datamodel

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

  1. … 2 more files in changeset.
JAL-3878 Add char[] constructor to Sequence

JAL-3860 prototype for highlight species/assembly/chromosome/position

  1. … 2 more files in changeset.
JAL-3982 JAL-3860 encapsulate genomic coordinates mapping/liftover logic

  1. … 1 more file in changeset.
JAL-3860 JAL-3892 extract genomic assembly mapping logic to static store

    • -0
    • +158
    ./GenomicAssemblies.java
  1. … 1 more file in changeset.
JAL-3746 apply copyright to source

  1. … 45 more files in changeset.
JAL-3438 spotless for 2.11.2.0

  1. … 647 more files in changeset.
JAL-3438 - all src and test run through spotless..

  1. … 654 more files in changeset.
Merge branch 'features/JAL-3417_sdppred_calcs' into features/r2_11_2_JAL-3417_sdppred

  1. … 1 more file in changeset.
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855 combined new logic for 2.11.2 3d-beacons with original hack to resolve PAE and CIF Conflicts: src/jalview/ws/dbsources/EBIAlfaFold.java

  1. … 5 more files in changeset.
JAL-3956 - PDBEntry objects constructed from 3D-Beacons have authoritative IDs overriding any embedded IDs

  1. … 2 more files in changeset.
JAL-819 update branch 'feature/JAL-819undeleteAutoannotation' from 2.11.2 develop

Conflicts:

src/jalview/api/AlignViewportI.java

src/jalview/gui/AnnotationLabels.java

  1. … 5 more files in changeset.
JAL-722 updated from 2.11.2 develop branch - needs further work before release

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/datamodel/Alignment.java

src/jalview/gui/AlignFrame.java

src/jalview/io/AlignFile.java

src/jalview/project/Jalview2XML.java

  1. … 10 more files in changeset.
Merge branch 'bug/JAL-3806_mappingCoversSequence_for2112' into develop Combines patches for JAL-3806 prior to redaction of shared CDS dataset sequences with patches for JAL-3673 Conflicts: src/jalview/datamodel/AlignedCodonFrame.java src/jalview/util/MappingUtils.java test/jalview/util/MappingUtilsTest.java

  1. … 2 more files in changeset.
JAL-3806 require mapping extent covers both sequence’s dataset sequence to avoid spurious mappings from overlapping CDS

  1. … 1 more file in changeset.
Merge branch 'task/JAL-3763_newDatasetForCds' into merge/develop_task/JAL-3763_newDatasetForCds

Conflicts:

src/jalview/analysis/AlignmentUtils.java

src/jalview/util/MapList.java

test/jalview/util/MapListTest.java

test/jalview/util/MappingUtilsTest.java

  1. … 6 more files in changeset.
JAL-3829 isCanonical should by default be false - ensure JalviewJS offers 3d-beacons search for example project

JAL-3919 use model format field to ensure we get the file extension correct when creating temp files for structure viewers

  1. … 4 more files in changeset.
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.