pl.poznan.put.structure.formats.StrandView Maven / Gradle / Ivy

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package pl.poznan.put.structure.formats;

import org.immutables.value.Value;
import pl.poznan.put.pdb.PdbNamedResidueIdentifier;
import pl.poznan.put.structure.DotBracketSymbol;

import java.util.List;

/** A strand which is defined as a fragment of a dot-bracket structure. */
@Value.Immutable
public abstract class StrandView implements Strand {
  @Override
  @Value.Parameter(order = 1)
  public abstract String name();

  @Override
  public final String description() {
    if (parent() instanceof DotBracketFromPdb) {
      final DotBracketFromPdb fromPdb = (DotBracketFromPdb) parent();
      final PdbNamedResidueIdentifier from = fromPdb.identifier(fromPdb.symbols().get(begin()));
      final PdbNamedResidueIdentifier to = fromPdb.identifier(fromPdb.symbols().get(end() - 1));
      return String.format("%s %s %s %s %s", from, to, sequence(), structure(), sequenceRY());
    }

    return String.format(
        "%d %d %s %s %s", begin() + 1, end(), sequence(), structure(), sequenceRY());
  }

  @Override
  @Value.Parameter(order = 3)
  public abstract int begin();

  @Override
  @Value.Parameter(order = 4)
  public abstract int end();

  /** @return The parent dot-bracket structure of this strand. */
  @Value.Parameter(order = 2)
  public abstract DotBracket parent();

  @Override
  @Value.Lazy
  public List symbols() {
    return parent().symbols().subList(begin(), end());
  }

  @Override
  public final String toString() {
    return String.format(">strand_%s\n%s\n%s", name(), sequence(), structure());
  }
}