Recipe 3.2. Editing a MS peak list

You want to edit a MS peak list.

MS peak list instances are immutable as no setters is able to modify it. The only way to modify a peak list pass by a manager that will handle it.

JPLMSPeakListManager manager = JPLMSPeakListManager.getInstance();

This manager provides setters to modify any PeakListImpl:

// the peak list to edit
pl = new PeakListImpl.Builder(masses).intensities(intensities).build();

// modify an mz
manager.setMzAt(pl, 2.9, 1);

// modify an intensity
manager.setIntensityAt(pl, 29, 1);

// add annotation
manager.addAnnotationAt(pl, new FragmentAnnotationImpl.Builder(
	PeptideTypeImpl.A, 2).build(), 1);

// remove all annotations at given peak
manager.removeAnnotationsAt(pl, 1);

Assert.assertFalse(pl.hasAnnotations());