jalview

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JAL-3761 more consistent parameter naming

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-3761 helper method reinstated to avoid code duplication

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-3761 locateInFrom/To revised with tests; unused methods removed

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    /src/jalview/datamodel/Mapping.java
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    /src/jalview/util/MapList.java
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    /test/jalview/util/MapListTest.java
JAL-3761 extra check that VCF feature is fully mappable to sequence

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    /src/jalview/io/vcf/VCFLoader.java
JAL-3761 debugged and working (but not tidied) locateInFrom2/To2

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    /test/jalview/util/MapListTest.java
JAL-3761 locateInFrom2 work in progress commit

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    /src/jalview/util/MapList.java
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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MapListTest.java
JAL-3761 unit test for MapList.countPos()

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    /test/jalview/util/MapListTest.java
JAL-3761 failing test, formatting, method renamed

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    /test/jalview/util/MapListTest.java
JAL-3761 failing tests for locateInFrom/To with overlapping ranges

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    /test/jalview/util/MapListTest.java
JAL-3751 only merge strictly contiguous ranges of mappings
JAL-3751 only merge strictly contiguous ranges of mappings
JAL-3751 only merge strictly contiguous ranges of mappings

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    /test/jalview/util/MapListTest.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-3700: Complement sequence correspondence is broken for CDS with shared dataset sequence
JAL-3700: Complement sequence correspondence is broken for CDS with shared dataset sequence
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown jar and version files

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    /getdown/lib/getdown-launcher-local.jar
JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown src files

Merge branch 'feature/JAL-3615gzipXfam' into develop

JAL-3746 bump release version for 2.11.2 series (currently on develop)

JAL-3679 Added externally specified plugins dir to J2sPlugin check

JAL-3679 Added externally specified plugins dir to J2sPlugin check

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

Decision made in the issue to just check release build_properties.

Decision made in the issue to just check release build_properties.