Class jalview.gui.AlignFrameTest

all > jalview.gui > AlignFrameTest

tests

failures

ignored

0.454s

duration

100%

successful

Tests
Standard output
Standard error

Test	Duration	Result
testChangeColour_background_groupsAndThresholds	0.203s	passed
testColourThresholdActions	0.047s	passed
testHideFeatureColumns	0.021s	passed
testNewView_colourThresholds	0.150s	passed
testNewView_dsRefPreserved	0.033s	passed

Java version: 11.0.25
Java Home: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
amd64 Linux 3.10.0-1160.24.1.el7.x86_64
loading services
Could not make Java version check
File format identified as Fasta
registry.getSupportedServices: [RNAalifoldWS, ClustalWS, ProbconsWS, ClustalOWS, DisemblWS, JronnWS, TcoffeeWS, IUPredWS, MSAprobsWS, GlobPlotWS, MafftWS, GLprobsWS, MuscleWS, AAConWS]
Attempting to connect with MafftWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@1afa82b3
Attempting to connect with MuscleWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@50990ea2
Attempting to connect with ClustalWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2aa2fae2
Attempting to connect with ClustalOWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@5266db9c
deregistering discoverer listener
ALL CLOSED
Attempting to connect with TcoffeeWS...
File format identified as Fasta
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@53e91c51
Attempting to connect with ProbconsWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@619a9f4d
Attempting to connect with MSAprobsWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@649368cc
Attempting to connect with GLprobsWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@79b48282
Attempting to connect with AAConWS...
deregistering discoverer listener
ALL CLOSED
File format identified as Fasta
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@52a94c60
Attempting to connect with RNAalifoldWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@6cbe81e0
Attempting to connect with JronnWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@261bedf6
Attempting to connect with DisemblWS...
deregistering discoverer listener
ALL CLOSED
File format identified as Fasta
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@22dc8cd4
Attempting to connect with GlobPlotWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@699fa70e
Attempting to connect with IUPredWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@1d47c9c3
deregistering discoverer listener
deregistering discoverer listener
ALL CLOSED
File format identified as Fasta
deregistering discoverer listener
deregistering discoverer listener
ALL CLOSED

INFO - Loaded Sequence Ontology from so-xp-simple.obo.zip (23ms)
Could not load jar:file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB665-JOB1/build/clover/clover-classes/!/.build_properties
INFO - Reloading services for jalview.ws2.client.ebi.JobDispatcherWSDiscoverer
INFO - Reloading services for jalview.ws2.client.slivka.SlivkaWSDiscoverer
INFO - Fetching list of services from https://www.compbio.dundee.ac.uk/slivka/
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Discovering jws1 services
INFO - Building web services menu for jpred4
INFO - Fetching list of services from https://www.ebi.ac.uk/Tools/services/rest/hmmer3_phmmer/
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
Invalid or corrupt date in property 'JALVIEW_NEWS_RSS_LASTMODIFIED' : value was 'Apr 23, 2014 2:53:26 PM'
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
Feb 28, 2025 2:54:35 PM compbio.ws.client.Jws2Client connectToRegistry
INFO: Connected to RegistryWS successfully!
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$new$1(AlignFrame.java:986) ~[clover-classes/:?]
	at jalview.ws2.client.api.AbstractWebServiceDiscoverer.fireServicesChanged(AbstractWebServiceDiscoverer.java:199) ~[clover-classes/:?]
	at jalview.ws2.client.api.AbstractWebServiceDiscoverer.lambda$startDiscoverer$1(AbstractWebServiceDiscoverer.java:178) ~[clover-classes/:?]
	at java.util.concurrent.CompletableFuture.uniHandle(CompletableFuture.java:930) [?:?]
	at java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:907) [?:?]
	at java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:506) [?:?]
	at java.util.concurrent.CompletableFuture.postFire(CompletableFuture.java:610) [?:?]
	at java.util.concurrent.CompletableFuture$UniHandle.tryFire(CompletableFuture.java:910) [?:?]
	at java.util.concurrent.CompletableFuture$Completion.exec(CompletableFuture.java:479) [?:?]
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290) [?:?]
	at java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
INFO - Reloading services for jalview.ws2.client.jpred4.JPred4WSDiscoverer
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Fetching list of services from https://www.compbio.dundee.ac.uk/jpred4/
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
java.lang.NullPointerException
	at jalview.gui.AppJmolBinding.releaseReferences(AppJmolBinding.java:175)
	at jalview.structure.StructureSelectionManager.removeStructureViewerListener(StructureSelectionManager.java:894)
	at jalview.gui.AlignmentPanel.closePanel(AlignmentPanel.java:1492)
	at jalview.gui.AlignFrame.closeMenuItem_actionPerformed(AlignFrame.java:2024)
	at jalview.gui.AlignFrame$6.internalFrameClosed(AlignFrame.java:1035)
	at java.desktop/javax.swing.JInternalFrame.fireInternalFrameEvent(JInternalFrame.java:1541)
	at java.desktop/javax.swing.JInternalFrame.dispose(JInternalFrame.java:1767)
	at java.desktop/javax.swing.JInternalFrame.setClosed(JInternalFrame.java:807)
	at jalview.gui.Desktop.closeAll_actionPerformed(Desktop.java:1498)
	at jalview.gui.AlignFrameTest.tearDown(AlignFrameTest.java:80)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethodConsideringTimeout(MethodInvocationHelper.java:69)
	at org.testng.internal.invokers.ConfigInvoker.invokeConfigurationMethod(ConfigInvoker.java:361)
	at org.testng.internal.invokers.ConfigInvoker.invokeConfigurations(ConfigInvoker.java:296)
	at org.testng.internal.invokers.TestInvoker.runConfigMethods(TestInvoker.java:823)
	at org.testng.internal.invokers.TestInvoker.runAfterConfigurations(TestInvoker.java:792)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:768)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1541)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	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)
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
Feb 28, 2025 2:54:36 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
Assuming project file with TEST is compatible with Jalview version 2.8.1
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
Warning - overwriting a sequenceSetId for a viewport!
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440)
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180)
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172)
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110)
	at jalview.gui.AlignFrame.lambda$buildWebServicesMenu$8(AlignFrame.java:4704)
	at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440)
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180)
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172)
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110)
	at jalview.gui.AlignFrame.lambda$buildWebServicesMenu$8(AlignFrame.java:4704)
	at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
Assuming project file with TEST is compatible with Jalview version 2.8.1
INFO - Rebuiling WS menu
Warning - overwriting a sequenceSetId for a viewport!
INFO - Building web service menu for slivka