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JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

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Merge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg' into develop

JAL-3829 JalviewJS workarounds/patches

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patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

Reviewing the alphafold + contact matrix patch for 2.11.2
Reviewing the alphafold + contact matrix patch for 2.11.2
JAL-3855 convenience method to check a URL will return a 200

JAL-3633 refactored/simplified LaunchUtils code

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JAL-3503 Added a Startup tab in Preferences, with gui for JVMMEMMAX and JVMMEMPC settings. Allowed jalview.bin.Launcher and getdown to read/use these memory settings at launch. Added channel.props to getdown appdir, used to determing correct .jalview_properties file. Refactored MemorySetting a bit, with more helper methods for the Preferences tab.

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JAL-3594 Allow a channel to use a different preferences file than .jalview_properties, with initial read from .jalview_properties

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Revert "Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch"

This reverts commit cb628aab46f9027e71b71203b322f96710e09990, reversing

changes made to a40669b2eeb34a6c760b63c172a31a194b456f24.

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JAL-3806 fix and test for one-to-many sequence mapping case

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JAL-3878 Initial preparation.

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JAL-3794 X and N are counted as DNA characters, but we also check how many Ns - if there were no real nucleotide characters we always return protein for poly-asparagine

JAL-3794 X and N are counted as DNA characters, but we also check how many Ns - if there were no real nucleotide characters we always return protein for poly-asparagine

JAL-3761 more consistent parameter naming

JAL-3761 more consistent parameter naming

Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

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JAL-3594 Adjustments to allow JalviewJS to use ChannelProperties, and new utils/channels dir for jalviewjs and jalviewjs-release

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JAL-3594 Images for splash screen

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JAL-3594 JAL-3728 Added taskbar icons to desktop and Java console. Changed "Jalview" to "app_name" in various appropriate places

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JAL-3594 added BG logo. Changed some named Jalviews to app_name property. Added test-release and default channels.

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JAL-3594 Default values for channel properties defined in code as fallback

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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.

JAL-3594 New jalview.util.ChannelProperties to get/cache values and images used in the application. Starting to tidy images in resources/images.

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    ./ChannelProperties.java
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JAL-3751 second occurrence of bug squashed

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JAL-3761 helper method reinstated to avoid code duplication