/**
* 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;
}
/** 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);
}
}