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Merge branch 'develop' into features/JAL-2909_bamImport_2_11_2

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JAL-3616 show name of structure viewer in ‘new view’ button

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JAL-3829 fetch 3D beacons now started by clicking button shown above the drop-down filter/manual input combo box.

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JAL-2909 mininal merge of bam import demo to Jalview 2.11.2 develop Merge remote-tracking branch 'origin/features/JAL-2909_bamImport2_11' into features/JAL-2909_bamImport_2_11_2

Conflicts:

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/AppletFormatAdapter.java

src/jalview/io/FileFormat.java

src/jalview/io/FileLoader.java

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JAL-3829 report when 3d-beacons doesn’t provide any models

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JAL-3829 alternative UX: need to select 3d-beacons from dropdown if db-refs need to be fetched

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JAL-3829 do better at detecting structure type, prompt to retrieve Uniprot ids for proteins without canonical Ids and show provider in the Structure Chooser’s cache view

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JAL-3774 combined changes from bug/JAL-3774_splitFrameFinder: i) fixed focus Finder from split frame. ii) missing i18n added, overlong translation shortened. iii) better translation.

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JAL-3739 (combined) commits from feature/JAL-3739_useFormFieldText

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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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Merge branch 'feature/JAL-3692enaEndpoint' into patch/for2.11.2/JAL-3821_ena_rna_moltype

JAL-3739 catch parameter errors and report to the user

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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-3774 better translation

JAL-3774 missing i18n added, overlong translation shortened

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JAL-3774 fixed focus Finder from split frame

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JAL-3719 Format->Colour Gaps option uses Overview gap colour logic pulled up to alignment viewport sequence renderer

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JAL-3719 Format->Colour Gaps option uses Overview gap colour logic pulled up to alignment viewport sequence renderer Conflicts: resources/lang/Messages.properties resources/lang/Messages_es.properties

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JAL-3490 merged with 2.11.2 develop

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Merge branch 'patch/Release_2_11_1_Branch_patch_JAL-3490' into releases/Release_2_11_1_Branch

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JAL-3676 More explicit tooltip about resetting log level on Console close. Also clarified code to set initial log level and re-set on close to previously set level.

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JAL-3676 More explicit tooltip about resetting log level on Console close. Also clarified code to set initial log level and re-set on close to previously set level.

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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); }