Dashboard

JAL-3878 Create WebServiceMenuBuilder which will replace PreferredServiceRegistry

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    /src/jalview/gui/WebServicesMenuBuilder.java
JAL-3878 Annotation comments and questions

JAL-3878 Add annotation operations to slivka discoverer.

JAL-3878 Fix sequences not being gathered when submitting without gaps.

JAL-3878 Rename annotation provider method to getAnnotations

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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Set job status to cancelled on job cancellation.

Despite job cancellation not being implemented in slivka client,

the job status should be updated to cancelled for the event to

be emitted to the ui updater.

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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Start interactive job by registering them with calcManager

JAL-3878 Fix progress updater bar to account for cancelled state.

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    /src/jalview/ws2/gui/ProgressBarUpdater.java
JAL-3878 Refactoring SeqAnnotationServiceCalcWorker.

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    /src/jalview/ws2/gui/ProgressBarUpdater.java
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    /src/jalview/ws2/operations/AnnotationServiceWorker.java
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    /src/jalview/ws2/operations/Operation.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'bug/r2_11_2/JAL-3904_structureviewermenu' into develop

JAL-3905 Fix: wait for response when sending mouseovers. Combined remove old label and add new label and also added warning in javadoc about out-of-order execution

JAL-3904 override buildActionMenu to add in additional menu actions after rebuild

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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/StructureViewerBase.java
JAL-3904 failing test

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    /src/jalview/gui/StructureViewerBase.java
JAL-3878 Add getCalcName to AlignCalcWorkerI.

getCalcName() can be used to identify services that run the calculator.

when an alternative calculator (different host or parameters) is created

the old ones sharing the name can be stopped.

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    /src/jalview/api/AlignCalcWorkerI.java
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    /src/jalview/workers/ConsensusThread.java
JAL-3878 Rename web service worker to more generic pollable task.

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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
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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/WebServiceWorkerI.java
Update annotation operation WIP

JAL-3878 Add dataset and viewport arguments to ResultSupplier.

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    /src/jalview/ws2/slivka/SlivkaWebService.java
SequencesInfo which is an individual object is doable, but I feel like it would be just a wrapper around a Map. What additional functionality would SequencesInfo have over a traditional Map? I'm n...

SequencesInfo which is an individual object is doable, but I feel like it would be just a wrapper around a Map. What additional functionality would SequencesInfo have over a traditional Map?

I'm not very familiar with serialization in java, I know there are libraries that can serialize beans to json or xml, but what are your expectations in this case?

one class with a static factory method seems to be better than two classes and an external mutable object.

one class with a static factory method seems to be better than two classes and an external mutable object.

JAL-3899 Replace prints with logger messages.

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    /src/jalview/analysis/SeqsetUtils.java
What's wrong with static classes? They are just like regular classes but within other class' namespace. That's non-static inner classes that are special. About factory pattern, I think it would be ...

What's wrong with static classes? They are just like regular classes but within other class' namespace. That's non-static inner classes that are special.
About factory pattern, I think it would be an overkill for a class that is only used by SeqsetUtils' methods.

yes, I see that, but do you really need a nested static class ? in line with my general comments re encapsulating the Map<String,SequenceInfo> further: perhaps it might make sense to simply apply a...

yes, I see that, but do you really need a nested static class ? in line with my general comments re encapsulating the Map<String,SequenceInfo> further: perhaps it might make sense to simply apply a factory pattern rather than have an internal bean that a generic map holds references to ?

(lets not get stuck on this though, the main thing is that the implementation works fine for now, though needs more work in order to save/restore sequenceInfo objects from Jalview project files)

Because it's instantiated in a static context e.g. uniquify and it does not need an instance of SeqsetUtils object to work.

Because it's instantiated in a static context e.g. uniquify and it does not need an instance of SeqsetUtils object to work.

we won't see this messages unless asserts are enabled. Cache.log.warn is perhaps better ?

we won't see this messages unless asserts are enabled. Cache.log.warn is perhaps better ?

it's a reasonable first pass, though stylistically all you've done is transformed a single concrete instance (Hashtable) to a more strongly typed verbose instance (Map<String,SequenceInfo>). Why no...

it's a reasonable first pass, though stylistically all you've done is transformed a single concrete instance (Hashtable) to a more strongly typed verbose instance (Map<String,SequenceInfo>). Why not go further and have a SequencesInfo object that records metadata for one or more sequences ?

There are also other requirements: SequenceInfo sets will need to be persisted for a web services job. You could expand JAL-3899 to incorporate this perhaps - JAL-1786 is the relevant epic for that.

why does this class need to be static ?

why does this class need to be static ?

this should probably be Cache.log.warn(..)

this should probably be Cache.log.warn(..)

JAL-3899 Refactor sequence de/uniquification.
JAL-3899 Refactor sequence de/uniquification.