Exemplo n.º 1
0
    /**
     * Add <code>count</code> H2 isotpes
     *
     * @param count the number of H2 to add
     * @return this builder
     */
    public final FragBuilder addH2(int count) {

      compositionBuilder.add(periodicTable.getAtom(AtomicSymbol.H, 2), count);
      return this;
    }
Exemplo n.º 2
0
  /** GlycanFragAnnotation Builder */
  public static class FragBuilder {

    static final PeriodicTable periodicTable = PeriodicTable.getInstance();

    private final int charge;
    private GlycanFragment fragment;
    private Mass neutralLoss = Mass.ZERO;
    private final Composition.Builder compositionBuilder = new Composition.Builder();

    /**
     * Construct a new FragBuilder
     *
     * @param charge the charge
     * @param fragment the glycan fragment
     */
    public FragBuilder(int charge, GlycanFragment fragment) {
      checkNotNull(fragment);
      this.charge = charge;
      this.fragment = fragment;
    }

    /**
     * Copy constructor
     *
     * @param src the GlycanFragAnnotation from which to copy the values
     */
    public FragBuilder(GlycanFragAnnotation src) {

      this.charge = src.getCharge();
      this.fragment = src.getFragment();
    }

    /**
     * Set the neutral loss
     *
     * @param neutralLoss the neutral loss
     * @return this builder
     */
    public final FragBuilder setNeutralLoss(Mass neutralLoss) {

      this.neutralLoss = neutralLoss;
      return this;
    }

    /**
     * Add <code>count</code> C13 isotopes
     *
     * @param count the number of C13 isotopes
     * @return this builder
     */
    public final FragBuilder addC13(int count) {

      compositionBuilder.add(periodicTable.getAtom(AtomicSymbol.C, 13), count);
      return this;
    }

    /**
     * Add <code>count</code> H2 isotpes
     *
     * @param count the number of H2 to add
     * @return this builder
     */
    public final FragBuilder addH2(int count) {

      compositionBuilder.add(periodicTable.getAtom(AtomicSymbol.H, 2), count);
      return this;
    }

    /**
     * Add the <code>isotope</code>
     *
     * @param isotope the isotope to add
     * @return this builder
     */
    public final FragBuilder addIsotope(Atom isotope) {

      checkArgument(!isotope.isDefaultIsotope());

      compositionBuilder.add(isotope, 1);
      return this;
    }

    /**
     * Add all the atoms from <code>isotopeComposition</code>
     *
     * @param isotopeComposition the atoms to add
     * @return this builder
     */
    public final FragBuilder addIsotopeComposition(Composition isotopeComposition) {

      compositionBuilder.addAll(isotopeComposition);
      return this;
    }

    /**
     * Build the CrossRingFragAnnotation annotation.
     *
     * @return the new CrossRingFragAnnotation
     */
    public final GlycanFragAnnotation build() {

      Composition fragIsotopeComposition =
          compositionBuilder.isEmpty()
              ? GlycanFragAnnotation.EMPTY_COMPOSITION
              : compositionBuilder.build();
      return new GlycanFragAnnotation(charge, fragment, fragIsotopeComposition, neutralLoss);
    }
  }