jalview/test

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Monday 11 Jan
5:08 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3117 raise AlignFrame or SplitFrame when Overview clicked

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    • +1
    ./gui/FreeUpMemoryTest.java
  2. … 4 more files in changeset.
Friday 08 Jan
4:05 pm

Jim Procter

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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    • +17
    ./datamodel/SequenceTest.java
Saturday 19 Dec 2020
7:22 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1713 restore project with no Overview, regardless of Preferences

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    • +46
    ./project/Jalview2xmlTests.java
  2. … 1 more file in changeset.
Thursday 17 Dec 2020
8:44 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1713 close and replace auto-opened Overview with restored Overview

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    • +3
    ./project/Jalview2xmlTests.java
  2. … 3 more files in changeset.
Monday 14 Dec 2020
7:58 pm

Jim Procter

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

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    ./datamodel/SequenceTest.java
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    • +2
    ./gui/AlignFrameTest.java
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    ./gui/AlignViewportTest.java
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    • +2
    ./gui/PairwiseAlignmentPanelTest.java
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    ./gui/PopupMenuTest.java
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    ./hmmer/HMMERTest.java
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    ./io/FileFormatsTest.java
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    ./project/Jalview2xmlTests.java
    • -9
    • +9
    ./renderer/seqfeatures/FeatureColourFinderTest.java
  10. … 48 more files in changeset.
5:24 pm

Ben Soares

JAL-3628 Test for doubly saved single backup file scheme

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    ./io/BackupFilesTest.java
    • -0
    • +112
    ./io/testProps_singlefilebackup.jvprops
Sunday 13 Dec 2020
12:32 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1713 unit test for save/restore Overview in project

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    • +92
    ./project/Jalview2xmlTests.java
Saturday 12 Dec 2020
2:39 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-1713 JAL-3119 JAL-3785 refactored get/set Overview bounds and title

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    • +41
    ./gui/AlignmentPanelTest.java
  2. … 5 more files in changeset.
Friday 11 Dec 2020
12:44 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3612 use _last_ drawn colour per feature type in Overview

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    • +54
    ./renderer/seqfeatures/FeatureColourFinderTest.java
  2. … 1 more file in changeset.
Thursday 10 Dec 2020
1:04 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

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

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    ./renderer/OverviewRendererTest.java
    • -49
    • +36
    ./renderer/OverviewResColourFinderTest.java
  3. … 6 more files in changeset.
Friday 04 Dec 2020
5:59 pm

Ben Soares

JAL-3775 added the Platform.isLinux() check for test HiDPISetting2

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    • +9
    ./bin/HiDPISettingTest2.java
5:35 pm

Ben Soares

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.

5:31 pm

Ben Soares

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.

Wednesday 02 Dec 2020
8:37 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3751 second occurrence of bug squashed

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    • +34
    ./util/MapListTest.java
  2. … 1 more file in changeset.
5:56 pm

Jim Procter

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.

5:53 pm

Jim Procter

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 ?

5:20 pm

Jim Procter

JAL-3608 cherry pick of 92cb745e7
JAL-3608 cherry pick of 92cb745e7
Tuesday 01 Dec 2020
2:52 pm

Ben Soares

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

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    ./bin/HiDPISettingTest1.java
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    ./bin/HiDPISettingTest2.java
    • -0
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    ./bin/hidpiTestProps.jvprops
  4. … 1 more file in changeset.
Thursday 26 Nov 2020
2:17 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

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

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    ./util/MapListTest.java
  2. … 2 more files in changeset.
Friday 20 Nov 2020
1:04 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3779 apply properties to all groups with given name, not just first

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    • +51
    ./io/AnnotationFileIOTest.java
  2. … 1 more file in changeset.
11:58 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3761 debugged and working (but not tidied) locateInFrom2/To2

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    ./util/MapListTest.java
  2. … 1 more file in changeset.
Thursday 12 Nov 2020
2:36 pm

Jim Procter

Merge branch 'feature/JAL-3469clinvarVCF' into spike/clinvar

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    ./io/vcf/VCFLoaderTest.java
  2. … 1 more file in changeset.
10:03 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3761 locateInFrom2 work in progress commit

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    ./util/MapListTest.java
  2. … 2 more files in changeset.
Thursday 29 Oct 2020
3:50 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3761 unit test for MapList.countPos()

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    • +64
    ./util/MapListTest.java
3:35 pm

Jim Procter

JAL-3759 fix compilation error for test

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    ./analysis/GroupingTest.java
11:30 am

gmungoc <g.m.carstairs@dundee.ac.uk>

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

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    ./util/MappingUtilsTest.java
  2. … 1 more file in changeset.
Wednesday 28 Oct 2020
11:24 pm

Jim Procter

JAL-3725 fix tests for EMBLFlatFile parser when mapping doesn’t include stop codon

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    • +8
    ./io/EmblFlatFileTest.java
Tuesday 27 Oct 2020
11:02 am

Jim Procter

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

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    • +2
    ./structure/Mapping.java
Thursday 22 Oct 2020
2:48 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3763 Javadoc, check for null, additional tests

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    ./datamodel/AlignedCodonFrameTest.java
  2. … 2 more files in changeset.
2:48 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3763 Javadoc, check for null, additional tests

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    ./datamodel/AlignedCodonFrameTest.java
  2. … 2 more files in changeset.