jalview

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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 Refactor sequence de/uniquification.

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JAL-2909 increase commandlinetests timeout

JAL-2909 fix up tests and ensure we don’t test bam as a writable format

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JAL-2909 pass a dummy sequence object to receive features. Ideally we should test that features look like they are expected too here !

JAL-3821 data file for failing test

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    ./io/J03321_rna.embl.txt
JAL-3821 less ambiguous base class name for EMBL and GenBank flat file parsers

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JAL-3821 failing test

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

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    ./ws/jabaws/DisorderAnnotExportImport.java
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    ./ws/jabaws/RNAStructExportImport.java
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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 updated response for P01308

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    ./fts/threedbeacons/p01308_tdb_resp.txt
JAL-3829 tests need to wait for dialog to be closed and background processes to finish before they can check functionality

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JAL-3829 TDBeacons fetcher needs a sequence with at least one canonical uniprot accession

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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-3761 listToArray became rangeListToArray

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    ./util/MappingUtilsTest.java
JAL-3829 parallel not welcome here

JAL-3829 test flakiness and human flakiness

JAL-3829 more info on test fail - seems to be flaky