Architecture

Architecture

The library is organized into three layers: controllers (entry points), model (domain objects and logic), and utilities.

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Package Overview

controller/
  IOController            ← file loading and saving (Singleton)
  TranslatorController    ← format translation (Singleton)
 
model/
  rnafile/
    RNAFile               ← representation of a loaded RNA file
    RNAFormat             ← enum of supported formats
    RNAFileConstructor    ← builds an RNAFile from disk (Singleton, ANTLR)
    RNAFileTranslator     ← translation logic between formats (static methods)
    RNAInputFileParserException ← parsing exception (unchecked)
 
  rnastructure/
    RNASecondaryStructure     ← secondary structure model
    WeakBond                  ← index pair representing a bond
    NonCanonicalEdgeFamily    ← non-canonical edge family
    NonCanonicalEdgeFamilyValues ← allowed values for edge families
 
  utils/
    Region                    ← region used in the pseudoknot algorithm
    RNAStatisticsCalculator   ← structure statistics (static methods)

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Key Classes

IOController (Singleton)

The main entry point for I/O operations.

Method	Description
loadFile(Path)	Parse and register a single file
loadDirectory(Path)	Parse and register all files in a directory
getRNAFileOf(Path)	Parse without registering
saveFiles(...)	Write files to disk, optionally with stats and ZIP
getLoadedRNAFiles()	Return an unmodifiable list of loaded files
deleteFile(RNAFile)	Remove a single file from the managed list
clearAllDataStructures()	Reset the controller state
getRecognizedFormat()	Return the current session's format

TranslatorController (Singleton)

Handles format conversion.

Method	Description
translate(RNAFile, RNAFormat)	Translate a file to the target format
getAvailableTranslations(RNAFormat)	List compatible target formats

RNAFile

Immutable representation of a parsed file. Key getters:

Method	Returns
getFormat()	RNAFormat
getFileName()	Original file name
getContent()	List<String> — raw lines
getStructure()	RNASecondaryStructure

RNASecondaryStructure

Method	Returns
getSize()	Number of nucleotides
getSequence()	Nucleotide sequence string
isPseudoknotted()	boolean
getWeakBonds()	List<WeakBond>

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Design Notes

• Singletons are stateful. IOController holds the list of loaded files and the recognized format. Always call clearAllDataStructures() between sessions with different formats.
• ANTLR4 parsing. Format detection happens at parse time from file content, not from the file extension.
• Translation returns new objects. translator.translate(...) never mutates the source RNAFile.
• 1-based indexing. All position indices start at 1, both internally and in all file formats.

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See Also

• Loading Files
• Format Translation
• Home