DEBUG - AUTHENTICATOR setting default Authenticator to null
DEBUG - AUTHENTICATOR setting property 'http.nonProxyHosts' to "null"
DEBUG - Setting proxy properties to: http.proxyHost=null, http.proxyPort=null, https.proxyHost=null, https.proxyPort=null
DEBUG - Ignoring SO:0001957 as obsolete and duplicated by SO:0001979
DEBUG - Ignoring SO:0000437 as obsolete and duplicated by SO:0000800
DEBUG - Ignoring SO:0000554 as obsolete and duplicated by SO:0000801
DEBUG - Ignoring SO:0000767 as obsolete and duplicated by SO:0000179
DEBUG - Ignoring SO:0000058 as obsolete and duplicated by SO:0000803
DEBUG - Ignoring SO:0001052 as obsolete and duplicated by SO:0001649
DEBUG - Ignoring SO:0000052 as obsolete and duplicated by SO:0000802
DEBUG - Ignoring SO:0001053 as obsolete and duplicated by SO:0001648
INFO - Loaded Sequence Ontology from so-xp-simple.obo.zip (34ms)
INFO - Linux platform only! You may have the following warning next: "WARNING: An illegal reflective access operation has occurred"
This is expected and cannot be avoided, sorry about that.
DEBUG - Got last known dimensions for : x:702 y:518 width:675 height:438
DEBUG - Got last known dimensions for JAVA_CONSOLE_: x:622 y:320 width:337 height:109
DEBUG - Downloading data from identifiers.org
DEBUG - Filechooser init thread started.
Could not load jar:file:/home/thomas/Studium/Master_2/java-hiwi/jalview/classes/!/.build_properties
DEBUG - Waiting around for old discovery thread to finish.
DEBUG - (Re)-Initialising the discovery URL list.
DEBUG - Starting news thread.
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 - Constructing news reader.
Jul 02, 2023 10:11:54 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Invalid or corrupt date in property 'JALVIEW_NEWS_RSS_LASTMODIFIED' : value was 'Apr 23, 2014 2:53:26 PM'
DEBUG - Exception downloading identifiers.org datahttps://www.jalview.org/services/identifiers
DEBUG - Filechooser init thread finished.
DEBUG - Aborting 1 JABAWS discovery threads.
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@6f85b2b8, jalview.ws.jws2.jabaws2.Jws2Instance@1823272, jalview.ws.jws2.jabaws2.Jws2Instance@14de54ca, jalview.ws.jws2.jabaws2.Jws2Instance@15ac9368, jalview.ws.jws2.jabaws2.Jws2Instance@308ab5ee, jalview.ws.jws2.jabaws2.Jws2Instance@37b19b42, jalview.ws.jws2.jabaws2.Jws2Instance@4ae5466f, jalview.ws.jws2.jabaws2.Jws2Instance@13908975, jalview.ws.jws2.jabaws2.Jws2Instance@7dfd07f9, jalview.ws.jws2.jabaws2.Jws2Instance@50a80744]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@6f85b2b8, jalview.ws.jws2.jabaws2.Jws2Instance@1823272, jalview.ws.jws2.jabaws2.Jws2Instance@14de54ca, jalview.ws.jws2.jabaws2.Jws2Instance@15ac9368, jalview.ws.jws2.jabaws2.Jws2Instance@308ab5ee, jalview.ws.jws2.jabaws2.Jws2Instance@37b19b42, jalview.ws.jws2.jabaws2.Jws2Instance@4ae5466f, jalview.ws.jws2.jabaws2.Jws2Instance@13908975, jalview.ws.jws2.jabaws2.Jws2Instance@7dfd07f9, jalview.ws.jws2.jabaws2.Jws2Instance@50a80744]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@6f85b2b8, jalview.ws.jws2.jabaws2.Jws2Instance@1823272, jalview.ws.jws2.jabaws2.Jws2Instance@14de54ca, jalview.ws.jws2.jabaws2.Jws2Instance@15ac9368, jalview.ws.jws2.jabaws2.Jws2Instance@308ab5ee, jalview.ws.jws2.jabaws2.Jws2Instance@37b19b42, jalview.ws.jws2.jabaws2.Jws2Instance@4ae5466f, jalview.ws.jws2.jabaws2.Jws2Instance@13908975, jalview.ws.jws2.jabaws2.Jws2Instance@7dfd07f9, jalview.ws.jws2.jabaws2.Jws2Instance@50a80744]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@6f85b2b8, jalview.ws.jws2.jabaws2.Jws2Instance@1823272, jalview.ws.jws2.jabaws2.Jws2Instance@14de54ca, jalview.ws.jws2.jabaws2.Jws2Instance@15ac9368, jalview.ws.jws2.jabaws2.Jws2Instance@308ab5ee, jalview.ws.jws2.jabaws2.Jws2Instance@37b19b42, jalview.ws.jws2.jabaws2.Jws2Instance@4ae5466f, jalview.ws.jws2.jabaws2.Jws2Instance@13908975, jalview.ws.jws2.jabaws2.Jws2Instance@7dfd07f9, jalview.ws.jws2.jabaws2.Jws2Instance@50a80744]
DEBUG - Old discovery thread has finished.
DEBUG - Firing service changed event for []
Rebuild WS Menu for service change
DEBUG - Firing service changed event for []
Rebuild WS Menu for service change
DEBUG - Firing service changed event for []
DEBUG - Firing service changed event for []
Rebuild WS Menu for service change
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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 - 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 - Displaying news.