Recipe 3.9. Rendering the alignment between an experimental spectrum and a theoretical spectrum generated from a peptide

You want to render the graph chart of the alignment between a peak list against theoretical peptide fragments.

The object MSPeptideMatchRenderer is making all the steps for you, from the generation of the theoretical spectrum to the rendering of the graph:

import org.expasy.jpl.msmatch.MSPeptideMatchRenderer;

// the experimental peak list that we want to match against the theoretical fragments
PeakList expPeakList = ...

// the peptide precursor that will be fragmented by the renderer
JPLIonizedPeptide peptide =
	JPLIonizedPeptide.newInstance(new Peptide.Builder(
		"EQVQSC({57})GPPPELLNGNVK").build(), 2);

// The builder defines the settings for:
// 1. the fragmentation of precursor (fragmenter, condition)
// 2. the matching of spectra (tolerance)
// 3. the rendering of the chart image (bgColor, dimension)
MSPeptideMatchRenderer renderer =
	new MSPeptideMatchRenderer.Builder().fragmenter(
		new PeptideFragmenter.Builder(EnumSet.of(
			FragmentationType.AX, FragmentationType.BY,
		    FragmentationType.CZ)).enableLoss().build())
		    .tolerance(0.1).bgColor(Color.gray).dimension(
		     new Dimension(500, 300)).build();

// setting the data
renderer.setData(peptide, expPeakList);

// rendering the chart
try {
	renderer.exportChart("/tmp/alignment");
} catch (ImageRenderingException e) {
	// no match -> nothing to render
	e.printStackTrace();
}

As the whole processing of fragmentation + matching is delegated internally to MSPeptideMatchFactory, you can also give it to the builder and define only the rendering parameters:

import org.expasy.jpl.msmatch.MSPeptideMatchFactory;
import org.expasy.jpl.msmatch.MSPeptideMatchRenderer;

// the experimental peak list that we want to match against the theoretical fragments
PeakList expPeakList = ...

// the peptide precursor that will be fragmented by the renderer
JPLIonizedPeptide peptide =
	JPLIonizedPeptide.newInstance(new Peptide.Builder(
		"EQVQSC({57})GPPPELLNGNVK").build(), 2);

// The builder defines the settings for:
// 1. the fragmentation of precursor (fragmenter, condition)
// 2. the matching of spectra (tolerance)
MSPeptideMatchFactory factory =
	new MSPeptideMatchFactory.Builder().fragmenter(
		new PeptideFragmenter.Builder(EnumSet.of(
			FragmentationType.AX, FragmentationType.BY,
		    FragmentationType.CZ)).enableLoss().build())
		    .tolerance(0.1).build();
		    
MSPeptideMatchRenderer renderer =
	new MSPeptideMatchRenderer.Builder(factory).bgColor(Color.gray)
		.dimension(new Dimension(500, 300)).build();

// setting the data
renderer.setData(peptide, expPeakList);

// rendering the chart
try {
	// the renderer will delegate the process to the factory (fragmentation + matching)
	// and then will render the alignment
	BufferedImage bi = renderer.render();
} catch (ImageRenderingException e) {
	// no match -> nothing to render
	e.printStackTrace();
}

Sometimes it is needed to edit the processed peak list before making the rendering. In this case, you have to call process() yourself:

MSPeptideMatchFactory factory =
	new MSPeptideMatchFactory.Builder().fragmenter(
		new PeptideFragmenter.Builder(EnumSet.of(
			FragmentationType.AX, FragmentationType.BY,
		    FragmentationType.CZ)).enableLoss().build())
		    .tolerance(0.1).build();
		    
// make the computation
factory.process(peptide, expPeakList);

// get the alignment spectra
PeakList apl = factory.getAnnotatedPeakList();
PeakList napl = factory.getNonAnnotatedPeakList();

// edit the spectra
.....

// new renderer
MSPeptideMatchRenderer renderer =
	new MSPeptideMatchRenderer.Builder(factory).build();
		
renderer.addDataSet(apl, "annot");
renderer.addDataSet(napl, "na");

// only render the modified alignment
renderer.render();

See also the recipe about processing the alignment of MS spectrum against peptide fragments.