jalview

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Commits this week: 15
Total Committers: 69
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Commits this week: 15

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Friday 27 Nov
5:24 pm

Ben Soares

JAL-3660 Fix for specified output format when using command line arg to convert a file

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    • -8
    • +29
    /src/jalview/bin/Jalview.java
Thursday 29 Oct
2:26 pm

Ben Soares

JAL-3248 Added mention of version 'TEST' in shadow jar filename in building.md/html since develop branch currently uses this by default.

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    • -1
    • +1
    /doc/building.html
    • -1
    • +1
    /doc/building.md
2:19 pm

Ben Soares

JAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename

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    • -5
    • +6
    /doc/building.html
    • -5
    • +8
    /doc/building.md
Wednesday 28 Oct
4:04 pm

Jim Procter

Merge branch 'portforward/JAL-3765_patch_to_2112' into develop

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12:18 pm

Ben Soares

JAL-3248 Added step to create the eclipse files before project import. Noted non-fatal NPEs during build with gradle 6.6+

Cherry pick from release, generated new building.html as it's a different process. Also added in a "**/*.md" into build.gradle (wasn't finding anything with "*.md")

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    • -1
    • +2
    /build.gradle
    • -3
    • +7
    /doc/building.html
    • -3
    • +11
    /doc/building.md
Tuesday 20 Oct
5:23 pm

Jim Procter

JAL-3765 fix test

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    • -0
    • +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
Thursday 15 Oct
3:01 pm

Ben Soares

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

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Tuesday 29 Sep
4:41 pm

Jim Procter

JAL-3760 fix tests for changed behaviour

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    • -4
    • +4
    /test/jalview/util/ComparisonTest.java
3:26 pm

Jim Procter

JAL-3760 refactor nucleotide proportion test to per-sequence and return false if any sequence appears protein-like

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    • -30
    • +39
    /src/jalview/util/Comparison.java
Monday 28 Sep
4:57 pm

Ben Soares

JAL-3753 ensure correct dependencies for shadowJar task

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    • -24
    • +24
    /build.gradle
12:12 pm

Ben Soares

Merge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar

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    • -1
    • +1
    /build.gradle
    • -1
    • +2
    /gradle.properties
Friday 25 Sep
9:39 am

Ben Soares

JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

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    • -1
    • +2
    /gradle.properties
Thursday 24 Sep
6:16 pm

Ben Soares

JAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...

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    • -1
    • +1
    /build.gradle
2:49 pm

Jim Procter

2:49 pm

Jim Procter

2:48 pm

Jim Procter

2:39 pm

Jim Procter

JAL-3751 only merge strictly contiguous ranges of mappings
JAL-3751 only merge strictly contiguous ranges of mappings
Wednesday 23 Sep
5:19 pm

Ben Soares

Merge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar

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4:49 pm

Ben Soares

JAL-3477 Added 10k leeway to amount of memory reserved for OS test for float rounding errors (needed to fix failing test)

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    • -11
    • +19
    /test/jalview/bin/MemorySettingTest.java
4:48 pm

Ben Soares

JAL-3753 Resources seen in tests and appropriate filters now being used as file opt-in rather than opt-out.

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    • -19
    • +28
    /build.gradle
Monday 21 Sep
12:01 pm

Jim Procter

Merge branch 'merge_review/JAL-3490_2_11_2_develop' into develop

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    • -3
    • +2
    /src/jalview/gui/AlignFrame.java
Sunday 20 Sep
8:33 pm

Ben Soares

JAL-3753 put resources in gradle run and test path

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    • -1
    • +0
    /.gitignore
    • -64
    • +75
    /build.gradle
Friday 18 Sep
6:18 pm

Ben Soares

JAL-3753 JAL-3754 first rejig

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    • -73
    • +90
    /build.gradle
    • -1
    • +0
    /gradle.properties
Wednesday 16 Sep
6:47 am

Jim Procter

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
Tuesday 15 Sep
12:58 pm

Jim Procter

Monday 14 Sep
11:24 pm

Ben Soares

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

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11:23 pm

Ben Soares

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/FJVL_VERSION
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    /getdown/lib/JVL_VERSION
    • binary
    /getdown/lib/getdown-core.jar
    • binary
    /getdown/lib/getdown-launcher-local.jar
    • binary
    /getdown/lib/getdown-launcher.jar
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar
11:23 pm

Ben Soares

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

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    /getdown/src/getdown/ant/pom.xml
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    /getdown/src/getdown/core/pom.xml
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    /getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
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    /getdown/src/getdown/launcher/pom.xml
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    /getdown/src/getdown/mvn_cmd
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    /getdown/src/getdown/pom.xml
6:11 pm

Ben Soares

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

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