jalview

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Commits this week: 14
Total Committers: 73
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Commits this week: 14

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Wednesday 20 Oct
5:05 pm

Mateusz Warowny

JAL-3878 Create WebServiceMenuBuilder which will replace PreferredServiceRegistry

Options
    • -26
    • +9
    /src/jalview/gui/AlignFrame.java
    • -0
    • +201
    /src/jalview/gui/WebServicesMenuBuilder.java
11:54 am

Mateusz Warowny

JAL-3878 Annotation comments and questions

Options
    • -0
    • +5
    /src/jalview/ws2/operations/AnnotationOperation.java
    • -15
    • +37
    /src/jalview/ws2/operations/AnnotationServiceWorker.java
Tuesday 19 Oct
2:40 pm

Mateusz Warowny

JAL-3878 Add annotation operations to slivka discoverer.

Options
    • -0
    • +16
    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
2:39 pm

Mateusz Warowny

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

Options
    • -0
    • +1
    /src/jalview/ws2/operations/AnnotationServiceWorker.java
2:33 pm

Mateusz Warowny

JAL-3878 Rename annotation provider method to getAnnotations

Options
    • -1
    • +1
    /src/jalview/ws2/slivka/SlivkaWebService.java
2:31 pm

Mateusz Warowny

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.

Options
    • -0
    • +1
    /src/jalview/ws2/slivka/SlivkaWebService.java
2:29 pm

Mateusz Warowny

JAL-3878 Start interactive job by registering them with calcManager

Options
    • -19
    • +26
    /src/jalview/ws2/operations/AnnotationOperation.java
2:25 pm

Mateusz Warowny

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

Options
    • -5
    • +2
    /src/jalview/ws2/gui/ProgressBarUpdater.java
Monday 18 Oct
5:04 pm

Mateusz Warowny <warownia1@gmail.com>

JAL-3878 Refactoring SeqAnnotationServiceCalcWorker.

Options
    • -0
    • +5
    /src/jalview/ws2/WSJobStatus.java
    • -0
    • +47
    /src/jalview/ws2/gui/ProgressBarUpdater.java
    • -0
    • +18
    /src/jalview/ws2/operations/AlignmentOperation.java
    • -84
    • +35
    /src/jalview/ws2/operations/AnnotationOperation.java
    • -0
    • +569
    /src/jalview/ws2/operations/AnnotationServiceWorker.java
    • -0
    • +6
    /src/jalview/ws2/operations/Operation.java
3:27 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

Options
3:27 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
3:04 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
    • -7
    • +24
    /src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
    • -1
    • +4
    /src/jalview/structures/models/AAStructureBindingModel.java
1:18 pm

Jim Procter <j.procter@dundee.ac.uk>

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

Options
    • -4
    • +15
    /src/jalview/gui/ChimeraViewFrame.java
    • -2
    • +9
    /src/jalview/gui/PymolViewer.java
    • -1
    • +7
    /src/jalview/gui/StructureViewerBase.java
12:39 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3904 failing test

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    • -0
    • +6
    /src/jalview/api/structures/JalviewStructureDisplayI.java
    • -1
    • +5
    /src/jalview/gui/StructureViewerBase.java
    • -2
    • +30
    /test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
Wednesday 13 Oct
2:30 pm

Mateusz Warowny <warownia1@gmail.com>

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.

Options
    • -3
    • +15
    /src/jalview/api/AlignCalcWorkerI.java
    • -0
    • +6
    /src/jalview/workers/ColumnCounterSetWorker.java
    • -0
    • +6
    /src/jalview/workers/ComplementConsensusThread.java
    • -0
    • +6
    /src/jalview/workers/ConsensusThread.java
    • -0
    • +6
    /src/jalview/workers/ConservationThread.java
    • -0
    • +6
    /src/jalview/workers/InformationThread.java
    • -0
    • +6
    /src/jalview/workers/StrucConsensusThread.java
    • -1
    • +7
    /src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
    • -2
    • +9
    /test/jalview/workers/AlignCaclManager2Test.java
12:58 pm

Mateusz Warowny <warownia1@gmail.com>

JAL-3878 Rename web service worker to more generic pollable task.

Options
    • -3
    • +3
    /src/jalview/viewmodel/AlignmentViewport.java
    • -0
    • +12
    /src/jalview/ws2/PollableTaskI.java
    • -0
    • +14
    /src/jalview/ws2/PollableTaskListenerI.java
    • -0
    • +126
    /src/jalview/ws2/PollingTaskExecutor.java
    • -133
    • +0
    /src/jalview/ws2/WebServiceExecutor.java
    • -14
    • +0
    /src/jalview/ws2/WebServiceThreadListenerI.java
    • -7
    • +3
    /src/jalview/ws2/WebServiceWorkerI.java
    • -4
    • +4
    /src/jalview/ws2/operations/AlignmentOperation.java
    • -4
    • +4
    /src/jalview/ws2/operations/AnnotationOperation.java
Saturday 09 Oct
2:01 pm

Mateusz Warowny

Update annotation operation WIP

Options
    • -2
    • +3
    /src/jalview/ws2/operations/AnnotationOperation.java
Thursday 07 Oct
2:31 pm

Mateusz Warowny

JAL-3878 Add dataset and viewport arguments to ResultSupplier.

Options
    • -1
    • +6
    /src/jalview/ws2/ResultSupplier.java
    • -1
    • +4
    /src/jalview/ws2/operations/AlignmentOperation.java
    • -4
    • +22
    /src/jalview/ws2/slivka/SlivkaWebService.java
12:53 pm

Mateusz Warowny

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?

11:57 am

Jim Procter

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.

11:34 am

Jim Procter

11:34 am

Mateusz Warowny

JAL-3899 Replace prints with logger messages.

Options
    • -10
    • +17
    /src/jalview/analysis/SeqsetUtils.java
11:31 am

Mateusz Warowny

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.

11:16 am

Jim Procter

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)

10:58 am

Mateusz Warowny

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.

8:56 am

Jim Procter

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 ?

8:53 am

Jim Procter

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.

8:42 am

Jim Procter

why does this class need to be static ?

why does this class need to be static ?

8:42 am

Jim Procter

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

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

8:39 am

Jim Procter

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