Details
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Type:
Bug
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Status: Closed
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Priority:
Blocker
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Resolution: Fixed
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Affects Version/s: 2.11.3.0
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Fix Version/s: 2.11.3.0
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Component/s: gui, jvdesktop, Structures
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Labels:
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Environment:Java version: 1.8.0_382
Java home: /usr/local/Cellar/openjdk@8/1.8.0-382_1/libexec/openjdk.jdk/Contents/Home/jre
Java arch: x86_64 Mac OS X 14.0
Jalview non-release version: TEST (Source git-commit:445dbb2523 [doc/JAL-4090_Release_2_11_3_0])
Setting initial log level to INFO
built as shadowJar
Description
it is possible to make Jalview hang if the Java console is open during long running Jmol operations involving lots of stdout activity (which are slower when console is open), and a user event triggers a command to be sent to Jmol.
Reproduce:
1. import attached alignment (epas1_aln.fa) and ensure Jmol is selected as structure viewer.
2. select all sequences, open 3d structure fetcher, discover 3d-beacons structures and import all alphafold structures - with superposition enabled.
3. As soon as viewer is displayed, start moving the mouse over sequences in the alignment window...
Symptom - Jmol causes the UI to become unresponsive when lots of stdout is being created due to thread starvation, but the additional act of sending commands to Jmol seems to cause an indirect deadlock.
Reproduce:
1. import attached alignment (epas1_aln.fa) and ensure Jmol is selected as structure viewer.
2. select all sequences, open 3d structure fetcher, discover 3d-beacons structures and import all alphafold structures - with superposition enabled.
3. As soon as viewer is displayed, start moving the mouse over sequences in the alignment window...
Symptom - Jmol causes the UI to become unresponsive when lots of stdout is being created due to thread starvation, but the additional act of sending commands to Jmol seems to cause an indirect deadlock.