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JAL-3746 release notes and what’s new for 2.11.2 - in progress

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JAL-3779 Added to documentation

JAL-3741 http to https (and jar to jvp for exampleFile defaults!) Conflicts: src/jalview/bin/Jalview.java src/jalview/gui/Desktop.java

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JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax

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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
JAL-3741 http to https (and jar to jvp for exampleFile defaults!)

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JAL-3675 update sequence fetcher service documentation for JAL-3692 (ENA Flatfile) and refreshed links for other endpoints.

JAL-3490 JAL-3675 release notes, update Find dialog image in help and tidy up documentation for 2.11.1.1

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JAL-3477 Added -help text for jvmmempc and jvmmemmax. Fixed typo and slight rewording in help/memory.html

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JAL-3477 Added -help text for jvmmempc and jvmmemmax. Fixed typo and slight rewording in help/memory.html

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JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax

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JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax

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JAL-3633 Help documentation updated

JAL-3633 Help documentation updated

JAL-3675 mention -open argument in the command line arguments table

JAL-3675 JAL-3570 JAL-3608 JAL-2983 release notes and docs

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JAL-3407 add and document ComputePeptideVariants.groovy

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JAL-3567 JAL-3407 document sequence features report and the additional info provided for virtual features. Also bumped release date to 22st April

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    ./seqfeaturereport.html
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    ./seqfeaturesrep.png
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JAL-3407 JAL-3187 help documentation for virtual features and tabbed feature settings for linked cds/protein views

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    ./linkedfeatsettings.png
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JAL-3407 JAL-3549 explicitly mention the ‘no features’ dialog, and how an existing selection affects the sort alignment by feature score/density

JAL-3376 documentation for standard attributes for variants from VCF

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JAL=3121 more data format validation/tests, help text tweak

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JAL-3121 update help page for GFF column 9 nested attributes

JAL-3474 removed all .cvsignore files stored in the repo

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JAL-3384 Added -out to showUsage and clarguments help text

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