List of estimateErrors() Examples

Examples of estimateErrors()

eu.isas.peptideshaker.recalibration.SpectrumRecalibrator.estimateErrors()

Estimates the file m/z errors and displays the progress in a waiting handler. Shall be done before calibration. The information generated can be cleared from the mapping using clearErrors(String spectrumFileName). The progress will only be updated, max value is the number of spectra @param spectrumFileName the name of the file of the run @param identification the corresponding identification @param annotationPreferences the annotation preferences to be used @param waitingHandler a waiting handler displaying the progress andallowing the user to cancel the process. Can be null @throws IOException @throws MzMLUnmarshallerException @throws SQLException @throws ClassNotFoundException @throws InterruptedException

                    waitingHandler.setSecondaryProgressCounter(0);
                    waitingHandler.setSecondaryProgressCounterIndeterminate(false);
                    waitingHandler.setMaxSecondaryProgressCounter(2 * spectrumFactory.getNSpectra(fileName));
                }


                spectrumRecalibrator.estimateErrors(fileName, identification, annotationPreferences, waitingHandler);
            }


            PSParameter psParameter = new PSParameter();
            identification.loadSpectrumMatchParameters(fileName, psParameter, waitingHandler);

                waitingHandler.resetSecondaryProgressCounter();
                waitingHandler.setSecondaryProgressCounterIndeterminate(false);
                waitingHandler.setMaxSecondaryProgressCounter(2 * spectrumFactory.getNSpectra(fileName));
            }


            spectrumRecalibrator.estimateErrors(fileName, identification, annotationPreferences, waitingHandler);


            // Debug part
            if (debug) {


                RunMzDeviation runMzDeviation = spectrumRecalibrator.getRunMzDeviations(fileName);

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Examples of estimateErrors()

Examples of eu.isas.peptideshaker.recalibration.SpectrumRecalibrator.estimateErrors()

Examples of eu.isas.peptideshaker.recalibration.SpectrumRecalibrator.estimateErrors()