Advanced Usage

Processing an InputStream Directly

Useful when the input comes from a network connection, a ZIP entry, or any source that is not a plain file:

InputStream rawStream = mySource.openStream();
BufferedInputStream bis = new BufferedInputStream(rawStream);
 
RnaUnifier unifier = new RnaUnifier();
String result = unifier.process(bis, ToolType.FR3D, true);

Building a Structure Programmatically

You can construct an ExtendedRNASecondaryStructure by hand without going through a parser — useful for testing or for integrating with other data sources:

ExtendedRNASecondaryStructure structure =
    new ExtendedRNASecondaryStructure.Builder()
        .setSequence("GCAUGC")
        .addPair(new Pair(0, 5, "G", "C", BondType.LEONTIS_WESTHOF_cWW))
        .addPair(new Pair(1, 4, "C", "G", BondType.LEONTIS_WESTHOF_cWW))
        .addPair(new Pair(0, 3, "G", "U", BondType.LEONTIS_WESTHOF_tWH))
        .addHeaderInfo("Source", "manual")
        .build();
 
BpseqExporter exporter = new BpseqExporter();
System.out.println(exporter.printExtendedBPSEQ(structure));

Inspecting Pairs After Parsing

After parsing, you can iterate over all pairs and filter by type:

RnaStructureParser parser = ParserFactory.getParser(ToolType.RNAPOLIS);
ExtendedRNASecondaryStructure structure;
try (InputStream is = new FileInputStream("input.txt")) {
    structure = parser.parse(is);
}
 
// All canonical pairs
structure.getCanonical().forEach(p ->
    System.out.println((p.getPos1() + 1) + " → " + (p.getPos2() + 1))
);
 
// All cHS pairs
structure.getPairs().stream()
    .filter(p -> p.getType() == BondType.LEONTIS_WESTHOF_cHS)
    .forEach(System.out::println);

Custom Exporter

If you need a different output format, extend BpseqExporter and inject your implementation:

public class MyExporter extends BpseqExporter {
    @Override
    public String printExtendedBPSEQ(ExtendedRNASecondaryStructure s) {
        // your custom logic
    }
}
 
RnaUnifier unifier = new RnaUnifier(new MyExporter());