Quick start

Quick Start

Parse a file with explicit tool type

import it.unicam.cs.bdslab.rna2dunifier.RnaUnifier;
import it.unicam.cs.bdslab.rna2dunifier.parser.ToolType;
 
import java.io.File;
 
public class Example {
    public static void main(String[] args) throws Exception {
        RnaUnifier unifier = new RnaUnifier();
 
        File inputFile = new File("path/to/barnaba_output.out");
 
        // true  → extended BPSEQ (all 12 LW families)
        // false → canonical BPSEQ only (cWW + tWW)
        String result = unifier.process(inputFile, ToolType.BARNABA, true);
 
        System.out.println(result);
    }
}

Parse a file with auto-detection

RnaUnifier unifier = new RnaUnifier();
File inputFile = new File("path/to/rnaview_output.txt");
 
// Tool type is inferred automatically from file content
String result = unifier.process(inputFile, true);
System.out.println(result);

Write the output directly to a file

RnaUnifier unifier = new RnaUnifier();
File inputFile  = new File("path/to/fr3d_output.json");
File outputFile = new File("path/to/output.bpseq");
 
unifier.processToFile(inputFile, ToolType.FR3D, outputFile, true);