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CHANGELOG.md

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0.0.9

  • (BREAKING) Renaming "UMAP" to more general "Projection" term This includes the data class, the visualizer, file handling and test cases
  • Updating dependencies

0.0.8

  • Adding testing strategy
  • Making toMap more generic for bio entities
  • Adding toString function for sequence
  • Adding preliminary OneHotEncodingEmbedder

0.0.7

  • Adding TypeNameMixin for all biological entities to be able to display the class name at runtime, even for optimized types in flutter web renderer

0.0.6

Features

  • Adding Cell and CellMeasurements data classes
  • Adding CellFCSParser stub

Maintenance

  • Changing bio_file_handler structure to be able to handle both string and binary file types (breaking changes for string converting and parsing)

0.0.5

Features

  • Adding EmbeddingsCombiner Is able to combine two embeddings via a combining function, currently multiply elementwise and concatenation. Enables ProteinProteinInteraction to provide the getEmbeddings interface.
  • Adding draft classes for AminoAcid and Atom to represent protein structure (work in progress)

Maintenance

  • Multiple lines for sequences in protein fasta files are now allowed and concatenated
  • File names are now automatically added to loaded entities (column name ExtractedDataset)
  • Renaming BiologicalEntity to BioEntity
  • Making nullableMerge applicable for non-comparable types
  • Adding toMap() and getEmbeddings() to BioEntity interface
  • Introducing functional error handling via fpdart, will be more widely adapted in future releases
  • Moving package to biocentral organization
  • Updating dependencies

0.0.4

Maintenance

  • Fixing image path in README

0.0.3

Maintenance

  • Fixing image path in README
  • Renaming umap example to example.dart
  • Fixing package description length

0.0.2

Maintenance

  • Adding BSD License

0.0.1

Initial release

Features

Widgets:

  • UMAP Visualizer

Biological Data Classes:

  • Protein
  • Sequence: AminoAcidSequence, NucleotideSequence
  • Protein-Protein Interaction
  • Taxonomy

Protein Representation and Data Analysis:

  • Embedding: PerSequence, PerResidue
  • UMAP

File handling:

  • Protein: fasta
  • ProteinProteinInteraction: fasta
  • Embedding: json
  • UMAPData: csv
  • CustomAttributes: csv