jalview

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Commits this week: 17
Total Committers: 73
Last Commit:
Commits this week: 17

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Tuesday 08 Mar
12:14 pm

Ben Soares

JAL-3103 Removed code and unused widgets for defaultBrowser

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    • -10
    • +0
    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java
12:03 pm

Ben Soares

JAL-3103 Remove BrowserLauncher2 and use Desktop.browse(url) with wrapper methods

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    • -1
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    /THIRDPARTYLIBS
    • binary
    /j11lib/BrowserLauncher2-1_3.jar
    • binary
    /j8lib/BrowserLauncher2-1_3.jar
    • -35
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    /resources/edu/stanford/ejalbert/launching/misc/linuxUnixConfig.properties
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    /resources/edu/stanford/ejalbert/launching/misc/sunOSConfig.properties
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    /resources/edu/stanford/ejalbert/launching/windows/windowsConfig.properties
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    • +1
    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java
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    • +54
    /src/jalview/util/BrowserLauncher.java
12:39 am

Ben Soares

JAL-3103 add BrowserLauncher2 LGPLv2.1 to THIRDPARTYLIBS

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    • +1
    /THIRDPARTYLIBS
12:34 am

Ben Soares

JAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-needed exception handling from jalview code for openURL. Change Default browser input to JComboBox populated by BrowserLauncher2

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    • -1
    • +3
    /build.gradle
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    • +35
    /resources/edu/stanford/ejalbert/launching/misc/linuxUnixConfig.properties
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    • +32
    /resources/edu/stanford/ejalbert/launching/misc/sunOSConfig.properties
    • -0
    • +51
    /resources/edu/stanford/ejalbert/launching/windows/windowsConfig.properties
    • -1
    • +1
    /resources/lang/Messages.properties
    • -1
    • +1
    /resources/lang/Messages_es.properties
    • -12
    • +19
    /src/jalview/gui/Help.java
    • -3
    • +9
    /src/jalview/gui/Preferences.java
    • -49
    • +73
    /src/jalview/gui/StructureViewerBase.java
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    • +16
    /src/jalview/io/HTMLOutput.java
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    /src/jalview/jbgui/GPreferences.java
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    • +36
    /src/jalview/util/BrowserLauncher.java
Monday 07 Mar
8:12 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

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8:07 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3647 release notes for JAL-1842 JAL-3509 JAL-3881, JAL-3884 JAL-3632 JAL-3633 and report JAL-3764 as a known issue

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    • -1
    • +41
    /help/help/html/releases.html
5:52 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3685 - two single quotes when replacements are present in i18n message

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    • -10
    • +10
    /resources/lang/Messages.properties
5:51 pm

Ben Soares

JAL-3103 Switched to (a wrapper around) BrowserLauncher2

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    • binary
    /j11lib/BrowserLauncher2-1_3.jar
    • binary
    /j8lib/BrowserLauncher2-1_3.jar
    • -0
    • +2
    /resources/lang/Messages.properties
    • -0
    • +2
    /resources/lang/Messages_es.properties
    • -2
    • +14
    /src/jalview/bin/Jalview.java
    • -32
    • +43
    /src/jalview/gui/Preferences.java
    • -924
    • +26
    /src/jalview/util/BrowserLauncher.java
Friday 04 Mar
5:19 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

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5:19 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3647 release notes for hdpi/laf scaling JAL-3608 JAL-3609 JAL-3552

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    • -1
    • +7
    /help/help/html/releases.html
4:38 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 structure mapping preference docs for JAL-3817

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    • -0
    • +7
    /help/help/html/features/preferences.html
3:57 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

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3:41 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3608 JAL-3830 tweaked the what’s new text and updated helpTOC

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    • +1
    /help/help/help.jhm
    • -2
    • +3
    /help/help/helpTOC.xml
    • -6
    • +4
    /help/help/html/whatsNew.html
3:26 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

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3:26 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3608 JAL-3830 simplified command line docs a bit

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    • -26
    • +51
    /help/help/html/features/commandline.html
2:36 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'doc/JAL-3608+JAL-3830_added_to_help_docs' into develop

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1:48 pm

Ben Soares

JAL-3830 added command line to whatsnew and releases

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    • -3
    • +9
    /help/help/html/releases.html
    • -0
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    /help/help/html/whatsNew.html
1:38 pm

Ben Soares

JAL-3830 Added new command line usage to docs

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    • -10
    • +87
    /help/help/html/features/commandline.html
1:19 pm

Mateusz Warowny

JAL-3878 Change visibility of WebService methods to public.

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    • -9
    • +9
    /src/jalview/ws2/api/WebService.java
12:19 pm

Ben Soares

JAL-3608 added to LaF documentation

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    • -1
    • +4
    /help/help/html/features/commandline.html
    • -0
    • +3
    /help/help/html/releases.html
Thursday 03 Mar
3:38 pm

Ben Soares

JAL-3830 fix broken/buggy install4j9 setting of executeSetupApp=false still running setupApp

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    • -1
    • +2
    /build.gradle
1:57 pm

Mateusz Warowny

JAL-3878 Create alignment service "backend" classes

JAL-3878 Implement AlignmentAction#perform method

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    • -3
    • +7
    /src/jalview/ws2/actions/alignment/AlignmentAction.java
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    • +114
    /src/jalview/ws2/actions/alignment/AlignmentJob.java
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    • +42
    /src/jalview/ws2/actions/alignment/AlignmentResult.java
    • -0
    • +219
    /src/jalview/ws2/actions/alignment/AlignmentTask.java
1:36 pm

Mateusz Warowny

JAL-3878 Remove unused JobStatus methods

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    • -11
    • +1
    /src/jalview/ws2/api/JobStatus.java
1:05 pm

Mateusz Warowny

JAL-3878 Create abstract base classes for non-interactive tasks

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    • +373
    /src/jalview/ws2/actions/AbstractPollableTask.java
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    • +193
    /src/jalview/ws2/actions/BaseJob.java
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    • +31
    /src/jalview/ws2/actions/ServiceInputInvalidException.java
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    /src/jalview/ws2/helpers/DelegateJobEventListener.java
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    • +60
    /src/jalview/ws2/helpers/TaskEventSupport.java
Wednesday 02 Mar
8:51 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

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8:50 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'bug/JAL-3962_awt_dll_problem' into develop

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8:50 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 release notes for JAL-3867

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    /help/help/html/releases.html
6:25 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3438 - all src and test run through spotless..

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    /src/com/stevesoft/pat/ChangeRule.java
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    /src/com/stevesoft/pat/Ctrl.java
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    /src/com/stevesoft/pat/Custom.java
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    /src/com/stevesoft/pat/FastBracket.java
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    /src/com/stevesoft/pat/FastMulti.java
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    /src/com/stevesoft/pat/FileRegex.java
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    /src/com/stevesoft/pat/Pattern.java
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    /src/com/stevesoft/pat/PopRule.java
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    /src/com/stevesoft/pat/Prop.java
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    /src/com/stevesoft/pat/PushRule.java
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    /src/com/stevesoft/pat/RegOpt.java
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    /src/com/stevesoft/pat/RegRes.java
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    /src/com/stevesoft/pat/Regex.java
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    /src/com/stevesoft/pat/RegexTokenizer.java
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    /src/com/stevesoft/pat/RegexWriter.java
  16. … 654 more files in changeset.
6:12 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 release note for JAL-3907 building Jalview with j17

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    /help/help/html/releases.html
6:09 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3746 release note for JAL-3618 Vaqua config so app directories can be opened

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    • +6
    /help/help/html/releases.html