jalview

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JAL-3816 bump version number and cut release notes

JAL-3815 default /etc/jalview_properties under utils/debian

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    /utils/debian/etc/jalview_properties
JAL-3815 default /etc/jalview_properties under utils/debian

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    /utils/debian/etc/jalview_properties
JAL-3251 debian build using maven, simplified build.gradle not needed

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    /utils/debian/build.gradle.debian
JAL-3521 Moved the debian build.gradle to utils/debian/build.gradle.debian

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    /utils/debian/build.gradle.debian
Merge branch 'task/JAL-3521_Slimmed_down_build.gradle_for_debian' into releases/Release_2_11_1_4_debianpatches

Merge branch 'releases/Release_2_11_1_4_debianpatches' into task/JAL-3521_Slimmed_down_build.gradle_for_debian

JAL-3814 don’t automatically launch the news browser when the desktop is first opened

JAL-3813 NOIDENTIFIERSSERVICE preference disables jalview pinging www.jalview.org/services/identifiers to get a list of URL link templates for viewing database crossreferences

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    /src/jalview/ws/utils/UrlDownloadClient.java
JAL-3812 new argument ‘-nohtmltemplates’ and user preference ‘NOHTMLTEMPLATES’ to disable download of templates from GitHub repository

JAL-3811 document SHOW_JWS2_SERVICES user preference and provide new menu option for ‘one off’ JABAWS discovery if preference is disabled.

JAL-3814 NONEWS property

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

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-2422 updated unit test for ChimeraX command change

JAL-2422 a fix and a fudge for two failing ChimeraX commands

JAL-3806 fix and test for one-to-many sequence mapping case

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    /test/jalview/util/MappingUtilsTest.java
JAL-3809 - Change CompletionStage to CompletableFuture.

Seems that swingjs doesn't have completion stages

properly implemented.

JAL-3809 - fixed param edit for msa but default is broken.

Edit settings dialog now works asynchronously. Everything

works properly in java. In javascript, edit settings dialog

works properly for msa services, but running without the

dialog does not work.

Annotation services do not add annotations to the seuqnces.

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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-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-3808 handle 1:1 mappings in exonerate gff2 using the ‘similarity’ feature extent to determine direction of mapping generated from alignment

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    /src/jalview/io/gff/ExonerateHelper.java
JAL-3808 example exonerate cdna2genome and coding2genome test data and test

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    /examples/testdata/test_cdna2genome_showquerygff.gff2
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    /examples/testdata/test_cdna2genome_showtargetgff.gff2
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    /examples/testdata/test_coding2genome_showquerygff.gff2
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    /examples/testdata/test_coding2genome_showtargetgff.gff2
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    /test/jalview/io/FeaturesFileTest.java
JAL-3878 Initial preparation.

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    /src/jalview/ws2/JalviewWebServiceI.java
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    /src/jalview/ws2/MenuEntryProviderI.java
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    /src/jalview/ws2/MsaMenuEntryProvider.java
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    /src/jalview/ws2/WSJobID.java
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    /src/jalview/ws2/WSJobState.java
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    /src/jalview/ws2/WSJobTrackerI.java
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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/WebServiceWorkerI.java
JAL-3807 JPred can now successfully submit and track the job.

This one should be compiling

JAL-3806 more lax allowance (3 positions) for stop codon

Implementing JPredThread methods and SlivkaJPredServiceInstance

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    /src/jalview/ws/JPredThread.java
Implementing JPredThread methods and SlivkaJPredServiceInstance

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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
Merge branch 'task/JAL-3796_notarization_no_uninstaller' into develop