jalview

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Commits this week: 4
Total Committers: 73
Last Commit:
Commits this week: 4

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Thursday 22 Apr 2021
3:20 pm

Ben Soares

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

Options
    • -2
    • +17
    /src/jalview/bin/HiDPISetting.java
Monday 19 Apr 2021
4:37 pm

Ben Soares

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

Options
    • -0
    • +10
    /src/jalview/bin/HiDPISetting.java
Sunday 18 Apr 2021
8:31 pm

Ben Soares

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

Options
    • -0
    • +10
    /src/jalview/bin/HiDPISetting.java
Tuesday 13 Apr 2021
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

Options
    • -3
    • +49
    /utils/getdown/bin/jalview.bat
Monday 12 Apr 2021
3:05 pm

Arnaud Gucciardi

JAL-3832 Gui working, with 3DBeacons parameters

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

Arnaud Gucciardi

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

Options
Tuesday 06 Apr 2021
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
3:23 pm

Jim Procter

JAL-3829 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 2021
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 2021
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 2021
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 2021
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 2021
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 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
    • -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 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

Options
    • -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
    • -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