Example for dishevelled-bio assembly gfa1 package

Gfa1Example.java

import static org.dishevelled.compress.Readers.reader;

import java.io.*;

import org.dishevelled.bio.assembly.gfa1.*;

void read(@Nullable File file) {

  // this Readers.reader method has some magic in it:
  //   if file is null, use stdin
  //   handles gzip, bgzf (block-gzipped), and bzip2 compression transparently
  try (BufferedReader reader = reader(file)) {

    // stream over reader, use callback for each parsed generic record
    Gfa1Reader.stream(reader, new Gfa1Listener() {
      @Override
      public boolean record(final Gfa1Record gfa1Record) {
        if (gfa1Record instanceof Path) {
          Path path = (Path) gfa1Record;

          // ...
        }

	// return true to continue processing
        return true;
      }
    });

    // or use the adapter specific type record callbacks

    Gfa1Reader.stream(reader, new Gfa1Adapter() {
      @Override
      public boolean path(final Path path) {

	// access required fields
        path.getName();
        path.getSegments();

        // access optional fields
        if (path.hasOverlaps()) {
          path.getOverlaps();
        }

        // access optional fields wrapped in Optional
        path.getOverlapsOpt().get();

	// return true to continue processing
        return true;
      }

      @Override
      public boolean segment(final Segment segment) {

        // access required fields
        path.getId();

        // access optional fields
        if (segment.hasSequence()) {
          segment.getSequence();
        }

        // access optional fields wrapped in Optional
        segment.getSequenceOpt().get();

	// access optional reserved tag fields (e.g. 'LN')
        if (segment.containsLn()) { // short field name version
          segment.getLn();
        }
        if (segment.containsLength()) { // long field name version
          segment.getLength();
        }

        // access optional reserved tag fields wrapped in Optional
        segment.getLnOpt().get();
        segment.getLengthOpt().get();

        // access optional non-reserved tag fields as String values, may return null
        String zz = segment.getTags().get("zz");

        // access typed optional non-reserved tag fields, may throw exception if type does not match
        if (segment.containsTagKey("zz")) {
          float f = segment.getTagFloat("zz");
        }

        // access typed optional non-reserved tag fields wrapped in Optional
        float f = segment.getTagFloatOpt("zz").getOrElse(0.0f);
      }
    });
  }
}