Class jalview.io.NewickFileTests
|
100%
successful |
| Test | Duration | Result |
|---|---|---|
| testTreeIO | 0.024s | passed |
| testTreeIO | 0.051s | passed |
| testTreeIO | 0.010s | passed |
'Tree with double escaped comma in node' :
('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)''|CK_Syn_MINOS11_750':1.063831);
Attempting to connect with MuscleWS...
'Tree with quotes' :
('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)|CK_Syn_MINOS11_750':1.063831);
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@4aa849b0
'Simple uniref50 newick' :
(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);
Attempting to connect with ClustalWS...
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 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 2:55:11 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 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$WorkQueue.topLevelExec(ForkJoinPool.java:1020) [?:?] at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) [?:?] at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) [?:?] at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) [?:?] INFO - Building web service menu for slivka WARN - java.lang.NullPointerException java.lang.NullPointerException: null at jalview.ws2.gui.WebServicesMenuManager.isActionEnabled(WebServicesMenuManager.java:440) ~[clover-classes/:?] at jalview.ws2.gui.WebServicesMenuManager.addEntriesForAction(WebServicesMenuManager.java:180) ~[clover-classes/:?] at jalview.ws2.gui.WebServicesMenuManager.addOneshotEntries(WebServicesMenuManager.java:172) ~[clover-classes/:?] at jalview.ws2.gui.WebServicesMenuManager.setServices(WebServicesMenuManager.java:110) ~[clover-classes/:?] at jalview.gui.AlignFrame.lambda$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) [?:?]