Loading files

Loading Files

All loading operations go through IOController, which is a stateful singleton. Acquire the instance once and reuse it:

IOController io = IOController.getInstance();

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Loading a Single File

RNAFile file = io.loadFile(Path.of("structure.bpseq"));
 
System.out.println("Detected format : " + file.getFormat());
System.out.println("Nucleotides     : " + file.getStructure().getSize());

loadFile parses the file, adds it to the internal list, and sets the session's recognized format.

⚠️ If a file with a different format from the already-loaded ones is loaded, an IllegalArgumentException is thrown.

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Loading a Directory

io.loadDirectory(Path.of("/data/structures/"));
 
List<RNAFile> files = io.getLoadedRNAFiles();
System.out.println("Loaded files  : " + files.size());
System.out.println("Shared format : " + io.getRecognizedFormat());

The method automatically ignores:

• Hidden files (names starting with .)
• Files inside subdirectories whose name contains a dot Subdirectories are not visited recursively.

All files in the directory must share the same format; the first non-conforming file causes an IllegalArgumentException.

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Building an RNAFile Without Registering It

To parse a file without adding it to the controller's managed list:

RNAFile file = io.getRNAFileOf(Path.of("single_structure.db"));

Useful for one-off inspection or when mixing files from different sessions.

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Format Detection

The format is detected from file content via the ANTLR4 parser, not from the file extension. A .txt file containing BPSEQ content is correctly recognized as BPSEQ.

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See Also

• Managing Loaded Files
• Format Translation
• Exception Handling
• Home