Examples with AlignmentParameters dulab.adap.workflow.AlignmentParameters used on opensource projects

Example 1 with AlignmentParameters

use of dulab.adap.workflow.AlignmentParameters in project mzmine2 by mzmine.

the class ADAP3AlignerTask method process.

/**
 * Call the alignment from the ADAP package.
 *
 * @param alignment an instance of {@link Project} containing all samples and peaks to be aligned.
 */
private void process() {
    AlignmentParameters params = new AlignmentParameters().sampleCountRatio(parameters.getParameter(ADAP3AlignerParameters.SAMPLE_COUNT_RATIO).getValue()).retTimeRange(parameters.getParameter(ADAP3AlignerParameters.RET_TIME_RANGE).getValue().getTolerance()).scoreTolerance(parameters.getParameter(ADAP3AlignerParameters.SCORE_TOLERANCE).getValue()).scoreWeight(parameters.getParameter(ADAP3AlignerParameters.SCORE_WEIGHT).getValue()).maxShift(2 * parameters.getParameter(ADAP3AlignerParameters.RET_TIME_RANGE).getValue().getTolerance()).eicScore(parameters.getParameter(ADAP3AlignerParameters.EIC_SCORE).getValue()).mzRange(parameters.getParameter(ADAP3AlignerParameters.MZ_RANGE).getValue().getMzTolerance());
    params.optimizationParameters = new OptimizationParameters().gradientTolerance(1e-6).alpha(1e-4).maxIterationCount(4000).verbose(false);
    alignment.alignSamples(params);
}