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Merged
s-t-h merged 29 commits into from
May 23, 2025
Merged

Merge dev into main #9

s-t-h merged 29 commits into from
May 23, 2025

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@s-t-h s-t-h commented May 23, 2025

Update to version v2.4.1.

s-t-h added 29 commits May 21, 2025 10:43
@s-t-h
Rename method Feature.getChildIdAndParent -> Feature.constructChildId
cf0b126
@s-t-h
Set default storage extension to .json.gz to compress files by default.
8b9596d
@s-t-h
Fix build output (storage) writing, if directory is specified as outp…
cab08f8 
…ut path.
@s-t-h
Fix bug with output file compression and renamed storage I/O methods …
06cafd9 
…for clarity.

Remove re-mapping of output stream during GFF3 parsing.
@s-t-h
Remove unused output stream properties.
20bc2f4
@s-t-h
Implement HDBSCAN clustering for sequence types of features.
831e408
@s-t-h
Rework of Logging system to use Java native Logger.
e98a877
@s-t-h
Rework of Logging system to use Java native Logger. Improved task `vi…
2daa321 
…ew` output handling to console.
@s-t-h
Bug fix with casting task view output parameter.
8ed2ae7
@s-t-h
Add project wide format methods to IO.
fa35f55
@s-t-h
Update IO format methods for numbers.
4f12784
@s-t-h
Added constants for attributes used during the Storage.updateStatisti…
748c30a 
…cs() method.
@s-t-h
Move key used to indicate sample occurrence to Attributable class its…
0d19bc1 
…elf.
@s-t-h
Downstream changes of previous commit.
8aaa449
@s-t-h
Update Storage.updateStatistics() method.
6ee6481
@s-t-h
Update GitHub workflow to generate JavaDoc.
530756b
@s-t-h
Add methods to retrieve internal map sizes (e.g., number of proteofor…
c6cf262 
…ms of feature).

Add mode to sort alleles and proteoforms by occurrence.
@s-t-h
Remove sortability of Feature.getAlleles() and Feature.getProteoforms…
ad64482 
…() methods.
@s-t-h
Implement method to obtain attribute or default value, if key is not …
0e651fc 
…associated with value.
@s-t-h
Remove unused method.
910745b
@s-t-h
Remove unused method.
c3628db
@s-t-h
Rename _uid properties to uid.
2840041 
Implement method to retrieve human readable sequence type name.
Simplify getFastaHeader() method.
UIDs are now prefixed with feature's name.
@s-t-h
Change SequenceType.getFastaHeader() to not end with line break.
a6b2f24
@s-t-h
Update Logging.getDate() doc. string.
78ae297
@s-t-h
Reformat
22201a1
@s-t-h
Adapt sequence type query methods to search for uid and name.
a690686
@s-t-h
Improve file and content naming of export methods.
f8e4dfb
@s-t-h
Improve file and content naming of export methods.
a25eb2b
@s-t-h
Update version tag.
507415e
@s-t-h s-t-h self-assigned this May 23, 2025
@s-t-h s-t-h added the enhancement New feature or request label May 23, 2025
@s-t-h s-t-h merged commit 77ce6bc into main May 23, 2025
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