Class jalview.gui.AlignViewportTest

all > jalview.gui > AlignViewportTest
10

tests
0

failures
0

ignored
0.322s

duration
100%

successful

Tests

Test Duration Result
testDeregisterMapping_onCloseView 0.067s passed
testDeregisterMapping_withNoReference 0.034s passed
testDeregisterMapping_withReference 0.053s passed
testGetConsensusSeq 0.036s passed
testHideRevealSequences 0s passed
testSetGetHasSearchResults 0.041s passed
testSetGlobalColourScheme 0.017s passed
testSetSelectionGroup 0.019s passed
testShowOrDontShowOccupancy 0.034s passed
testUpdateConservation_qualityOnly 0.021s passed

Standard output

Attempting to connect with MuscleWS...
File format identified as Fasta
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@a1b6f60
Attempting to connect with ClustalWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@4ba19632
Attempting to connect with ClustalOWS...
File format identified as Fasta
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2d0ed257
File format identified as Fasta
Attempting to connect with TcoffeeWS...
File format identified as Fasta
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@4556b6eb
File format identified as Fasta
File format identified as Fasta
File format identified as Fasta
registry.getSupportedServices: [RNAalifoldWS, AAConWS, MuscleWS, ClustalWS, ClustalOWS, DisemblWS, MSAprobsWS, MafftWS, GLprobsWS, IUPredWS, TcoffeeWS, GlobPlotWS, ProbconsWS, JronnWS]
Attempting to connect with MafftWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@7cd2d42a
File format identified as Fasta
Attempting to connect with MuscleWS...
File format identified as Fasta
Attempting to connect with ClustalWS...
File format identified as Fasta
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@50d2d3dc
Attempting to connect with ClustalOWS...
File format identified as Fasta
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@747c1aa6
Attempting to connect with TcoffeeWS...
File format identified as Fasta

Standard error

DEBUG - Waiting around for old discovery thread to finish.
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.
Aug 13, 2020 12:06:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 1998207317
Warning - overwriting a sequenceSetId for a viewport!
Aug 13, 2020 12:06:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Aborting 1 JABAWS discovery threads.
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@fd22970, jalview.ws.jws2.jabaws2.Jws2Instance@241d64b4, jalview.ws.jws2.jabaws2.Jws2Instance@a1b6f60, jalview.ws.jws2.jabaws2.Jws2Instance@4ba19632, jalview.ws.jws2.jabaws2.Jws2Instance@2d0ed257]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@fd22970, jalview.ws.jws2.jabaws2.Jws2Instance@241d64b4, jalview.ws.jws2.jabaws2.Jws2Instance@a1b6f60, jalview.ws.jws2.jabaws2.Jws2Instance@4ba19632, jalview.ws.jws2.jabaws2.Jws2Instance@2d0ed257]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@fd22970, jalview.ws.jws2.jabaws2.Jws2Instance@241d64b4, jalview.ws.jws2.jabaws2.Jws2Instance@a1b6f60, jalview.ws.jws2.jabaws2.Jws2Instance@4ba19632, jalview.ws.jws2.jabaws2.Jws2Instance@2d0ed257]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@fd22970, jalview.ws.jws2.jabaws2.Jws2Instance@241d64b4, jalview.ws.jws2.jabaws2.Jws2Instance@a1b6f60, jalview.ws.jws2.jabaws2.Jws2Instance@4ba19632, jalview.ws.jws2.jabaws2.Jws2Instance@2d0ed257]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@fd22970, jalview.ws.jws2.jabaws2.Jws2Instance@241d64b4, jalview.ws.jws2.jabaws2.Jws2Instance@a1b6f60, jalview.ws.jws2.jabaws2.Jws2Instance@4ba19632, jalview.ws.jws2.jabaws2.Jws2Instance@2d0ed257]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@fd22970, jalview.ws.jws2.jabaws2.Jws2Instance@241d64b4, jalview.ws.jws2.jabaws2.Jws2Instance@a1b6f60, jalview.ws.jws2.jabaws2.Jws2Instance@4ba19632, jalview.ws.jws2.jabaws2.Jws2Instance@2d0ed257]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@fd22970, jalview.ws.jws2.jabaws2.Jws2Instance@241d64b4, jalview.ws.jws2.jabaws2.Jws2Instance@a1b6f60, jalview.ws.jws2.jabaws2.Jws2Instance@4ba19632, jalview.ws.jws2.jabaws2.Jws2Instance@2d0ed257]
Rebuild WS Menu for service change
DEBUG - Old discovery thread has finished.
DEBUG - Firing service changed event for []
Aug 13, 2020 12:06:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Aug 13, 2020 12:06:19 PM compbio.ws.client.Jws2Client connectToRegistry
INFO: Connected to RegistryWS successfully!
Aug 13, 2020 12:06:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!