jalview

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Merge branch 'to_merge/r2_11_2/JAL-3904_improved_alignpanelAPI_autoshowview' into develop

JAL-3551 pymol docs - work in progress

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    /help/help/html/features/pymol.html
JAL-3929 don’t use the url encoded pdbId in feature group when transferring features from associated structure to a sequence

JAL-3616 update messages/tooltips/menu items to use getViewerName() for chimera/x/pymol

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    /src/jalview/gui/ChimeraViewFrame.java
JAL-3551 JAL-3931 view pymol commands/responses in Log.trace

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    /src/jalview/ext/pymol/PymolManager.java
JAL-3931 remove % and - from ids so Pymol doesn’t strip them out and truncate the structure identifier that Jalview uses to refer to each file

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    /src/jalview/gui/PymolBindingModel.java
JAL-3929 URLencode pdbid to remove problematic characters - propagate urlEncoded ID to the features transferred from the structure file

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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/ws/dbsources/EBIAlfaFold.java
JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations. Better for response.varfile installation of Jalview

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    /utils/install4j/file_associations_auto-install4j8.xml
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    /utils/install4j/file_associations_template-install4j8.xml
JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations. Better for response.varfile installation of Jalview

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    /utils/install4j/file_associations_auto-install4j8.xml
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    /utils/install4j/file_associations_template-install4j8.xml
Merge branch 'develop' into task/JAL-3911_getdown_improvements

JAL-3904 use new AlignPanel API method

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    /src/jalview/gui/ViewSelectionMenu.java
JAL-3904 simple method to make an alignPanel the currently viewed one in the alignframe

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

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    /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