jalview

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JAL-3848 patched SwingJS runtime rebuilt

JAL-3948 - temporarily add the ojdk8 calendardata file (GPL licensed)

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    /resources/sun/util/resources/CalendarData.properties
Merge branch 'improvement/JAL-3848_slivka_0.8_updated_jslib' of https://source.jalview.org/git/jalview into improvement/JAL-3848_slivka_0.8_updated_jslib

JAL-3848 j2s 3.2.10-v1 slivka-java-client jslib

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    /utils/jalviewjs/libjs/slivka-client-site.zip
JAL-3848 nominal build of slivka 0.8 compatible java client library

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    /utils/jalviewjs/libjs/slivka-client-site.zip
Merge branch 'bug/JAL-3849_aacon-parameters' into improvement/JAL-3848_slivka_0.8

JAL-3690 Remove references to old AlignCalcManager.

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    /src/jalview/api/AlignCalcManagerI.java
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    /src/jalview/workers/AlignCalcWorker.java
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    /test/jalview/gui/AlignViewportTest.java
JAL-3849 Remove join() which blocked the ui.

JAL-3848 SlivkaParamSet: reformat code and add service description.

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    /src/jalview/ws/slivkaws/SlivkaParamSet.java
JAL-3848 Update slivka client library.

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    /src/jalview/ws/slivkaws/SlivkaParamSet.java
JAL-3847 set default behaviour as exclude when dealing with duplicate entries in jars and zips

JAL-3743 JAL-3745 Fixed NullPointerExceptions happening with linkCheck and jalviewjsTranspile tasks when gradle >= 6.6

Merge branch 'bug/JAL-3809_ws_params_dialog_fix' into alpha/JAL-3066_Jalview_212_slivka-integration

Merge branch 'bug/JAL-3810_annotation_ws_stopping_abruptly' into bug/JAL-3809_ws_params_dialog_fix

Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3810 - Add trace method to javascript implementation of Logger

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    /src/jalview/javascript/log4j/Logger.java
JAL-3810 - Replace log.trace() calls with log.debug()

JAL-3809 - Fixed param edit dialog for jalviewjs.

Edit settings dialog now works asynchronously.

Annotation services still do not add annotations to the sequences.

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/WsJobParameters.java
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    /src/jalview/ws/jws2/MsaWSClient.java
JAL-3690 Introduce AlignCalcManager2 tests.

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    /src/jalview/api/AlignCalcManagerI2.java
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    /test/jalview/workers/AlignCaclManager2Test.java
Merge branch 'Jalview-JS/develop' into feature/JAL-3690_callback-based-web-services

Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3690 AlignCalcManager - add full support for oneshot workers

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    /src/jalview/workers/AlignCalcManager2.java
JAL-3690 AACon ws menu entry fix.

JAL-3690 Allow unregistered workers to be run with CalcManager.

JAL-3690 Fix typo in enum name in slivka client.

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    /utils/jalviewjs/libjs/slivka-client-site.zip
Merge remote-tracking branch 'origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services' into feature/JAL-3690_callback-based-web-services

JAL-3690 Fixed slivka wsmenu categories.

JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

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    /swingjs/ver/3.2.10-j11/DEV_NOTES.txt
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    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
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    /swingjs/ver/3.2.10-j11/differences.txt
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    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.10-j11/timestamp
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    /swingjs/ver/3.2.10/DEV_NOTES.txt
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    /swingjs/ver/3.2.10/SwingJS-site.zip
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    /swingjs/ver/3.2.10/_j2sclasslist.txt
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    /swingjs/ver/3.2.10/differences.txt
  1. … 24 more files in changeset.
JAL-3690 recoded AWSThread to use javax.swing.Timer (see https://github.com/BobHanson/java2script/issues/195#issuecomment-747695834 )- web service submission works, but doesn’t seem to be happening as a background task.