Class jalview.io.RNAMLfileTest

all > jalview.io > RNAMLfileTest

tests

failures

ignored

0.120s

duration

100%

successful

Tests
Standard output
Standard error

Test	Duration	Result
testRnamlToStockholmIO	0.120s	passed

Reading file: examples/testdata/rna-alignment.xml
File format identified as Rnaml
Attempting to connect with ClustalOWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@44e995d0
Attempting to connect with TcoffeeWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@12e75baa
Attempting to connect with ProbconsWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@154f9849
Attempting to connect with MSAprobsWS...
Output file in 'Stockholm':
# STOCKHOLM 1.0
#=GR /rna-alignmen.0/1-295 SS .....(((.(((((((((...[[[[.((((((((((.....)))))(((((....)))).)((...(((((...........(((((...((((....)))).)))..)).......((((((.......))))))(((((((((....))).))))).)..)))..)))))))))))))...((((......((((((...(((((.]]]]))))))))))).....))))......((((((((....))))))))...........................)))))))).
/rna-alignmen.0/1-295         gaggaaaguccgggCUCCAUAGGGCAGAGUGCCAGGUAACGCCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAGAAAACAACCGCCUAAGCGCGCAAGCGCCGGUAAGGGUGAAAAGGUGCGGUAAGAGCGCACCGCACGGCUGGCAACAGUUCGUGGCUAGGUAAACCCCACUCGGAGCAAGACCAAAUAGGGAUCCAUUGGCGUGGCCCGCGCUGGAUCCGGGUAGGUUGCUAAAGGCGGCCAGCGAUGGUCGUCGUAGAGGAAUGACUGUCCUCGacagaacccggcuua
#=GR /rna-alignmen.1/1-250 SS ..............((((...[[[[.((((((((((.....)))))(((((....)))).)((...(((((............(((((((((((((....)))))))))))..))........((((((.......))))))(((((((((....)))))))).).)))..)))))))))))))...((((((((((.....(((.]]]])))...))))))))....)).............(....)
/rna-alignmen.1/1-250         gaggaaaguccggacUUCGCAGAAAAAGGUGCCAGUGAAAAACUGGGGGCCGUAAGGCUACGGAAAGUGUAACAGAAAACAAACCGCUAAUUCUACCUAGGUAAGAUUAGACAGGAUGAAAAUGUCGAGCUUAUGGCUCGACCUCUUUGUGGAAACACAAGGACGCUGCAAACCCCACCUGAAGCAAGAAAGAGUUCGUUUCAGUUUUUCGCUCAGGAACUCUUAGAGUCGCUCGAGGAUUUUGGUGAC
//

<<EOF

Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@7e77f70b
Attempting to connect with GLprobsWS...
File format identified as Stockholm
Check sequence: /rna-alignmen.0/1-295
Check sequence: /rna-alignmen.1/1-250

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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
INFO - Building web services menu for jobs dispatcher
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
INFO - Building web services menu for jpred4
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
WARN - java.lang.NullPointerException
java.lang.NullPointerException: null
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?]
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?]
	at jalview.gui.AlignFrame.lambda$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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?]
	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?]
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?]
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?]
INFO - Reloading services for jalview.ws2.client.jpred4.JPred4WSDiscoverer
INFO - Fetching list of services from https://www.compbio.dundee.ac.uk/jpred4/
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440)
	at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180)
	at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172)
	at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110)
	at jalview.gui.AlignFrame.lambda$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)
Feb 28, 2025 2:55:11 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:55:11 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:55:11 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Feb 28, 2025 2:55:11 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!

Class jalview.io.RNAMLfileTest

Tests