edu.umn.msi.tropix.proteomics.itraqquantitation.QuantitationTrainingOptions.java Source code

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Here is the source code for edu.umn.msi.tropix.proteomics.itraqquantitation.QuantitationTrainingOptions.java

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/********************************************************************************
 * Copyright (c) 2009 Regents of the University of Minnesota
 *
 * This Software was written at the Minnesota Supercomputing Institute
 * http://msi.umn.edu
 *
 * All rights reserved. The following statement of license applies
 * only to this file, and and not to the other files distributed with it
 * or derived therefrom.  This file is made available under the terms of
 * the Eclipse Public License v1.0 which accompanies this distribution,
 * and is available at http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 * Minnesota Supercomputing Institute - initial API and implementation
 *******************************************************************************/

package edu.umn.msi.tropix.proteomics.itraqquantitation;

import java.io.File;

import org.apache.commons.lang.builder.ToStringBuilder;

import com.google.common.base.Joiner;
import com.google.common.collect.ImmutableList;

import edu.umn.msi.tropix.proteomics.itraqquantitation.impl.InputReport;
import edu.umn.msi.tropix.proteomics.itraqquantitation.options.QuantificationType;
import edu.umn.msi.tropix.proteomics.itraqquantitation.training.QuantificationTrainingOptions;

public class QuantitationTrainingOptions {
    private final ImmutableList<File> inputMzxmlFiles;
    private final InputReport inputReport;
    private final File outputFile;
    private final QuantificationType quantificationType;
    private final QuantificationTrainingOptions trainingOptions;

    public static final class QuantitationOptionsBuilder {
        private final ImmutableList<File> inputMzxmlFiles;
        private final InputReport inputReport;
        private File outputFile = new File("quantification_output.csv");
        private QuantificationTrainingOptions trainingOptions;
        private QuantificationType quantificationType = QuantificationType.FOUR_PLEX;

        private QuantitationOptionsBuilder(final Iterable<File> inputMzxmlFiles, final InputReport inputReport) {
            this.inputMzxmlFiles = ImmutableList.copyOf(inputMzxmlFiles);
            this.inputReport = inputReport;
        }

        public QuantitationOptionsBuilder withTrainingOptions(final QuantificationTrainingOptions trainingOptions) {
            this.trainingOptions = trainingOptions;
            return this;
        }

        public QuantitationOptionsBuilder ofType(final QuantificationType quantificationType) {
            this.quantificationType = quantificationType;
            return this;
        }

        public QuantitationOptionsBuilder is4Plex() {
            this.quantificationType = QuantificationType.FOUR_PLEX;
            return this;
        }

        public QuantitationOptionsBuilder is8Plex() {
            this.quantificationType = QuantificationType.EIGHT_PLEX;
            return this;
        }

        public QuantitationOptionsBuilder withOutput(final File outputFile) {
            this.outputFile = outputFile;
            return this;
        }

        public QuantitationTrainingOptions get() {
            return new QuantitationTrainingOptions(inputMzxmlFiles, inputReport, outputFile, quantificationType,
                    trainingOptions);
        }
    }

    public static QuantitationOptionsBuilder forInput(final Iterable<File> inputMzxmlFiles,
            final InputReport inputReport) {
        return new QuantitationOptionsBuilder(inputMzxmlFiles, inputReport);
    }

    public QuantitationTrainingOptions(final ImmutableList<File> inputMzxmlFiles,
            final InputReport inputScaffoldReport, final File outputFile,
            final QuantificationType quantificationType, final QuantificationTrainingOptions trainingOptions) {
        this.inputMzxmlFiles = inputMzxmlFiles;
        this.inputReport = inputScaffoldReport;
        this.outputFile = outputFile;
        this.quantificationType = quantificationType;
        this.trainingOptions = trainingOptions;
    }

    public ImmutableList<File> getInputMzxmlFiles() {
        return inputMzxmlFiles;
    }

    public InputReport getInputScaffoldReport() {
        return inputReport;
    }

    public File getOutputFile() {
        return outputFile;
    }

    public QuantificationType getQuantificationType() {
        return quantificationType;
    }

    public QuantificationTrainingOptions getTrainingOptions() {
        return trainingOptions;
    }

    public String toString() {
        return "QuantitationTrainingOptions[mzxmlFiles" + Joiner.on(",").join(inputMzxmlFiles) + ",report="
                + inputReport + ", outputFile=" + outputFile + ", type=" + quantificationType.getValue()
                + ",weights=" + ToStringBuilder.reflectionToString(trainingOptions) + "]";
    }

}