Activity jalview/src

2:01 pm

Mateusz Warowny

Update annotation operation WIP

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./jalview/ws2/operations/AnnotationOperation.java
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./jalview/ws2/.../AnnotationOperation.java

2:31 pm

Mateusz Warowny

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a047722
changed 3 files
JAL-3878_web_services_overhaul

JAL-3878 Add dataset and viewport arguments to ResultSupplier.

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./jalview/ws2/ResultSupplier.java
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./jalview/ws2/ResultSupplier.java
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./jalview/ws2/operations/AlignmentOperation.java
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./jalview/ws2/.../AlignmentOperation.java
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./jalview/ws2/slivka/SlivkaWebService.java
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./jalview/ws2/slivka/SlivkaWebService.java

12:53 pm

Mateusz Warowny

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Re: CR-JAL-254
commented on review

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.

11:34 am

Jim Procter

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CR-JAL-254
resumed reviewing

11:34 am

Mateusz Warowny

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e7e676c
changed 1 file
alpha/JAL-3899_deuniquify_refactor CR-JAL-254

JAL-3899 Replace prints with logger messages.

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./jalview/analysis/SeqsetUtils.java
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./jalview/analysis/SeqsetUtils.java

11:31 am

Mateusz Warowny

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Re: CR-JAL-254
replied to Jim Procter

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

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Re: CR-JAL-254
replied to Jim Procter

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

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Re: CR-JAL-254
commented on review

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

8:53 am

Jim Procter

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Re: CR-JAL-254
commented on review

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