jalview

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Commits this week: 2
Total Committers: 73
Last Commit:
Commits this week: 2

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Thursday 25 Mar 2021
7:27 pm

Ben Soares

JAL-3633 new getdown jars

Options
    • 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
7:27 pm

Ben Soares

JAL-3633 refactored/simplified LaunchUtils code

Options
    • -13
    • +3
    /getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
    • -41
    • +0
    /getdown/src/getdown/core/src/main/java/jalview/bin/LaunchUtils.java
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    • +17
    /getdown/src/getdown/core/src/main/java/jalview/util/ChannelProperties.java
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    • +56
    /getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java
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    • +11
    /getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/ProxyUtil.java
    • -41
    • +0
    /src/jalview/bin/LaunchUtils.java
    • -2
    • +3
    /src/jalview/bin/Launcher.java
    • -6
    • +17
    /src/jalview/util/ChannelProperties.java
    • -0
    • +56
    /src/jalview/util/LaunchUtils.java
3:49 pm

Arnaud Gucciardi

TDB.executeRequest fix & test passed

Options
    • -4
    • +4
    /src/jalview/fts/core/FTSRestResponse.java
    • -11
    • +10
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -8
    • +38
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
2:47 pm

Arnaud Gucciardi

Added (and passed !)all the FTS tests from test.fts.core

Options
    • -0
    • +149
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
2:20 pm

Arnaud Gucciardi

Created 3Dbeacons data_columns.txt Test passed for data columns

Options
    • -0
    • +44
    /resources/fts/tdbeacons_data_columns.txt
    • -0
    • +10
    /src/jalview/fts/core/FTSRestResponse.java
    • -27
    • +119
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -6
    • +63
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
2:11 am

Ben Soares

JAL-3633 new getdown jars

Options
    • 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
2:11 am

Ben Soares

JAL-3633 getdown reads jalview_properties for proxy settings

Options
    • -0
    • +1
    /build.gradle
    • -2
    • +12
    /getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/ProxyPanel.java
    • -1
    • +43
    /getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/ProxyUtil.java
Wednesday 24 Mar 2021
1:49 am

Ben Soares

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

Options
    • -7
    • +9
    /build.gradle
    • -2
    • +5
    /gradle.properties
    • -0
    • +50
    /utils/getdown/bin/jalview.ps1
    • -0
    • +132
    /utils/getdown/bin/jalview.sh
    • -132
    • +0
    /utils/getdown/jalviewc
    • -50
    • +0
    /utils/getdown/jalviewc.ps1
    • -23
    • +43
    /utils/install4j/install4j8_template.install4j
Saturday 20 Mar 2021
11:51 am

Ben Soares

JAL-3503 Changed decimal display of memory in Prefences

Options
    • -2
    • +2
    /src/jalview/bin/MemorySetting.java
Friday 19 Mar 2021
11:19 pm

Ben Soares

JAL-3594 Making default .jalview_properties file separate. Now .jalview_nonrelease_properties

Options
    • -1
    • +1
    /utils/channels/default/resources/channel.props
11:18 pm

Ben Soares

JAL-3503 missed a widget being disabled

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    • -0
    • +1
    /src/jalview/jbgui/GPreferences.java
10:54 pm

Ben Soares

JAL-3503 New getdown version and jar files

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    • -1
    • +1
    /getdown/lib/FJVL_VERSION
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    • +1
    /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
10:53 pm

Ben Soares

JAL-3503 Added a Startup tab in Preferences, with gui for JVMMEMMAX and JVMMEMPC settings. Allowed jalview.bin.Launcher and getdown to read/use these memory settings at launch. Added channel.props to getdown appdir, used to determing correct .jalview_properties file. Refactored MemorySetting a bit, with more helper methods for the Preferences tab.

Options
    • -0
    • +7
    /build.gradle
    • -1
    • +1
    /getdown/src/getdown/ant/pom.xml
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    • +1
    /getdown/src/getdown/core/pom.xml
    • -1
    • +22
    /getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
    • -0
    • +41
    /getdown/src/getdown/core/src/main/java/jalview/bin/LaunchUtils.java
    • -70
    • +179
    /getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java
    • -0
    • +277
    /getdown/src/getdown/core/src/main/java/jalview/util/ChannelProperties.java
    • -0
    • +585
    /getdown/src/getdown/core/src/main/java/jalview/util/StringUtils.java
    • -1
    • +1
    /getdown/src/getdown/launcher/pom.xml
    • -1
    • +1
    /getdown/src/getdown/mvn_cmd
    • -1
    • +1
    /getdown/src/getdown/pom.xml
    • -0
    • +1
    /gradle.properties
    • -0
    • +11
    /resources/lang/Messages.properties
    • -0
    • +11
    /resources/lang/Messages_es.properties
    • -0
    • +41
    /src/jalview/bin/LaunchUtils.java
  16. … 6 more files in changeset.
Wednesday 17 Mar 2021
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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    • -3
    • +3
    /build.gradle
    • -4
    • +1
    /gradle.properties
    • -12
    • +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
    • -3
    • +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)

Options
    • -0
    • +74
    /utils/getdown/jalviewc-windows
Monday 15 Mar 2021
4:56 pm

Ben Soares

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

Options
    • -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
11:59 am

Arnaud Gucciardi

added untracked parsing attempts files

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    • -0
    • +1
    /src/jalview/fts/service/threedbeacons/.gitignore
    • -0
    • +2
    /test/jalview/fts/threedbeacons/.gitignore
11:56 am

Arnaud Gucciardi

Adding tests for 3DB, currently 2/4 corrects on PanelTest

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    • -2
    • +2
    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
    • -2
    • +81
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
    • -2
    • +4
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
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    /test/jalview/fts/service/pdb/PDBFTSPanelTest.java
    • -0
    • +76
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
    • -0
    • +68
    /test/jalview/fts/threedbeacons/TDBeaconsPanelTest.java
10:29 am

Jim Procter

Merge branch 'releases/Release_2_11_1_Branch'

Options
Sunday 14 Mar 2021
1:29 am

Ben Soares

JAL-3830 minor fix in powershell wrapper

Options
    • -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

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

Ben Soares

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

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    • -9
    • +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 2021
8:41 pm

Ben Soares

JAL-3830 powershell wrapper tested and fixed

Options
    • -4
    • +6
    /utils/getdown/jalviewc.ps1
6:26 pm

Ben Soares

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

Options
    • -1
    • +1
    /build.gradle
    • -0
    • +1
    /gradle.properties
    • -10
    • +15
    /utils/getdown/jalviewc
    • -14
    • +49
    /utils/getdown/jalviewc-macos
    • -0
    • +28
    /utils/getdown/jalviewc.ps1
1:09 am

Ben Soares

JAL-3830 unix and macos wrappers. Symbolic link to jalviewc-macos in Contents/MacOS/jalviewc.

Options
    • -1
    • +14
    /build.gradle
    • -1
    • +3
    /gradle.properties
    • -0
    • +28
    /utils/getdown/jalviewc
    • -0
    • +34
    /utils/getdown/jalviewc-macos
    • -2
    • +3
    /utils/install4j/install4j8_template.install4j
    • -28
    • +0
    /utils/install4j/macos_jalview
Thursday 11 Mar 2021
6:51 pm

Ben Soares

JAL-3523 Advanced the getdown version number

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    • +1
    /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
    • -1
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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/launcher/pom.xml
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    /getdown/src/getdown/mvn_cmd
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    /getdown/src/getdown/pom.xml
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar