jalview.gui > SeqPanelTest

tests

failures

ignored

0.433s

duration

90%

successful

Failed tests
Tests
Standard output
Standard error

Failed tests

testFindMousePosition_wrapped_scales_longSequence

java.lang.AssertionError: expected [17] but found [20]
	at org.testng.Assert.fail(Assert.java:94)
	at org.testng.Assert.failNotEquals(Assert.java:496)
	at org.testng.Assert.assertEquals(Assert.java:125)
	at org.testng.Assert.assertEquals(Assert.java:372)
	at org.testng.Assert.assertEquals(Assert.java:382)
	at jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequence(SeqPanelTest.java:940)
	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:145)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:92)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	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:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)

Tests

Test	Duration	Result
testAmbiguousAminoAcidGetsStatusMessage	0.054s	passed
testFindColumn_unwrapped	0.042s	passed
testFindColumn_wrapped	0.026s	passed
testFindMousePosition_wrapped_annotations	0.016s	passed
testFindMousePosition_wrapped_noAnnotations	0.027s	passed
testFindMousePosition_wrapped_scaleAbove	0.019s	passed
testFindMousePosition_wrapped_scales_longSequence	0.234s	failed
testGetEditStatusMessage	0.001s	passed
testGetEditStatusMessage_lockedEditing	0s	passed
testSetStatusReturnsNearestResiduePosition	0.014s	passed

Standard output

File format identified as Fasta
registry.getSupportedServices: [MSAprobsWS, DisemblWS, TcoffeeWS, RNAalifoldWS, MafftWS, IUPredWS, GlobPlotWS, ProbconsWS, AAConWS, JronnWS, ClustalWS, MuscleWS, ClustalOWS, GLprobsWS]
File format identified as Fasta
File format identified as Fasta
File format identified as Fasta
File format identified as Fasta
File format identified as Pfam
registry.getSupportedServices: [MSAprobsWS, DisemblWS, TcoffeeWS, RNAalifoldWS, MafftWS, IUPredWS, GlobPlotWS, ProbconsWS, AAConWS, JronnWS, ClustalWS, MuscleWS, ClustalOWS, GLprobsWS]
Attempting to connect with MafftWS...

Standard error

DEBUG - Scanning news items: newsnew=false and lastDate is null
DEBUG - Will show jalview news automatically
DEBUG - Completed construction of reader.
DEBUG - Completed news thread.
DEBUG - Constructing news reader.
Invalid or corrupt date in property 'JALVIEW_NEWS_RSS_LASTMODIFIED' : value was 'Apr 23, 2014 2:53:26 PM'
DEBUG - Displaying news.
DEBUG - (Re)-Initialising the discovery URL list.
DEBUG - Setting default services
DEBUG - A MsaWS service called Muscle Multiple Protein Sequence Alignment exists at http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS

DEBUG - A MsaWS service called MAFFT Multiple Sequence Alignment exists at http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS

DEBUG - A MsaWS service called ClustalW Multiple Sequence Alignment exists at http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS

DEBUG - A SecStrPred service called JPred Secondary Structure Prediction exists at http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred

DEBUG - No service endpoints to use for service discovery.
DEBUG - Filechooser init thread finished.
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
DEBUG - Old discovery thread has finished.
DEBUG - Scanning news items: newsnew=false and lastDate is null
DEBUG - Will show jalview news automatically
DEBUG - Completed construction of reader.
DEBUG - Completed news thread.
java.io.IOException: No sequences found (PFAM input)
	at jalview.io.PfamFile.parse(PfamFile.java:121)
	at jalview.io.AlignFile.doParse(AlignFile.java:208)
	at jalview.io.AlignFile.<init>(AlignFile.java:185)
	at jalview.io.AlignFile.<init>(AlignFile.java:170)
	at jalview.io.AlignFile.<init>(AlignFile.java:156)
	at jalview.io.PfamFile.<init>(PfamFile.java:47)
	at jalview.io.FileFormat$2.getReader(FileFormat.java:54)
	at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:205)
	at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:155)
	at jalview.io.FormatAdapter.readFile(FormatAdapter.java:234)
	at jalview.io.FileLoader.run(FileLoader.java:381)
	at jalview.io.FileLoader._LoadFileWaitTillLoaded(FileLoader.java:211)
	at jalview.io.FileLoader.LoadFileWaitTillLoaded(FileLoader.java:164)
	at jalview.io.FileLoader.LoadFileWaitTillLoaded(FileLoader.java:147)
	at jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequence(SeqPanelTest.java:922)
	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:145)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:92)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	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:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Failed to read alignment using the 'Pfam' reader.
java.io.IOException: No sequences found (PFAM input)
Jul 02, 2023 10:11:59 AM compbio.ws.client.Jws2Client connectToRegistry
INFO: Connected to RegistryWS successfully!