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RNA2DFormatIO — Wiki

Version: 0.0.1 | Java: 21+ | Group: it.unicam.cs.bdslab

Java library for reading, writing, and converting RNA secondary structure files. Supports automatic format detection via ANTLR4 and translation across all major formats.

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Quick Navigation

Section	Description
Requirements & Integration	Dependencies, Maven setup
Supported Formats	AAS, BPSEQ, CT, DB, FASTA and variants
Architecture	Package and class overview
Loading Files	Single files, directories, standalone parsing
Format Translation	Conversion matrix, translate API
Saving Files	Output options, statistics, ZIP
Structure Statistics	Nucleotide and bond analysis
Managing Loaded Files	List, remove, reset
Exception Handling	Error types and robust patterns
Examples	Complete working code examples
Notes & Limitations	Thread safety, edge cases

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Main Entry Points

IOController io = IOController.getInstance();
TranslatorController translator = TranslatorController.getInstance();

Both are stateful singletons. Call io.clearAllDataStructures() between sessions with different formats.

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At a Glance

// Load → Translate → Save in three lines
IOController io = IOController.getInstance();
RNAFile source = io.loadFile(Path.of("structure.bpseq"));
RNAFile db = TranslatorController.getInstance().translate(source, RNAFormat.DB);
io.saveFiles(List.of(db), Path.of("/output/"), false, true, "result");