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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.

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.
JAL-3899 Update usages of uniquify and deuniquify.

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tmp

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JAL-2909 JAL-3894 hack in support to import regions of an unindexed SAM file.

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JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

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JAL-3829 ignore the fake ID generated when a PDB format file without embedded ID is imported for an existing PDBEntry

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JAL-3829 ensure nulls are not wildcards when retrieving annotation by calcId/label/description

JAL-3829 store 3db metadata on PDBEntry so it can be shown in Cache/etc

JAL-3829 allow PDBEntry with file and ID with mismatching case to override one without a file

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JAL-2226 new method to search for annotation matching particular description as well as calcId and label

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JAL-3863 promote non-canonical version of dbref to a canonical one

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JAL-3863 passing test to verify a uniprot accession with canonical flag set is transferred via the DBRefFetcher (and the SequenceI.transferAnnotation method it calls)

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JAL-3929 generalised Alphafold retrieval mechanism to be reused for PDBEntrys with retrieval URIs discovered via 3d beacons

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JAL-3829 generalised Alphafold retrieval mechanism to be reused for PDBEntrys with retrieval URIs discovered via 3d beacons

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JAL-3863 mark first accession retrieved from Uniprot as the canonical accession

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JAL-3863 mark first accession retrieved from Uniprot as the canonical accession

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JAL-3929 3d-beacons structure chooser logic (not yet finished)

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JAL-3829 3d-beacons structure chooser logic (not yet finished)

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patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available