Class jalview.project.Jalview2xmlTests

File format identified as Jalview
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 571.7/847.2
processors available: 8
useCommandThread: false

FileManager.getAtomSetCollectionFromFile(/tmp/viewerSession10586014307412424899.tmp)
FileManager opening file /tmp/viewerSession10586014307412424899.tmp
Time for openFile(/tmp/viewerSession10586014307412424899.tmp): 35 ms
FileManager opening file /tmp/viewerSession10586014307412424899.tmp
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure

FileManager.getAtomSetCollectionFromFile(/tmp/jalview_pdb9944754333758982161.txt)
FileManager opening file /tmp/jalview_pdb9944754333758982161.txt
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
Time for openFile(/tmp/jalview_pdb9944754333758982161.txt): 155 ms
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 250.2/843.1
processors available: 8
useCommandThread: false
unrecognized SET parameter in Jmol state script (set anyway): usearcball
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
measurement[0] = [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
registry.getSupportedServices: [MSAprobsWS, DisemblWS, TcoffeeWS, RNAalifoldWS, MafftWS, IUPredWS, GlobPlotWS, ProbconsWS, AAConWS, JronnWS, ClustalWS, MuscleWS, ClustalOWS, GLprobsWS]
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 249.5/832.6
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
Attempting to connect with MafftWS...
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 273.3/832.6
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Attempting to connect with MuscleWS...
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 197.7/591.4
processors available: 8
useCommandThread: false
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 7 ms
Attempting to connect with ClustalWS...
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 182.7/591.4
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 11 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4
File format identified as Jalview
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 196.3/591.4
processors available: 8
useCommandThread: false
Attempting to connect with ClustalOWS...
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 7 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 197.6/591.4
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 204.9/591.4
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Attempting to connect with TcoffeeWS...
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 210.0/784.3
processors available: 8
useCommandThread: false
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
Attempting to connect with ProbconsWS...
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 211.4/622.9
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 8 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@1b439676
File format identified as Fasta
Writing jar entry uniref50.fa.xml
Writing jar entry 1605169249  Dataset for examples/uniref50.fa.xml
File format identified as Jalview
Attempting to connect with MSAprobsWS...
Per sequence colourscheme (Background) successfully applied and recovered.
Per sequence (Group) colourscheme successfully applied and recovered.
File format identified as Jalview
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 247.5/622.9
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 8 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 205.8/622.9
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
Attempting to connect with GLprobsWS...
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 215.7/622.9
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Attempting to connect with AAConWS...
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 218.3/622.9
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@306605f3
Attempting to connect with RNAalifoldWS...
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 218.8/622.9
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 10 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3
ALL CLOSED
File format identified as Jalview
Attempting to connect with JronnWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@7756c072
Attempting to connect with DisemblWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6
Attempting to connect with GlobPlotWS...
File format identified as Jalview
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0
ALL CLOSED
File format identified as Fasta
Writing jar entry 0uniref50.fa.xml
Attempting to connect with IUPredWS...
Writing jar entry 1uniref50.fa.xml
Writing jar entry 2uniref50.fa.xml
Writing jar entry 1422170098  Dataset for examples/uniref50.fa.xml
ALL CLOSED
File format identified as Jalview
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e
File format identified as Stockholm
Writing jar entry RF00031_folded.stk.xml
Writing jar entry 133573226  Dataset for examples/RF00031_folded.stk.xml
File format identified as Jalview
Read in same number of annotations as originally present (61)
File format identified as Fasta
Writing jar entry Copied From Clipboard.xml
Writing jar entry 2144260895  Dataset for Copied From Clipboard.xml
File format identified as Jalview
ALL CLOSED
File format identified as Fasta
Writing jar entry uniref50.fa.xml
Writing jar entry 1412950730  Dataset for examples/uniref50.fa.xml
ALL CLOSED
File format identified as Jalview
ALL CLOSED
File format identified as Jalview
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 469.0/622.9
processors available: 8
useCommandThread: false

FileManager.getAtomSetCollectionFromFile(/tmp/viewerSession8698801992219104833.tmp)
FileManager opening file /tmp/viewerSession8698801992219104833.tmp
Time for openFile(/tmp/viewerSession8698801992219104833.tmp): 24 ms
FileManager opening file /tmp/viewerSession8698801992219104833.tmp
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure

FileManager.getAtomSetCollectionFromFile(/tmp/jalview_pdb8759265862018532884.txt)
FileManager opening file /tmp/jalview_pdb8759265862018532884.txt
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
Time for openFile(/tmp/jalview_pdb8759265862018532884.txt): 117 ms
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 8 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
unrecognized SET parameter in Jmol state script (set anyway): usearcball
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 184.1/618.7
processors available: 8
useCommandThread: false
measurement[0] = [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 7 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 187.8/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 209.2/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 205.7/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 211.2/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 7 ms
JMOL CREATE IMAGE
JMOL CREATE IMAGE
Writing jar entry viewer__jalview_pre2_4_512,285,363,36539670237879784822408527692980 (JMOL)
Writing jar entry 1A70 (1A70)
Writing jar entry MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry MAFFT Multiple Sequence Alignment of Retrieved from Uniprot_1.xml
Writing jar entry MAFFT Multiple Sequence Alignment of Retrieved from Uniprot_2.xml
Writing jar entry MAFFT Multiple Sequence Alignment of Retrieved from Uniprot_3.xml
Writing jar entry MAFFT Multiple Sequence Alignment of Retrieved from Uniprot_4.xml
Writing jar entry 1493184635  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 1493184635  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 1493184635  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 1493184635  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 1493184635  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
ALL CLOSED
File format identified as Jalview
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 260.4/618.7
processors available: 8
useCommandThread: false

FileManager.getAtomSetCollectionFromFile(/tmp/viewerSession14510576418154856812.tmp)
FileManager opening file /tmp/viewerSession14510576418154856812.tmp
Time for openFile(/tmp/viewerSession14510576418154856812.tmp): 13 ms
FileManager opening file /tmp/viewerSession14510576418154856812.tmp
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure

FileManager.getAtomSetCollectionFromFile(/tmp/jalview_pdb13400392571764953370.txt)
FileManager opening file /tmp/jalview_pdb13400392571764953370.txt
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
Time for openFile(/tmp/jalview_pdb13400392571764953370.txt): 103 ms
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 186.8/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
measurement[0] = [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 204.6/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 208.2/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 214.4/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 213.4/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
ALL CLOSED
File format identified as Fasta
Writing jar entry Copied From Clipboard.xml
Writing jar entry 1610397354  Dataset for Copied From Clipboard.xml
ALL CLOSED
File format identified as Jalview
ALL CLOSED
File format identified as Fasta
Writing jar entry 0uniref50.fa.xml
Writing jar entry 1uniref50.fa.xml
Writing jar entry 1101625662  Dataset for examples/uniref50.fa.xml
ALL CLOSED
File format identified as Jalview
ALL CLOSED
File format identified as PDB
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 270.5/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
ELECTRON TRANSPORT                      06-FEB-13   3W5V
CROSS-LINKED COMPLEX BETWEEN FERREDOXIN AND FERREDOXIN-NADP+ R
found biomolecule 1: A, D
biomolecule 1: number of transforms: 1
found biomolecule 2: C, B
biomolecule 2: number of transforms: 1
FAD = FLAVIN-ADENINE DINUCLEOTIDE
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 1 21 1
3W5V
reading 6290 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
6290 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 15 ms

blah
Writing jar entry 3W5V (3W5V)
Writing jar entry 3W5V.pdb.xml
Writing jar entry 1495183399  Dataset for examples/3W5V.pdb.xml
ALL CLOSED
File format identified as Jalview
blah
ALL CLOSED
File format identified as Jalview
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 227.3/618.7
processors available: 8
useCommandThread: false

FileManager.getAtomSetCollectionFromFile(/tmp/viewerSession5676766598047557317.tmp)
FileManager opening file /tmp/viewerSession5676766598047557317.tmp
Time for openFile(/tmp/viewerSession5676766598047557317.tmp): 149 ms
FileManager opening file /tmp/viewerSession5676766598047557317.tmp
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure

FileManager.getAtomSetCollectionFromFile(/tmp/jalview_pdb18185198564634452783.txt)
FileManager opening file /tmp/jalview_pdb18185198564634452783.txt
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
Time for openFile(/tmp/jalview_pdb18185198564634452783.txt): 114 ms
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 4 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
unrecognized SET parameter in Jmol state script (set anyway): usearcball
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 191.0/618.7
processors available: 8
useCommandThread: false
measurement[0] = [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 189.0/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 212.9/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 208.9/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 214.9/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
JMOL CREATE IMAGE
JMOL CREATE IMAGE
Writing jar entry viewer__jalview_pre2_4_512,285,363,36539670237879784822408527699312 (JMOL)
Writing jar entry 1A70 (1A70)
Writing jar entry 0MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 1MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 2MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 3MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 4MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
Writing jar entry 695623985  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
ALL CLOSED
File format identified as Jalview
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 200.5/618.7
processors available: 8
useCommandThread: false

FileManager.getAtomSetCollectionFromFile(/tmp/viewerSession339132126933373274.tmp)
FileManager opening file /tmp/viewerSession339132126933373274.tmp
Time for openFile(/tmp/viewerSession339132126933373274.tmp): 5 ms
FileManager opening file /tmp/viewerSession339132126933373274.tmp
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure

FileManager.getAtomSetCollectionFromFile(/tmp/jalview_pdb13557344470912884982.txt)
FileManager opening file /tmp/jalview_pdb13557344470912884982.txt
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
Time for openFile(/tmp/jalview_pdb13557344470912884982.txt): 116 ms
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 2 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 194.7/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
measurement[0] = [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 206.2/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 212.2/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 7 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 225.0/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 5 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 220.9/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
File format identified as Fasta
Writing jar entry uniref50.fa.xml
Writing jar entry 1122624359  Dataset for examples/uniref50.fa.xml
File format identified as Jalview
T-Coffee score shading successfully recovered from project.
File format identified as Jalview
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 246.3/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 11 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 212.6/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 3 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 222.6/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 224.0/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53  2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 226.8/618.7
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
IRON-SULFUR PROTEIN                     19-MAR-98   1A70
SPINACH FERREDOXIN
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 21 21 21
1A70
reading 817 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
817 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 6 ms

Rebuild WS Menu for service change
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DEBUG - Constructing news reader.
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DEBUG - Filechooser init thread finished.
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DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276993655
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.22303180396702378797848224085276993655
Warning - overwriting a sequenceSetId for a viewport!
Allocating Jmol Viewer: 
DEBUG - Exception downloading identifiers.org datahttps://www.jalview.org/services/identifiers
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> load FILES "/tmp/viewerSession10586014307412424899.tmp"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> set hoverDelay=0.1

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276993655
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.21107449396702378797848224085276993655
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:14 AM compbio.ws.client.Jws2Client connectToRegistry
INFO: Connected to RegistryWS successfully!
DEBUG - Scanning news items: newsnew=false and lastDate is Sun Jul 02 11:13:13 CEST 2023
DEBUG - Completed construction of reader.
DEBUG - Completed news thread.
Jul 02, 2023 10:13:15 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Unhandled callback MEASURE [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276993655
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.20906159396702378797848224085276993655
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276993655
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.30823587396702378797848224085276993655
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:15 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276993655
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.9472175396702378797848224085276993655
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:16 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.getTabBounds(BasicTabbedPaneUI.java:1733)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.getTabBounds(BasicTabbedPaneUI.java:1668)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.repaintTab(BasicTabbedPaneUI.java:2338)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.setFocusIndex(BasicTabbedPaneUI.java:2322)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.focusGained(BasicTabbedPaneUI.java:4116)
	at java.desktop/java.awt.AWTEventMulticaster.focusGained(AWTEventMulticaster.java:227)
	at java.desktop/java.awt.Component.processFocusEvent(Component.java:6524)
	at java.desktop/java.awt.Component.processEvent(Component.java:6391)
	at java.desktop/java.awt.Container.processEvent(Container.java:2263)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5011)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4843)
	at java.desktop/java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1950)
	at java.desktop/java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:1050)
	at java.desktop/java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:674)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4892)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4843)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:772)
	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.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:95)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:743)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742)
	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)
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276996764
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.22303180396702378797848224085276996764
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276996764
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.21107449396702378797848224085276996764
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:17 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276996764
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.20906159396702378797848224085276996764
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276996764
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.30823587396702378797848224085276996764
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:17 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276996764
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.9472175396702378797848224085276996764
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:18 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.getTabBounds(BasicTabbedPaneUI.java:1733)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.getTabBounds(BasicTabbedPaneUI.java:1668)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.repaintTab(BasicTabbedPaneUI.java:2338)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.setFocusIndex(BasicTabbedPaneUI.java:2322)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.focusGained(BasicTabbedPaneUI.java:4116)
	at java.desktop/java.awt.AWTEventMulticaster.focusGained(AWTEventMulticaster.java:227)
	at java.desktop/java.awt.Component.processFocusEvent(Component.java:6524)
	at java.desktop/java.awt.Component.processEvent(Component.java:6391)
	at java.desktop/java.awt.Container.processEvent(Container.java:2263)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5011)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4843)
	at java.desktop/java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1950)
	at java.desktop/java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:1050)
	at java.desktop/java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:674)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4892)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4843)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:772)
	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.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:95)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:743)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742)
	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)
DEBUG - Scanning news items: newsnew=false and lastDate is Sun Jul 02 11:13:13 CEST 2023
DEBUG - Saved last read date as 2 Jul 2023, 11:13:13
DEBUG - Scanning news items: newsnew=false and lastDate is Sun Jul 02 11:13:13 CEST 2023
DEBUG - Saved last read date as 2 Jul 2023, 11:13:13
DEBUG - Scanning news items: newsnew=false and lastDate is Sun Jul 02 11:13:13 CEST 2023
DEBUG - Saved last read date as 2 Jul 2023, 11:13:13
DEBUG - BACKUPFILES using temp file /tmp/JalviewTest15869114384156449677.jvp9982257472993027995.tmp_newfile
DEBUG - BACKUPFILES moving /tmp/JalviewTest15869114384156449677.jvp to /tmp/JalviewTest15869114384156449677.jvp_BACKUPFILESTESTTMP000001 was successful
DEBUG - Created new dataset ds01 for alignment 64670494
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 131513837098803
DEBUG - Setting viewport's view id : 1315138370.127016117398803
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:18 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276998942
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.22303180396702378797848224085276998942
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Not enabling Google Tracking.
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276998942
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.21107449396702378797848224085276998942
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276998942
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.20906159396702378797848224085276998942
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:19 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276998942
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.30823587396702378797848224085276998942
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:20 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276998942
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.9472175396702378797848224085276998942
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:21 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Assuming project file with null is compatible with Jalview version null
Assuming project file with null is compatible with Jalview version 2.8.3
Assuming project file with 2.8.3 is compatible with Jalview version null
Assuming project file with Development Build is compatible with Jalview version null
Assuming project file with DEVELOPMENT BUILD is compatible with Jalview version null
Assuming project file with Development Build is compatible with Jalview version 2.8.3
Assuming project file with Test is compatible with Jalview version null
Assuming project file with TEST is compatible with Jalview version null
Assuming project file with Test is compatible with Jalview version 2.8.3
Assuming project file with Automated Build is compatible with Jalview version null
Assuming project file with Automated Build is compatible with Jalview version 2.8.3
Assuming project file with AUTOMATED BUILD is compatible with Jalview version 2.8.3
Invalid version format found: For input string: "3B1"
Invalid version format found: For input string: "3B1"
DEBUG - Created new dataset ds01 for alignment 993304233
DEBUG - Setting viewport's sequence set id : 17735918861253
DEBUG - Setting viewport's view id : 1773591886.3392269031253
Warning - overwriting a sequenceSetId for a viewport!
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
DEBUG Notice:  Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)
Jul 02, 2023 10:13:21 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 15045532551253
DEBUG - Setting viewport's view id : 1504553255.2288834531253
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 15045532551253
DEBUG - Setting viewport's view id : 1504553255.3545527701253
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 15045532551253
DEBUG - Setting viewport's view id : 1504553255.14330432921253
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 15045532551253
DEBUG - Setting viewport's view id : 1504553255.11565581831253
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 20385051711253
DEBUG - Setting viewport's view id : 2038505171.16404697981253
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:21 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 20385051711253
DEBUG - Setting viewport's view id : 2038505171.4340028561253
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 20385051711253
DEBUG - Setting viewport's view id : 2038505171.12978027721253
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Created new dataset ds01 for alignment 616786272
DEBUG - Setting viewport's sequence set id : 15045532551844
DEBUG - Setting viewport's view id : 1504553255.11565581831844
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:21 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Setting viewport's sequence set id : 15045532551844
DEBUG - Setting viewport's view id : 1504553255.2288834531844
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 1787852645
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 1787852645
Warning - overwriting a sequenceSetId for a viewport!
Jul 02, 2023 10:13:22 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Created new dataset ds01 for alignment 1854210091
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 17878526452182
DEBUG - Setting viewport's view id : 1787852645.7771935512182
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 17878526452182
DEBUG - Setting viewport's view id : 1787852645.13263698202182
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 17878526452182
DEBUG - Setting viewport's view id : 1787852645.20865883622182
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - BACKUPFILES using temp file /tmp/JalviewTest2367249496997871162.jvp4816914864626019876.tmp_newfile
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
Rebuild WS Menu for service change
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
Rebuild WS Menu for service change
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
Rebuild WS Menu for service change
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
Rebuild WS Menu for service change
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
Rebuild WS Menu for service change
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@2e7b54f4, jalview.ws.jws2.jabaws2.Jws2Instance@1f76f962, jalview.ws.jws2.jabaws2.Jws2Instance@cbd8bee, jalview.ws.jws2.jabaws2.Jws2Instance@42ae6f4, jalview.ws.jws2.jabaws2.Jws2Instance@41bb999a, jalview.ws.jws2.jabaws2.Jws2Instance@42d0de36, jalview.ws.jws2.jabaws2.Jws2Instance@1b439676, jalview.ws.jws2.jabaws2.Jws2Instance@4d223d76, jalview.ws.jws2.jabaws2.Jws2Instance@306605f3, jalview.ws.jws2.jabaws2.Jws2Instance@d532ff6, jalview.ws.jws2.jabaws2.Jws2Instance@6db1d0e0, jalview.ws.jws2.jabaws2.Jws2Instance@28cf1d1e, jalview.ws.jws2.jabaws2.Jws2Instance@7756c072, jalview.ws.jws2.jabaws2.Jws2Instance@2245abc3]
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
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
DEBUG - BACKUPFILES moving /tmp/JalviewTest2367249496997871162.jvp to /tmp/JalviewTest2367249496997871162.jvp_BACKUPFILESTESTTMP000001 was successful
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
DEBUG - Created new dataset ds01 for alignment 135937179
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 5933747002476
DEBUG - Setting viewport's view id : 593374700.12705257232476
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Exception during web service menu building process.
java.lang.NullPointerException: null
	at jalview.ws.jws2.Jws2Client.registerAAConWSInstance(Jws2Client.java:212) ~[classes/:?]
	at jalview.ws.jws2.SequenceAnnotationWSClient.attachWSMenuEntry(SequenceAnnotationWSClient.java:164) ~[classes/:?]
	at jalview.ws.jws2.jabaws2.Jws2Instance.attachWSMenuEntry(Jws2Instance.java:236) ~[classes/:?]
	at jalview.ws.jws2.Jws2Discoverer.addEnumeratedServices(Jws2Discoverer.java:574) ~[classes/:?]
	at jalview.ws.jws2.Jws2Discoverer.populateWSMenuEntry(Jws2Discoverer.java:408) ~[classes/:?]
	at jalview.ws.jws2.Jws2Discoverer.attachWSMenuEntry(Jws2Discoverer.java:345) ~[classes/:?]
	at jalview.gui.AlignFrame$20$1.run(AlignFrame.java:4305) [classes/:?]
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313) [?:?]
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770) [?:?]
	at java.awt.EventQueue$4.run(EventQueue.java:721) [?:?]
	at java.awt.EventQueue$4.run(EventQueue.java:715) [?:?]
	at java.security.AccessController.doPrivileged(Native Method) ~[?:?]
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) [?:?]
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:740) [?:?]
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) [?:?]
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) [?:?]
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) [?:?]
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) [?:?]
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [?:?]
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:90) [?:?]
DEBUG - BACKUPFILES using temp file /tmp/JalviewTest10973155325384099301.jvp307324009990299461.tmp_newfile
DEBUG - BACKUPFILES moving /tmp/JalviewTest10973155325384099301.jvp to /tmp/JalviewTest10973155325384099301.jvp_BACKUPFILESTESTTMP000001 was successful
DEBUG - Created new dataset ds01 for alignment 1141392503
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 11470142492809
DEBUG - Setting viewport's view id : 1147014249.8880890292809
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Created new dataset ds01 for alignment 89001633
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 15396396912920
DEBUG - Setting viewport's view id : 1539639691.2696390142920
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527692980
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.2230318039670237879784822408527692980
Warning - overwriting a sequenceSetId for a viewport!
Allocating Jmol Viewer: 
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> load FILES "/tmp/viewerSession8698801992219104833.tmp"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> set hoverDelay=0.1

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527692980
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.2110744939670237879784822408527692980
Warning - overwriting a sequenceSetId for a viewport!
Unhandled callback MEASURE [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527692980
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.2090615939670237879784822408527692980
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527692980
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.3082358739670237879784822408527692980
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527692980
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.947217539670237879784822408527692980
Warning - overwriting a sequenceSetId for a viewport!
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.getTabBounds(BasicTabbedPaneUI.java:1733)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.getTabBounds(BasicTabbedPaneUI.java:1668)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.repaintTab(BasicTabbedPaneUI.java:2338)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.setFocusIndex(BasicTabbedPaneUI.java:2322)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.focusGained(BasicTabbedPaneUI.java:4116)
	at java.desktop/java.awt.AWTEventMulticaster.focusGained(AWTEventMulticaster.java:227)
	at java.desktop/java.awt.Component.processFocusEvent(Component.java:6524)
	at java.desktop/java.awt.Component.processEvent(Component.java:6391)
	at java.desktop/java.awt.Container.processEvent(Container.java:2263)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5011)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4843)
	at java.desktop/java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1950)
	at java.desktop/java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:1050)
	at java.desktop/java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:674)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4892)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4843)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:772)
	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.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:95)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:743)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742)
	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)
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> write STATE "/tmp/JMOL2059350686330000215.spt"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
Error writing Jalview project
java.util.zip.ZipException: duplicate entry: 1493184635  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
	at java.base/java.util.zip.ZipOutputStream.putNextEntry(ZipOutputStream.java:233)
	at java.base/java.util.jar.JarOutputStream.putNextEntry(JarOutputStream.java:109)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:1686)
	at jalview.project.Jalview2XML.writeDatasetFor(Jalview2XML.java:815)
	at jalview.project.Jalview2XML.saveAllFrames(Jalview2XML.java:691)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:623)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:575)
	at jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews(Jalview2xmlTests.java:433)
	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.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
	at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
	at org.testng.TestRunner.privateRun(TestRunner.java:771)
	at org.testng.TestRunner.run(TestRunner.java:621)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
	at org.testng.SuiteRunner.run(SuiteRunner.java:259)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
	at org.testng.TestNG.run(TestNG.java:1009)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:145)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:92)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	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:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Error writing Jalview project
java.util.zip.ZipException: duplicate entry: 1493184635  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
	at java.base/java.util.zip.ZipOutputStream.putNextEntry(ZipOutputStream.java:233)
	at java.base/java.util.jar.JarOutputStream.putNextEntry(JarOutputStream.java:109)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:1686)
	at jalview.project.Jalview2XML.writeDatasetFor(Jalview2XML.java:815)
	at jalview.project.Jalview2XML.saveAllFrames(Jalview2XML.java:691)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:623)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:575)
	at jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews(Jalview2xmlTests.java:433)
	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.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
	at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
	at org.testng.TestRunner.privateRun(TestRunner.java:771)
	at org.testng.TestRunner.run(TestRunner.java:621)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
	at org.testng.SuiteRunner.run(SuiteRunner.java:259)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
	at org.testng.TestNG.run(TestNG.java:1009)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:145)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:92)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	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:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Error writing Jalview project
java.util.zip.ZipException: duplicate entry: 1493184635  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
	at java.base/java.util.zip.ZipOutputStream.putNextEntry(ZipOutputStream.java:233)
	at java.base/java.util.jar.JarOutputStream.putNextEntry(JarOutputStream.java:109)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:1686)
	at jalview.project.Jalview2XML.writeDatasetFor(Jalview2XML.java:815)
	at jalview.project.Jalview2XML.saveAllFrames(Jalview2XML.java:691)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:623)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:575)
	at jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews(Jalview2xmlTests.java:433)
	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.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
	at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
	at org.testng.TestRunner.privateRun(TestRunner.java:771)
	at org.testng.TestRunner.run(TestRunner.java:621)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
	at org.testng.SuiteRunner.run(SuiteRunner.java:259)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
	at org.testng.TestNG.run(TestNG.java:1009)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:145)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:92)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	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:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Error writing Jalview project
java.util.zip.ZipException: duplicate entry: 1493184635  Dataset for MAFFT Multiple Sequence Alignment of Retrieved from Uniprot.xml
	at java.base/java.util.zip.ZipOutputStream.putNextEntry(ZipOutputStream.java:233)
	at java.base/java.util.jar.JarOutputStream.putNextEntry(JarOutputStream.java:109)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:1686)
	at jalview.project.Jalview2XML.writeDatasetFor(Jalview2XML.java:815)
	at jalview.project.Jalview2XML.saveAllFrames(Jalview2XML.java:691)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:623)
	at jalview.project.Jalview2XML.saveState(Jalview2XML.java:575)
	at jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews(Jalview2xmlTests.java:433)
	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.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
	at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
	at org.testng.TestRunner.privateRun(TestRunner.java:771)
	at org.testng.TestRunner.run(TestRunner.java:621)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
	at org.testng.SuiteRunner.run(SuiteRunner.java:259)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
	at org.testng.TestNG.run(TestNG.java:1009)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:145)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:92)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	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:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
DEBUG - Created new dataset ds01 for alignment 1274761773
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276929806078
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.21107449396702378797848224085276929806078
Warning - overwriting a sequenceSetId for a viewport!
Allocating Jmol Viewer: 
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> load FILES "/tmp/viewerSession14510576418154856812.tmp"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> set hoverDelay=0.1

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
Unhandled callback MEASURE [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276929806078
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.20906159396702378797848224085276929806078
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276929806078
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.30823587396702378797848224085276929806078
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276929806078
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.9472175396702378797848224085276929806078
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276929806078
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.22303180396702378797848224085276929806078
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - reusing DseqFor ID
DEBUG - Created new dataset ds01 for alignment 928970794
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 3640323818526
DEBUG - Setting viewport's view id : 364032381.5894824878526
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 303824502
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Created new dataset ds01 for alignment 646427520
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 3038245028635
DEBUG - Setting viewport's view id : 303824502.11867771828635
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 3038245028635
DEBUG - Setting viewport's view id : 303824502.6757853448635
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Created new dataset ds01 for alignment 1845890526
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 11830332519181
DEBUG - Setting viewport's view id : 1183033251.1018187409181
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527699312
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.2230318039670237879784822408527699312
Warning - overwriting a sequenceSetId for a viewport!
Allocating Jmol Viewer: 
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> load FILES "/tmp/viewerSession5676766598047557317.tmp"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> set hoverDelay=0.1

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527699312
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.2110744939670237879784822408527699312
Warning - overwriting a sequenceSetId for a viewport!
Unhandled callback MEASURE [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527699312
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.2090615939670237879784822408527699312
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527699312
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.3082358739670237879784822408527699312
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 32038447815156893765406141098684336046856092601561375251543984656269718347347550035996250606097223418125197189434639670237879784822408527699312
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.947217539670237879784822408527699312
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> write STATE "/tmp/JMOL10150460120754591725.spt"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - Created new dataset ds01 for alignment 1307555224
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 3203844781515689376540614109868433604685609260156137525154398465626971834734755003599625060609722341812519718943463967023787978482240852769931212276
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.223031803967023787978482240852769931212276
Warning - overwriting a sequenceSetId for a viewport!
Allocating Jmol Viewer: 
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> load FILES "/tmp/viewerSession339132126933373274.tmp"

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> set hoverDelay=0.1

DEBUG - <<Jmol<< pending
DEBUG - >>Jmol>> History on
DEBUG - <<Jmol<< pending
Unhandled callback MEASURE [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm]
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 3203844781515689376540614109868433604685609260156137525154398465626971834734755003599625060609722341812519718943463967023787978482240852769931212276
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.94721753967023787978482240852769931212276
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 3203844781515689376540614109868433604685609260156137525154398465626971834734755003599625060609722341812519718943463967023787978482240852769931212276
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.308235873967023787978482240852769931212276
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 3203844781515689376540614109868433604685609260156137525154398465626971834734755003599625060609722341812519718943463967023787978482240852769931212276
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.209061593967023787978482240852769931212276
Warning - overwriting a sequenceSetId for a viewport!
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 3203844781515689376540614109868433604685609260156137525154398465626971834734755003599625060609722341812519718943463967023787978482240852769931212276
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.211074493967023787978482240852769931212276
Warning - overwriting a sequenceSetId for a viewport!
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: Index 4 out of bounds for length 4
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.paintTabArea(BasicTabbedPaneUI.java:897)
	at java.desktop/javax.swing.plaf.basic.BasicTabbedPaneUI.paint(BasicTabbedPaneUI.java:860)
	at java.desktop/javax.swing.plaf.metal.MetalTabbedPaneUI.paint(MetalTabbedPaneUI.java:933)
	at java.desktop/javax.swing.plaf.metal.MetalTabbedPaneUI.update(MetalTabbedPaneUI.java:814)
	at java.desktop/javax.swing.JComponent.paintComponent(JComponent.java:797)
	at java.desktop/javax.swing.JComponent.paint(JComponent.java:1074)
	at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:907)
	at java.desktop/javax.swing.JComponent.paint(JComponent.java:1083)
	at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:907)
	at java.desktop/javax.swing.JComponent.paint(JComponent.java:1083)
	at java.desktop/javax.swing.JLayeredPane.paint(JLayeredPane.java:590)
	at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:907)
	at java.desktop/javax.swing.JComponent.paint(JComponent.java:1083)
	at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:907)
	at java.desktop/javax.swing.JComponent.paint(JComponent.java:1083)
	at java.desktop/javax.swing.JComponent.paintChildren(JComponent.java:907)
	at java.desktop/javax.swing.JComponent.paint(JComponent.java:1083)
	at java.desktop/javax.swing.JLayeredPane.paint(JLayeredPane.java:590)
	at java.desktop/javax.swing.JComponent.paintToOffscreen(JComponent.java:5255)
	at java.desktop/javax.swing.RepaintManager$PaintManager.paintDoubleBufferedImpl(RepaintManager.java:1643)
	at java.desktop/javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1618)
	at java.desktop/javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1556)
	at java.desktop/javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:262)
	at java.desktop/javax.swing.RepaintManager.paint(RepaintManager.java:1323)
	at java.desktop/javax.swing.JComponent._paintImmediately(JComponent.java:5203)
	at java.desktop/javax.swing.JComponent.paintImmediately(JComponent.java:5013)
	at java.desktop/javax.swing.RepaintManager$4.run(RepaintManager.java:865)
	at java.desktop/javax.swing.RepaintManager$4.run(RepaintManager.java:848)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
	at java.desktop/javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:848)
	at java.desktop/javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:823)
	at java.desktop/javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:772)
	at java.desktop/javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1890)
	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)
DEBUG - BACKUPFILES using temp file /tmp/JalviewTest5197505952790733927.jvp17157718248011286778.tmp_newfile
DEBUG - BACKUPFILES moving /tmp/JalviewTest5197505952790733927.jvp to /tmp/JalviewTest5197505952790733927.jvp_BACKUPFILESTESTTMP000001 was successful
DEBUG - Created new dataset ds01 for alignment 2134316666
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 182014652814394
DEBUG - Setting viewport's view id : 1820146528.63050763614394
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276914476
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.22303180396702378797848224085276914476
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276914476
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.21107449396702378797848224085276914476
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276914476
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.20906159396702378797848224085276914476
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276914476
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.30823587396702378797848224085276914476
Warning - overwriting a sequenceSetId for a viewport!
DEBUG - Setting viewport's sequence set id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346396702378797848224085276914476
DEBUG - Setting viewport's view id : 320384478151568937654061410986843360468560926015613752515439846562697183473475500359962506060972234181251971894346.9472175396702378797848224085276914476
Warning - overwriting a sequenceSetId for a viewport!