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Agreed. I seem to remember (this was a while ago now) that I found isAMacAndNotJS() and thought it might be an important distinction. Sounds like it's just redundant? Can tidy this another time then.

Agreed. I seem to remember (this was a while ago now) that I found isAMacAndNotJS() and thought it might be an important distinction. Sounds like it's just redundant? Can tidy this another time then.

Agree this is just touching on a much bigger task. However... The reason I /needed/ to do this rather than just /wanted/ to do this is that several of the classes I've been working on (e.g. jalview...

Agree this is just touching on a much bigger task.
However...
The reason I /needed/ to do this rather than just /wanted/ to do this is that several of the classes I've been working on (e.g. jalview.bin.Launcher, jalview.bin.HiDPISetting, jalview.bin.MemorySetting) run very early on (especially jalview.bin.Launcher!). This means Cache.log has perhaps not yet been initialised, so a Cache.log.debug doesn't log (unless you count reams of NullPointerExceptions as logging!).

In the case of HiDPISetting and MemorySetting that also get used in Getdown, where there is no jalview.bin.Cache, they currently have to use System.out and System.err [or maybe I could stub jalview.bin.Cache too]. I'd prefer them to use Cache.log when they can so this is an attempt at starting to decouple jalview.bin.Cache from other jalview things so it can be used standalone within Getdown. The main reason for wanting to do that is to have shared code to read the preferences between Jalview and Getdown.

I think there are lots of things that could be tidied up (particularly the overloading and additional logging functions via Cache which don't really reduce code at point of use, but are certainly u...

I think there are lots of things that could be tidied up (particularly the overloading and additional logging functions via Cache which don't really reduce code at point of use, but are certainly useful in spirit), but now is most definitely not the time to optimise and beautify code.

Ben Soares as far as I can see the only thing missing after this branch is merged to develop is this logic. I just did a quick test and it appears 'Platform.isAMac()' returns false under JalviewJS,...

Ben Soares as far as I can see the only thing missing after this branch is merged to develop is this logic. I just did a quick test and it appears 'Platform.isAMac()' returns false under JalviewJS, so probably not a dealbreaker. Do you agree ?

JAL-3608 cherry pick of 92cb745e7
JAL-3608 cherry pick of 92cb745e7
doesn't matter for 2.11.1.1 but should be dropped for 2.11.2 unless it really is needed.

doesn't matter for 2.11.1.1 but should be dropped for 2.11.2 unless it really is needed.

Ben Soares - I don't think you need this. The logger provides a overload to pass exceptions which will give the full stack trace - e.g. catch (Exception ex) { Cache.log.debug("ignored raised except...

Ben Soares - I don't think you need this. The logger provides a overload to pass exceptions which will give the full stack trace - e.g. catch (Exception ex) { Cache.log.debug("ignored raised exception during blah",ex); }

JAL-3628 Cache.getStackTraceAsString
JAL-3628 Cache.getStackTraceAsString
changed

changed

Should be ENA Flatfile retrieval failed

Should be ENA Flatfile retrieval failed

JAL-3692: Update ENA endpoint for EMBL/CDS sequence retrieval
JAL-3692: Update ENA endpoint for EMBL/CDS sequence retrieval
[Added TRACE above] I've added: if currentlLogLevel is not null and an instanceof Level, and can't be selected then it gets added to the Combo and then selected. This will allow all levels to be se...

[Added TRACE above] I've added:
if currentlLogLevel is not null and an instanceof Level, and can't be selected then it gets added to the Combo and then selected. This will allow all levels to be set in .jalview_properties without over-complicating the combo for other users.

I've added TRACE (and moved it above DEBUG as I think that preserves the verbosity order). Also see below comment in setChosenLogLevelCombo()

I've added TRACE (and moved it above DEBUG as I think that preserves the verbosity order). Also see below comment in setChosenLogLevelCombo()

Happy to see you look back at the log level property again https://source.jalview.org/crucible/static/ogdo0b/2static/images/wiki/icons/emoticons/smile.gif

Happy to see you look back at the log level property again

this will override the log level set via .jalview_properties - I occasionally use TRACE, for instance - so the combo should allow other levels.

this will override the log level set via .jalview_properties - I occasionally use TRACE, for instance - so the combo should allow other levels.

There might be a need to enable more levels - perhaps TRACE ?

There might be a need to enable more levels - perhaps TRACE ?

guess this can be deleted

guess this can be deleted

JAL-3676 Added Log Level ComboBox and Copy to Clipboard button in Java Console
JAL-3676 Added Log Level ComboBox and Copy to Clipboard button in Java Console
JAL-3390: Option to hide unmapped residues in structure viewer
JAL-3390: Option to hide unmapped residues in structure viewer
I suggest we close this. It's all ancient history now.

I suggest we close this. It's all ancient history now.

technically, the method field is any value taken by AlignmentSorter.sortByFeature() - ie FEATURE_SCORE, FEATURE_LABEL, FEATURE_DENSITY.

technically, the method field is any value taken by AlignmentSorter.sortByFeature() - ie FEATURE_SCORE, FEATURE_LABEL, FEATURE_DENSITY.

JAL-3549: 'Undo' menu item is added for null Sort by Feature Score/Density action
JAL-3549: 'Undo' menu item is added for null Sort by Feature Score/Density action
I have added a large number of commits to this review which were tagged "JAL-3253-applet" or "Jalview-JS/develop-3253" or similar. This should be just the issue id for JIRA to associate the commit ...

I have added a large number of commits to this review which were tagged "JAL-3253-applet" or "Jalview-JS/develop-3253" or similar. This should be just the issue id for JIRA to associate the commit with the issue.