jalview

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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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    • -3
    • +3
    /src/jalview/datamodel/AlignedCodonFrame.java
    • -1
    • +6
    /src/jalview/gui/PopupMenu.java
    • -0
    • +63
    /test/jalview/datamodel/AlignedCodonFrameTest.java
2:48 pm

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

JAL-3763 Javadoc, check for null, additional tests

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    • -3
    • +3
    /src/jalview/datamodel/AlignedCodonFrame.java
    • -1
    • +6
    /src/jalview/gui/PopupMenu.java
    • -0
    • +63
    /test/jalview/datamodel/AlignedCodonFrameTest.java
10:40 am

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

JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

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    • -1
    • +6
    /src/jalview/datamodel/AlignedCodonFrame.java
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    • +4
    /src/jalview/datamodel/SearchResults.java
    • -26
    • +129
    /test/jalview/datamodel/AlignedCodonFrameTest.java
10:40 am

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

JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

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    • -1
    • +6
    /src/jalview/datamodel/AlignedCodonFrame.java
    • -2
    • +4
    /src/jalview/datamodel/SearchResults.java
    • -26
    • +129
    /test/jalview/datamodel/AlignedCodonFrameTest.java
Wednesday 21 Oct 2020
4:24 pm

Jim Procter

JAL-3766 release notes for JAL-3611 JAL-3765

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    • -0
    • +5
    /help/help/html/releases.html
4:21 pm

Jim Procter

Merge branch 'releases/Release_2_11_1_Branch' of http://source.jalview.org/git/jalview into releases/Release_2_11_1_Branch

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4:20 pm

Jim Procter

Merge branch 'bug/JAL-3765_Find_bugs_in_21112' into releases/Release_2_11_1_Branch

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4:20 pm

Jim Procter

JAL-3766 cut new patch release

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    • +1
    /RELEASE
    • -0
    • +17
    /help/help/html/releases.html
    • -2
    • +2
    /help/help/html/whatsNew.html
4:14 pm

Jim Procter

Merge branch 'releases/Release_2_11_1_Branch'

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3:18 pm

Mateusz Warowny

JAL-3690 Documentation for AlignCalcListener

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    • +27
    /src/jalview/api/AlignCalcListener.java
2:54 pm

Mateusz Warowny

JAL-3690 Catch and notify about worker cancellation separately.

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    • -0
    • +1
    /src/jalview/api/AlignCalcListener.java
    • -0
    • +17
    /src/jalview/workers/AlignCalcManager2.java
2:51 pm

Mateusz Warowny

JAL-3690 Fix concurrent modification exception when workers are cancelled

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    • -26
    • +32
    /src/jalview/workers/AlignCalcManager2.java
2:45 pm

Mateusz Warowny

JAL-3690 Documentation for AlignCalcManagerI2

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    • -0
    • +88
    /src/jalview/api/AlignCalcManagerI2.java
Tuesday 20 Oct 2020
5:23 pm

Jim Procter

JAL-3765 fix test

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    • -0
    • +13
    /test/jalview/analysis/FinderTest.java
5:23 pm

Jim Procter

JAL-3765 fix test

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    • -10
    • +13
    /test/jalview/analysis/FinderTest.java
5:13 pm

Jim Procter

fix for JAL-3765

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    • -1
    • +1
    /src/jalview/analysis/Finder.java
5:13 pm

Jim Procter

fix for JAL-3765

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    • -1
    • +1
    /src/jalview/analysis/Finder.java
Monday 19 Oct 2020
6:07 pm

Jim Procter

JAL-3765 simple test that findAll finds all matches for a pattern when it is present multiple times in a sequence

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    • -0
    • +10
    /test/jalview/analysis/FinderTest.java
11:59 am

Jim Procter

not related to JAL-3765 ! Actually related to JAL-3675!

not related to JAL-3765 ! Actually related to JAL-3675!

Thursday 15 Oct 2020
3:01 pm

Ben Soares

Merge branch 'develop' into blocker/JAL-3611_space_character_in_jalview_install_path

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11:02 am

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

JAL-3763 unused method removed

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    • -34
    • +0
    /src/jalview/datamodel/AlignedCodonFrame.java
Thursday 08 Oct 2020
3:30 pm

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

JAL-3700 JAL-3763 create datasets for test sequences

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    • -4
    • +8
    /test/jalview/util/MappingUtilsTest.java
3:30 pm

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

JAL-3700 JAL-3763 create datasets for test sequences

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    • -4
    • +8
    /test/jalview/util/MappingUtilsTest.java
3:29 pm

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

JAL-3763 failsafe check for null

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    • -0
    • +4
    /src/jalview/datamodel/AlignedCodonFrame.java
3:29 pm

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

JAL-3763 failsafe check for null

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    • -0
    • +4
    /src/jalview/datamodel/AlignedCodonFrame.java
3:06 pm

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

JAL-3763 refactored getCoveringMapping for virtual feature discovery

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    • +65
    /src/jalview/datamodel/AlignedCodonFrame.java
    • -7
    • +7
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
3:06 pm

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

JAL-3763 refactored getCoveringMapping for virtual feature discovery

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    • -25
    • +65
    /src/jalview/datamodel/AlignedCodonFrame.java
    • -7
    • +7
    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
3:05 pm

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

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

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    • -55
    • +41
    /src/jalview/analysis/AlignmentUtils.java
3:05 pm

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

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

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    • -55
    • +41
    /src/jalview/analysis/AlignmentUtils.java
8:40 am

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

JAL-3761 failing test, formatting, method renamed

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    /src/jalview/util/MapList.java
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    • +19
    /test/jalview/util/MapListTest.java