pl.poznan.put.pdb.PdbExpdtaLine Maven / Gradle / Ivy

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package pl.poznan.put.pdb;

import org.immutables.value.Value;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import java.util.Locale;
import java.util.Objects;

/** A representation of EXPDTA line in PDB files. */
@Value.Immutable
public abstract class PdbExpdtaLine implements Serializable {
  // @formatter:off
  //  COLUMNS       DATA TYPE      FIELD         DEFINITION
  //  ------------------------------------------------------------------------------------
  //  1 -  6       Record name    "EXPDTA"
  //  9 - 10       Continuation   continuation  Allows concatenation of multiple records.
  // 11 - 79       SList          technique     The experimental technique(s) with
  //                                            optional comment describing the
  //                                            sample or experiment.
  // @formatter:on
  private static final String FORMAT = "EXPDTA    %-70s"; // NON-NLS
  private static final String RECORD_NAME = "EXPDTA";

  /**
   * Parses text as an EXPDTA line in PDB format.
   *
   * @param line EXPDTA line in PDB format.
   * @return An instance of this class.
   */
  public static PdbExpdtaLine parse(final String line) {
    final String recordName = line.substring(0, 6).trim();

    if (!Objects.equals(PdbExpdtaLine.RECORD_NAME, recordName)) {
      throw new PdbParsingException("PDB line does not start with EXPDTA");
    }

    final List experimentalTechniques = new ArrayList<>();
    for (final String techniqueFullName : line.substring(10).trim().split(";")) {
      final ExperimentalTechnique technique =
          ExperimentalTechnique.fromFullName(techniqueFullName.trim());
      if (technique == ExperimentalTechnique.UNKNOWN) {
        throw new PdbParsingException("Failed to parse line: " + line);
      }
      experimentalTechniques.add(technique);
    }
    return ImmutablePdbExpdtaLine.of(experimentalTechniques);
  }

  /** @return The value of the {@code experimentalTechniques} attribute */
  @Value.Parameter(order = 1)
  public abstract List experimentalTechniques();

  @Override
  public final String toString() {
    return toPdb();
  }

  /** @return A line in PDB format. */
  public final String toPdb() {
    final StringBuilder builder = new StringBuilder();

    if (experimentalTechniques().isEmpty()) {
      builder.append(ExperimentalTechnique.UNKNOWN);
    } else {
      builder.append(experimentalTechniques().get(0).getPdbName());
      for (int i = 1; i < experimentalTechniques().size(); i++) {
        builder.append("; ");
        builder.append(experimentalTechniques().get(i).getPdbName());
      }
    }
    return String.format(Locale.US, PdbExpdtaLine.FORMAT, builder);
  }
}