jalview

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Commits this week: 4
Total Committers: 70
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Commits this week: 4

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Thursday 25 Feb
3:57 pm

Mungo Carstairs

3:56 pm

Mungo Carstairs

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no sma...

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no small job) to change all dialogs to this pattern.

There are still numerous dialogs that have not been changed to either pattern (so won't work in SwingJS): see comment at https://issues.jalview.org/browse/?focusedCommentId=20525&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#JAL-3048comment-20525.

2:21 pm

Mungo Carstairs

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

2:17 pm

Mungo Carstairs

It would be good to add Javadoc to this method

It would be good to add Javadoc to this method

2:14 pm

Mungo Carstairs

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

Wednesday 24 Feb
4:45 pm

Jim Procter

4:43 pm

Jim Procter

JAL-3818 process Jmol callbacks in AWT thread
JAL-3818 process Jmol callbacks in AWT thread
Thursday 11 Feb
5:06 pm

Mungo Carstairs

Or can it be compiled to Java 8 bytecode?

Or can it be compiled to Java 8 bytecode?

3:00 pm

Mungo Carstairs

'var' is since Java 10. We are still supporting Java 8 runtime which will not run this code (sadly). Compile with JDK 8 to find other occurrences (also Preferences, line 596 is not Java 8 compatibl...

'var' is since Java 10. We are still supporting Java 8 runtime which will not run this code (sadly).
Compile with JDK 8 to find other occurrences (also Preferences, line 596 is not Java 8 compatible syntax).

2:27 pm

Mungo Carstairs

Above statement is a duplicate - should only be inside the check for service != null. It fails with NPE if service is null.

Above statement is a duplicate - should only be inside the check for service != null. It fails with NPE if service is null.

2:26 pm

Mungo Carstairs

startjob and canceljob are only referenced in jbinit() so should be local variables in that method.

startjob and canceljob are only referenced in jbinit() so should be local variables in that method.

2:17 pm

Mungo Carstairs

Field startJob used to be the return value of showRunDialog(). As it no longer is, it can be removed.

Field startJob used to be the return value of showRunDialog(). As it no longer is, it can be removed.

12:29 pm

Mungo Carstairs

JAL-3809: Edit web service parameters dialog does not work in jalviewjs
JAL-3809: Edit web service parameters dialog does not work in jalviewjs
Friday 08 Jan
4:53 pm

Ben Soares

JAL-3419 improved look of tabs

Options
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    • +9
    /src/jalview/bin/Jalview.java
12:02 pm

Ben Soares

JAL-3416 Added FlatLightLaf, use with -Dlaf=flat property

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    • binary
    /j11lib/flatlaf-0.46.jar
    • -3
    • +16
    /src/jalview/bin/Jalview.java
Monday 14 Dec 2020
11:18 pm

Ben Soares

JAL-3280 Fixed the version checking URL formulation (getdown build_properties) for jalviewjs, can also use it for jalviewjs in future

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    • -13
    • +35
    /src/jalview/bin/Cache.java
5:56 pm

Ben Soares

JAL-3783 Reverting to using groovy-all-2.4.12-indy.jar to fix serious problem with Groovy console using shadowJar

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    /j11lib/groovy-2.5.7.jar
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    /j11lib/groovy-all-2.4.12-indy.jar
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    /j11lib/groovy-ant-2.5.7.jar
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    /j11lib/groovy-bsf-2.5.7.jar
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    /j11lib/groovy-cli-commons-2.5.7.jar
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    /j11lib/groovy-cli-picocli-2.5.7.jar
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    /j11lib/groovy-console-2.5.7.jar
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    /j11lib/groovy-datetime-2.5.7.jar
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    /j11lib/groovy-dateutil-2.5.7.jar
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    /j11lib/groovy-docgenerator-2.5.7.jar
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    /j11lib/groovy-groovydoc-2.5.7.jar
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    /j11lib/groovy-groovysh-2.5.7.jar
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    /j11lib/groovy-jaxb-2.5.7.jar
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    /j11lib/groovy-jmx-2.5.7.jar
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    /j11lib/groovy-json-2.5.7.jar
  16. … 12 more files in changeset.
5:24 pm

Ben Soares

JAL-3628 Test for doubly saved single backup file scheme

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    • +71
    /test/jalview/io/BackupFilesTest.java
    • -0
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    /test/jalview/io/testProps_singlefilebackup.jvprops
4:12 pm

Ben Soares

JAL-3594 Allow setting of getdownappbase and getdowndistdir properties for DEVELOP channel, and change DEVELOP version to be VERSION-dDATE instead of VERSION-develop. dDATE will help users know when Jalview Develop applicaiton updated

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    • -7
    • +25
    /build.gradle
    • -1
    • +14
    /src/jalview/bin/Cache.java
Friday 11 Dec 2020
8:27 pm

Ben Soares

JAL-3594 Defintely want SplashScreen to appear in the Desktop window otherwise it might not be closeable

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    • -2
    • +4
    /src/jalview/gui/SplashScreen.java
5:19 pm

Ben Soares

JAL-3594 Changed building.md to describe -PCHANNEL=JALVIEWJS and JALVIEWJS-TEST

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    • +5
    /doc/building.md
5:14 pm

Ben Soares

JAL-3594 Changed building.md to reflect change of name of channel_properties to channel.props

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    /doc/building.md
5:02 pm

Ben Soares

JAL-3594 Adjustments to allow JalviewJS to use ChannelProperties, and new utils/channels dir for jalviewjs and jalviewjs-release

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    /build.gradle
    • -7
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    /src/jalview/gui/SplashScreen.java
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    /src/jalview/util/ChannelProperties.java
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    /utils/channels/default/resources/channel.props
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    /utils/channels/default/resources/channel_properties
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    • +18
    /utils/channels/develop/resources/channel.props
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    /utils/channels/develop/resources/channel_properties
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    /utils/channels/jalviewjs-release
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    • +22
    /utils/channels/jalviewjs/channel_gradle.properties
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    /utils/channels/jalviewjs/images/UoD_banner-28.png
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    /utils/channels/jalviewjs/images/UoD_banner-32.png
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    /utils/channels/jalviewjs/images/barton_group-30.png
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    /utils/channels/jalviewjs/images/barton_group-62.png
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    /utils/channels/jalviewjs/images/barton_group-white-512.png
  16. … 36 more files in changeset.
4:34 pm

Ben Soares

JAL-3775 JAL-3633 Make java.net.Authenticator code conditional on not being JalviewJS

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    • -65
    • +86
    /src/jalview/bin/Cache.java
    • -39
    • +50
    /src/jalview/jbgui/GPreferences.java
Thursday 10 Dec 2020
7:56 pm

Ben Soares

Merge branch 'task/JAL-3594_updated--CHANNEL_cosmetics' into develop

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7:53 pm

Ben Soares

JAL-3594 Better Jalview Develop banner

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    /utils/channels/develop/images/jalview_develop_banner.xcf
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    /utils/channels/develop/resources/images/jalview_develop_banner.png
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    /utils/channels/test-release/images/jalview_test-release_banner.xcf
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    /utils/channels/test-release/resources/channel_properties
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    /utils/channels/test-release/resources/images/jalview_banner.png
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    /utils/channels/test-release/resources/images/jalview_test-release_banner.png
10:49 am

Ben Soares

JAL-3594 Documentation added to building.md for using the utils/channels/... folders

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    • +28
    /doc/building.md
10:05 am

Ben Soares

Merge branch 'task/JAL-3594_updated--CHANNEL_cosmetics' into develop

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9:56 am

Ben Soares

Merge branch 'merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into develop

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    • -0
    • +5
    /build.gradle
Wednesday 09 Dec 2020
8:21 pm

Ben Soares

JAL-3594 Improved About banners for develop and test-release

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    /utils/channels/develop/images/jalview_develop_banner.xcf
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    /utils/channels/develop/resources/images/jalview_develop_banner.png
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    /utils/channels/test-release/resources/images/jalview_banner.png