Auto detection

Auto-Detection of Tool Type

When no ToolType is provided, RnaUnifier delegates to ParserFactory.detectTool(). This method peeks at the first 4 096 bytes of the stream and applies the following heuristics in priority order:

Priority	Signal	Detected tool
1	Contains BEGIN_base-pair	RNAVIEW
2	Contains Residue conformations	MCANNOTATE
3	Contains > and seq	RNAPOLIS
4	JSON with key "annotations"	FR3D
5	JSON with key "pairs"	X3DNA
6	Lines matching N_INT_INT N_INT_INT XXc pattern	BARNABA
7	Lines with ? separator and W:WC-style tokens	BPNET

If no signature matches, an IllegalArgumentException is thrown.

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Stream Requirements

The InputStream passed to detectTool (or to any auto-detecting process overload) must support mark()/reset(). A BufferedInputStream always satisfies this requirement.

If you are passing a raw FileInputStream, wrap it first:

try (BufferedInputStream bis = new BufferedInputStream(new FileInputStream(myFile))) {
    String result = unifier.process(bis, true);
}

Note: RnaUnifier.process(File, boolean) wraps the file internally, so you do not need to do this manually when passing a File object.

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