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JAL-3117 raise AlignFrame or SplitFrame when Overview clicked

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JAL-3794 new test for recognition of protein or DNA with ambiguity characters, including the ‘all N’ case (that should be protein..).

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    ./jalview/datamodel/SequenceTest.java
JAL-1713 restore project with no Overview, regardless of Preferences

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    ./jalview/project/Jalview2xmlTests.java
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JAL-1713 close and replace auto-opened Overview with restored Overview

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    ./jalview/project/Jalview2xmlTests.java
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Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

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    ./jalview/gui/AlignViewportTest.java
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    ./jalview/gui/PairwiseAlignmentPanelTest.java
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    ./jalview/project/Jalview2xmlTests.java
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JAL-3628 Test for doubly saved single backup file scheme

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    ./jalview/io/BackupFilesTest.java
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    ./jalview/io/testProps_singlefilebackup.jvprops
JAL-1713 unit test for save/restore Overview in project

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    ./jalview/project/Jalview2xmlTests.java
JAL-1713 JAL-3119 JAL-3785 refactored get/set Overview bounds and title

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    ./jalview/gui/AlignmentPanelTest.java
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JAL-3612 use _last_ drawn colour per feature type in Overview

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JAL-1713 refactorings to allow save/restore Overview to/from project

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    ./jalview/renderer/OverviewResColourFinderTest.java
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JAL-3775 added the Platform.isLinux() check for test HiDPISetting2

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-3751 second occurrence of bug squashed

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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-3609 JAL-3775 Tests for jalview.bin.HiDPISetting

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    ./jalview/bin/HiDPISettingTest1.java
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    ./jalview/bin/HiDPISettingTest2.java
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    ./jalview/bin/hidpiTestProps.jvprops
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JAL-3761 locateInFrom/To revised with tests; unused methods removed

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    ./jalview/util/MapListTest.java
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JAL-3779 apply properties to all groups with given name, not just first

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

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    ./jalview/util/MapListTest.java
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Merge branch 'feature/JAL-3469clinvarVCF' into spike/clinvar

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JAL-3761 locateInFrom2 work in progress commit

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

JAL-3759 fix compilation error for test

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

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

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-3763 Javadoc, check for null, additional tests

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JAL-3763 Javadoc, check for null, additional tests

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