Examples with FractionParameters com.compomics.util.parameters.identification.advanced.FractionParameters used on opensource projects

Example 1 with FractionParameters

use of com.compomics.util.parameters.identification.advanced.FractionParameters in project peptide-shaker by compomics.

the class PeptideShaker method proteinMapChanged.

/**
 * Processes the identifications if a change occurred in the protein map.
 *
 * @param identification the identification object containing the
 * identification matches
 * @param waitingHandler the waiting handler
 * @param identificationParameters the identification parameters
 * @param sequenceProvider a protein sequence provider
 */
public void proteinMapChanged(Identification identification, WaitingHandler waitingHandler, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider) {
    FastaParameters fastaParameters = identificationParameters.getFastaParameters();
    FractionParameters fractionParameters = identificationParameters.getFractionParameters();
    matchesValidator.attachProteinProbabilities(identification, sequenceProvider, fastaParameters, metrics, waitingHandler, fractionParameters);
}

Example 2 with FractionParameters

use of com.compomics.util.parameters.identification.advanced.FractionParameters in project peptide-shaker by compomics.

the class PeptideShaker method spectrumMapChanged.

/**
 * Processes the identifications if a change occurred in the PSM map.
 *
 * @param identification the identification object containing the
 * identification matches
 * @param waitingHandler the waiting handler
 * @param processingPreferences the processing preferences
 * @param identificationParameters the identification parameters
 * @param sequenceProvider a protein sequence provider
 * @param spectrumProvider the spectrum provider
 * @param projectType the project type
 */
public void spectrumMapChanged(Identification identification, WaitingHandler waitingHandler, ProcessingParameters processingPreferences, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, ProjectType projectType) {
    FastaParameters fastaParameters = identificationParameters.getFastaParameters();
    FractionParameters fractionParameters = identificationParameters.getFractionParameters();
    TargetDecoyMap peptideMap = new TargetDecoyMap();
    TargetDecoyMap proteinMap = new TargetDecoyMap();
    matchesValidator.setPeptideMap(peptideMap);
    matchesValidator.setProteinMap(proteinMap);
    attachSpectrumProbabilitiesAndBuildPeptidesAndProteins(sequenceProvider, identificationParameters.getSequenceMatchingParameters(), projectType, fastaParameters, waitingHandler);
    matchesValidator.fillPeptideMaps(identification, metrics, waitingHandler, identificationParameters, sequenceProvider, spectrumProvider);
    peptideMap.estimateProbabilities(waitingHandler);
    matchesValidator.attachPeptideProbabilities(identification, fastaParameters, waitingHandler);
    matchesValidator.fillProteinMap(identification, spectrumProvider, waitingHandler);
    proteinMap.estimateProbabilities(waitingHandler);
    matchesValidator.attachProteinProbabilities(identification, sequenceProvider, fastaParameters, metrics, waitingHandler, fractionParameters);
}

Example 3 with FractionParameters

use of com.compomics.util.parameters.identification.advanced.FractionParameters in project peptide-shaker by compomics.

the class PeptideShaker method peptideMapChanged.

/**
 * Processes the identifications if a change occurred in the peptide map.
 *
 * @param identification the identification object containing the
 * identification matches
 * @param waitingHandler the waiting handler
 * @param identificationParameters the identification parameters
 * @param sequenceProvider a protein sequence provider
 * @param spectrumProvider the spectrum provider
 */
public void peptideMapChanged(Identification identification, WaitingHandler waitingHandler, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider) {
    FastaParameters fastaParameters = identificationParameters.getFastaParameters();
    FractionParameters fractionParameters = identificationParameters.getFractionParameters();
    TargetDecoyMap proteinMap = new TargetDecoyMap();
    matchesValidator.setProteinMap(proteinMap);
    matchesValidator.attachPeptideProbabilities(identification, fastaParameters, waitingHandler);
    matchesValidator.fillProteinMap(identification, spectrumProvider, waitingHandler);
    proteinMap.estimateProbabilities(waitingHandler);
    matchesValidator.attachProteinProbabilities(identification, sequenceProvider, fastaParameters, metrics, waitingHandler, fractionParameters);
}