jalview

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Commits this week: 3
Total Committers: 72
Last Commit:
Commits this week: 3

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Today
3 hrs ago

Ben Soares

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

Options
    • -3
    • +49
    /utils/getdown/bin/jalview.bat
Monday 12 Apr
3:05 pm

Arnaud Gucciardi

JAL-3832 Gui working, with 3DBeacons parameters

Options
    • -3
    • +3
    /resources/fts/tdbeacons_data_columns.txt
    • -2
    • +4
    /src/jalview/fts/core/FTSDataColumnPreferences.java
    • -11
    • +14
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
9:17 am

Arnaud Gucciardi

Merge branch 'arnaud/develop' into arnaud/JAL-3929_spike, to insert the previous changes

Options
Tuesday 06 Apr
3:23 pm

Jim Procter

JAL-3929 forgot to add in the dummy 3d-beacons db proxy

Options
    • -0
    • +521
    /src/jalview/ws/dbsources/TDBeacons.java
3:04 pm

Jim Procter

JAL-3832 dummy 3d-beacons database client and code to create the TDBeaconsFTSPanel via the sequence fetcher dropdown menu

Options
    • -0
    • +6
    /src/jalview/gui/SequenceFetcher.java
    • -0
    • +2
    /src/jalview/ws/SequenceFetcher.java
2:25 pm

Arnaud Gucciardi

JAL-3829 more testing wit tdbeacons data columns and FTSclient

Options
    • -1
    • +4
    /resources/fts/tdbeacons_data_columns.txt
    • -0
    • +2
    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
    • -4
    • +3
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -0
    • +3
    /test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
    • -8
    • +10
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
    • -2
    • +7
    /test/jalview/gui/StructureChooserTest.java
Thursday 01 Apr
2:28 pm

Arnaud Gucciardi

JAL-3829 attempt to fix my changes to follow the Jira issue

Options
    • -0
    • +3
    /resources/fts/tdbeacons_data_columns.txt
    • -9
    • +10
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -3
    • +3
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
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).

Options
    • -2
    • +3
    /build.gradle
    • -1
    • +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
Monday 29 Mar
1:39 pm

Arnaud Gucciardi

fixed last commit

Options
    • -10
    • +9
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -2
    • +2
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
9:51 am

Arnaud Gucciardi

Request now parses the whole structures, need to fix the result

Options
    • -6
    • +6
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
    • -21
    • +16
    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
    • -0
    • +8
    /test/jalview/fts/service/pdb/PDBFTSPanelTest.java
    • -1
    • +1
    /test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
Friday 26 Mar
5:30 pm

Ben Soares

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

Options
    • -1
    • +11
    /utils/install4j/install4j8_template.install4j
Thursday 25 Mar
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
    • -6
    • +17
    /getdown/src/getdown/core/src/main/java/jalview/util/ChannelProperties.java
    • -0
    • +56
    /getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java
    • -20
    • +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
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
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
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

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

Ben Soares

JAL-3503 New getdown version and jar files

Options
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    • +1
    /getdown/lib/FJVL_VERSION
    • -1
    • +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
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    • +7
    /build.gradle
    • -1
    • +1
    /getdown/src/getdown/ant/pom.xml
    • -1
    • +1
    /getdown/src/getdown/core/pom.xml
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    • +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
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    • +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
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    • +1
    /getdown/src/getdown/mvn_cmd
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    • +1
    /getdown/src/getdown/pom.xml
    • -0
    • +1
    /gradle.properties
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    • +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
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.

Options
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    • +3
    /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

Options
    • -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
4:56 pm

Ben Soares

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

Options
    • -1
    • +31
    /utils/install4j/install4j8_template.install4j