All Activity

Merge branch 'develop' into task/JAL-3911_getdown_improvements

JAL-3878 Use annotations from the representative sequence in the new alignment.

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    /src/jalview/ws2/gui/JPredMenuBuilder.java
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    /src/jalview/ws2/operations/JPredWorker.java
JAL-3594 correct Jalview Develop logo SVG added in [not actually used in application]

JAL-3927 Make url checks asynchronous in preferences dialog

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    /src/jalview/gui/SlivkaPreferences.java
JAL-3878 Add jpred operation and worker to the services.

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    /src/jalview/ws2/gui/JPredMenuBuilder.java
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    /src/jalview/ws2/operations/JPredOperation.java
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    /src/jalview/ws2/operations/JPredWorker.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3553 added filesize to json

JAL-3878 Make openEditsParamsDialog an interface static method.

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    /src/jalview/ws2/gui/AnnotationMenuBuilder.java
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    /src/jalview/ws2/gui/MenuEntryProviderI.java
JAL-3066 Fix ambiguous assertEquals casting values to double.

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    /test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
JAL-3878 Add annotation operation and worker to the services.

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    /src/jalview/ws2/gui/AnnotationMenuBuilder.java
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    /src/jalview/ws2/gui/ProgressBarUpdater.java
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    /src/jalview/ws2/operations/AnnotationWorker.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Handle nulls when filtering annotation workers by name.

JAL-3066 Vastly updated testng libs

    • binary
    /utils/testnglibs/testng-7.4.0-sources.jar
    • binary
    /utils/testnglibs/testng-7.4.0.jar
    • binary
    /utils/testnglibs/testng-sources.jar
JAL-3878 Move common poll method to upper class AbstractWorker

JAL-3878 Add methods to get and remove workers by their calc name.

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    /src/jalview/api/AlignCalcManagerI2.java
JAL-3878 Add multiple sequence operation.

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    /src/jalview/ws2/gui/AlignmentMenuBuilder.java
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    /src/jalview/ws2/gui/AlignmentProgressUpdater.java
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    /src/jalview/ws2/gui/WebServiceInfoUpdater.java
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    /src/jalview/ws2/operations/AlignmentWorker.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Create abstract workers and their utility classes.

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    /src/jalview/ws2/operations/AbstractPollableWorker.java
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    /src/jalview/ws2/operations/AbstractWorker.java
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    /src/jalview/ws2/operations/Operation.java
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    /src/jalview/ws2/operations/WSJobList.java
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    /src/jalview/ws2/operations/WebServiceWorkerI.java
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    /src/jalview/ws2/operations/WebServiceWorkerListener.java
JAL-3926 disable autosearch by default

JAL-3878 Create pollable task and executor it can be run with.

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    /src/jalview/ws2/PollableTaskI.java
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    /src/jalview/ws2/PollableTaskListenerI.java
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    /src/jalview/ws2/PollingTaskExecutor.java
JAL-3553 now creating a json file for use on website. It's easier to parse all the info here than on the website!

JAL-3878 Add ws menu builder and attach to the align frame.

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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws2/WebServiceDiscovererI.java
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    /src/jalview/ws2/gui/WebServicesMenuBuilder.java
JAL-3878 Add slivka's implementations of web service and discoverer.

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    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Create backbone for new web services

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    /src/jalview/ws2/WSJob.java
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    /src/jalview/ws2/WSJobStatus.java
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    /src/jalview/ws2/WebServiceDiscovererI.java
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    /src/jalview/ws2/WebServiceI.java
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    /src/jalview/ws2/gui/MenuEntryProviderI.java
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    /src/jalview/ws2/operations/AbstractOperation.java
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    /src/jalview/ws2/operations/Operation.java
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    /src/jalview/ws2/operations/OperationStub.java
JAL-3066 Remove redundant throws declaration from SlivkaParamSet constructor.

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    /src/jalview/ws/slivkaws/SlivkaParamSet.java
JAL-3923 JAL-3878 disable clover for CI builds

JAL-3922 convert selection events in Jmol to highlights in Jalview - still need to ignore selection events performed as part of Jalview manipulating Jmol.

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/gui/AppJmolBinding.java
JAL-3878 Add RNAalifold service discovery.

JAL-3553 copy sha256sums to a versioned filename too when created

JAL-3553 added customized labels for install4j output.txt

Merge branch 'JAL-3866_RNAalifold-slivka-client' into alpha/JAL-3066_Jalview_212_slivka-integration

Merge branch 'alpha/JAL-3899_deuniquify_refactor' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3553 improve the labels in install4j's output.txt and make a versioned filename output-JALVIEW_VERSION.txt