jalview

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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-3700 mapped sequence group includes short (or all gapped) sequences

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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MappingUtilsTest.java
JAL-3725 fix tests for EMBLFlatFile parser when mapping doesn’t include stop codon

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    /test/jalview/io/EmblFlatFileTest.java
JAL-3725 patch EMBL flat file to exclude stop codon from the mapping (for 2.11.1.3 - needs cherry-pick to 2.11.2)

update test for JAL-3763 redact shared DS sequences for contiguous CDS

JAL-3768 noticed failure of test when run as part of suite via gradle - whilst patching JAL-3700 JAL-3748 JAL-3763 for 2.11.1.3

JAL-3700 JAL-3748 JAL-3763 don’t add stop codon via alignAs if guide peptide doesn’t include C terminus.

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    /src/jalview/analysis/AlignmentUtils.java
JAL-3763 Javadoc, check for null, additional tests

JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

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    /src/jalview/datamodel/SearchResults.java
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    /test/jalview/datamodel/AlignedCodonFrameTest.java
JAL-3700 JAL-3763 create datasets for test sequences

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    /test/jalview/util/MappingUtilsTest.java
JAL-3763 failsafe check for null

JAL-3763 refactored getCoveringMapping for virtual feature discovery

JAL-3763 always make a new dataset sequence for CDS sequence

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    /src/jalview/analysis/AlignmentUtils.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-3748 not testing for sequence’s containment in mapped range breaks CDS reconstruction but allows testAlignProteinAsDna_incompleteStartCodon to pass

JAL-3748 fix compilation error

JAL-3748 maximal test for JAL-3748 using covid19 CDS/Protein

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    /test/jalview/gui/SplitFrameTest.java
JAL-3748 more tests verifying reconstruction of AlignemntView for linked CDS/Protein alignment and selected region

JAL-3748 reusable assert to trace specific issues with recovering the correct Sequence/Mapping (highlights points of failure for AlignmentUtilsTests with patch

JAL-3748 allow AlignedCodonFrame.covers to optionally only require coverage for either originating or mapped sequence.

JAL-3748 test data for SplitFrameTest

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    /examples/testdata/MN908947.jvp
JAL-3748 don’t trash start/end on SequenceI reconstructed from a SeqCigar via SeqsetUtils.SeqCharacterUnhash

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    /src/jalview/analysis/SeqsetUtils.java