jalview

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Commits this week: 18
Total Committers: 72
Last Commit:
Commits this week: 18

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Wednesday 21 Jul
12:50 pm

Ben Soares

JAL-3850 fixed full class name

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    • -2
    • +2
    /build.gradle
12:32 pm

Ben Soares

JAL-3850 using reflection for SimpleHttpFileServerFactory

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    • -1
    • +7
    /build.gradle
Tuesday 06 Jul
5:42 pm

Jim Procter

5:42 pm

Jim Procter

WIP
WIP
Friday 18 Jun
3:29 pm

Ben Soares

JAL-3594 Updated the Jalview Develop getdown splashscreen image with Geoff's license free photo

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    • binary
    /utils/channels/develop/images/jalview_develop_getdown_background.png
    • binary
    /utils/channels/develop/images/jalview_develop_getdown_background.xcf
    • binary
    /utils/channels/develop/images/jalview_develop_getdown_background_error.png
    • binary
    /utils/channels/develop/images/jalview_develop_getdown_background_initialising.png
Wednesday 09 Jun
4:53 pm

Jim Procter

JAL-3840 don’t update the modal residue count for gaps

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    • -1
    • +6
    /src/jalview/datamodel/ResidueCount.java
4:40 pm

Jim Procter

fixes JAL-3840

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    • +1
    /src/jalview/datamodel/ResidueCount.java
4:35 pm

Jim Procter

JAL-3840 failing test - show that addGaps overflows

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    • +1
    /src/jalview/datamodel/ResidueCount.java
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    • +12
    /test/jalview/datamodel/ResidueCountTest.java
Tuesday 08 Jun
5:11 pm

Ben Soares

Merge branch 'develop' into improvement/JAL-3830_macOS_bundle_wrapper

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    • -5
    • +4
    /build.gradle
Monday 26 Apr
8:00 pm

Ben Soares

JAL-3248 Moved old README to doc/old_README and put pointers in new README for deskopt application building and JalviewJS building

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    • -71
    • +4
    /README
    • -0
    • +72
    /doc/old_README
5:56 pm

Ben Soares

JAL-3743 JAL-3745 Fixed NullPointerExceptions happening with linkCheck and jalviewjsTranspile tasks when gradle >= 6.6

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    • -5
    • +4
    /build.gradle
Thursday 22 Apr
3:20 pm

Ben Soares

JAL-3833 Allow setHiDPI and setHiDPIScale to work more usefully in real life

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    • -2
    • +17
    /src/jalview/bin/HiDPISetting.java
Sunday 18 Apr
8:31 pm

Ben Soares

JAL-3833 cap the scaling used by HiDPISetting for incorrect DPI values or incorrect height/width values

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    • -0
    • +10
    /src/jalview/bin/HiDPISetting.java
Tuesday 13 Apr
5:40 pm

Ben Soares

JAL-3830 Improved jalview.bat to find either pwsh.exe or powershell.exe, and give better messages to the user

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    • -3
    • +49
    /utils/getdown/bin/jalview.bat
Wednesday 31 Mar
11:16 pm

Ben Soares

JAL-3830 BAT file wrapper around powershell, so jalview works in command prompt. Added install4j option for installer to add Jalview's bin dir to Path in Windows. Added install4j option to create symlink to bash script to user's local bin (first of ~/bin, ~/.local/bin, ~/local/bin, ~/opt/bin that exists. First two of these usually automatically in PATH).

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    • -2
    • +3
    /build.gradle
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    • +1
    /gradle.properties
    • -0
    • +4
    /utils/getdown/bin/jalview.bat
    • -32
    • +84
    /utils/install4j/install4j8_template.install4j
Tuesday 30 Mar
1:43 am

Ben Soares

JAL-3830 Follow all SymbolicLinks in Windows powershell wrapper

Options
    • -4
    • +41
    /utils/getdown/bin/jalview.ps1
Friday 26 Mar
5:30 pm

Ben Soares

JAL-3830 delete channel.props and channel.propsv when uninstalling

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    • -1
    • +11
    /utils/install4j/install4j8_template.install4j
Wednesday 24 Mar
1:49 am

Ben Soares

JAL-3830 Moved wrappers to bin/jalview.* and make a symlink bin/jalview. Install4j script now jalviewg

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    • -7
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    /build.gradle
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    • +5
    /gradle.properties
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    • +50
    /utils/getdown/bin/jalview.ps1
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    • +132
    /utils/getdown/bin/jalview.sh
    • -132
    • +0
    /utils/getdown/jalviewc
    • -50
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    /utils/getdown/jalviewc.ps1
    • -23
    • +43
    /utils/install4j/install4j8_template.install4j
Wednesday 17 Mar
11:15 pm

Ben Soares

JAL-3830 Allow paths to start with '~'. Make path check more succinct.

Options
    • -3
    • +3
    /utils/getdown/jalviewc
9:06 pm

Ben Soares

JAL-3830 Now using a single universal bash script (jalviewc) for bash in linux, macos, cygwin and WSL. It keeps things together.

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    /build.gradle
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    • +1
    /gradle.properties
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    • +111
    /utils/getdown/jalviewc
    • -69
    • +0
    /utils/getdown/jalviewc-macos
    • -74
    • +0
    /utils/getdown/jalviewc-windows
    • -27
    • +3
    /utils/install4j/install4j8_template.install4j
12:30 am

Ben Soares

JAL-3830 add the windows bash script to getdown files and install4j installers

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    • -1
    • +1
    /build.gradle
    • -1
    • +2
    /gradle.properties
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    • +15
    /utils/install4j/install4j8_template.install4j
12:22 am

Ben Soares

JAL-3830 bash script that works in both cygwin and WSL (Windows Subsystem for Linux)

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    • -0
    • +74
    /utils/getdown/jalviewc-windows
Monday 15 Mar
4:56 pm

Ben Soares

JAL-3830 Delete wrapper scripts and getdown *v files when uninstalling

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    • -1
    • +31
    /utils/install4j/install4j8_template.install4j
3:21 pm

Ben Soares

JAL-3830 powershell wrapper tested on linux, macos and windows including spaces in paths. This is the way.

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    • -10
    • +26
    /utils/getdown/jalviewc.ps1
Sunday 14 Mar
1:29 am

Ben Soares

JAL-3830 minor fix in powershell wrapper

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    • -1
    • +1
    /utils/getdown/jalviewc.ps1
1:27 am

Ben Soares

JAL-3830 powershell follows symlinks as they do exist in NTFS, and of course in linux

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    • -3
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    /utils/getdown/jalviewc.ps1
12:28 am

Ben Soares

JAL-3830 Powershell wrapper now works cross-platform. Who needs bash?!

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    • +13
    /utils/getdown/jalviewc.ps1
12:27 am

Ben Soares

JAL-3830 Make wrapper scripts executable

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    • -1
    • +10
    /utils/install4j/install4j8_template.install4j
Friday 12 Mar
8:41 pm

Ben Soares

JAL-3830 powershell wrapper tested and fixed

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    • +6
    /utils/getdown/jalviewc.ps1
6:26 pm

Ben Soares

JAL-3830 improved bash scripts. Added powershell script. Needs testing

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    /build.gradle
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    /gradle.properties
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    • +15
    /utils/getdown/jalviewc
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    • +49
    /utils/getdown/jalviewc-macos
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    • +28
    /utils/getdown/jalviewc.ps1