Examples with PeptideAndProteinBuilder com.compomics.util.experiment.identification.protein_inference.PeptideAndProteinBuilder used on opensource projects

Example 1 with PeptideAndProteinBuilder

use of com.compomics.util.experiment.identification.protein_inference.PeptideAndProteinBuilder in project peptide-shaker by compomics.

the class PeptideShaker method attachSpectrumProbabilitiesAndBuildPeptidesAndProteins.

/**
 * Attaches the spectrum posterior error probabilities to the spectrum
 * matches and creates peptides and proteins.
 *
 * @param sequenceProvider a protein sequence provider
 * @param sequenceMatchingPreferences the sequence matching preferences
 * @param projectType the project type
 * @param fastaParameters the FASTA parsing parameters
 * @param waitingHandler the handler displaying feedback to the user
 */
private void attachSpectrumProbabilitiesAndBuildPeptidesAndProteins(SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingPreferences, ProjectType projectType, FastaParameters fastaParameters, WaitingHandler waitingHandler) {
    waitingHandler.setSecondaryProgressCounterIndeterminate(false);
    waitingHandler.setMaxSecondaryProgressCounter(identification.getSpectrumIdentificationSize());
    PeptideAndProteinBuilder peptideAndProteinBuilder = new PeptideAndProteinBuilder(identification);
    identification.getSpectrumIdentification().values().stream().flatMap(keys -> keys.stream()).parallel().map(key -> identification.getSpectrumMatch(key)).forEach(spectrumMatch -> attachSpectrumProbabilitiesAndBuildPeptidesAndProteins(spectrumMatch, peptideAndProteinBuilder, sequenceProvider, sequenceMatchingPreferences, projectType, fastaParameters, waitingHandler));
    waitingHandler.setSecondaryProgressCounterIndeterminate(true);
}