jalview

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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
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.
JAL-3899 Update usages of uniquify and deuniquify.

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    /src/jalview/io/packed/JalviewDataset.java
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    /src/jalview/ws/jws1/JPredThread.java
tmp

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    /src/jalview/io/packed/JalviewDataset.java
JAL-3899 Refactor sequence de/uniquification.

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    /src/jalview/analysis/SeqsetUtils.java
JAL-3416 make flat default laf for linux

JAL-3878 Annotation operation skeleton.

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    /src/jalview/ws2/operations/AnnotationOperation.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3416 updated FlatLaf to 1.6 and added some tabbed pane properties

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    /j11lib/flatlaf-1.6.jar
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    /j8lib/flatlaf-1.6.jar
Merge branch 'develop' into JAL-3416_different_look_and_feel_on_linux

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

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    /src/jalview/datamodel/CigarParser.java
Merge branch 'develop' into features/JAL-2909_bamImport_2_11_2

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3616 show name of structure viewer in ‘new view’ button

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    /src/jalview/jbgui/GStructureChooser.java