<commit_before>/*
 * Copyright 2006-2012 The MZmine 2 Development Team
 * 
 * This file is part of MZmine 2.
 * 
 * MZmine 2 is free software; you can redistribute it and/or modify it under the
 * terms of the GNU General Public License as published by the Free Software
 * Foundation; either version 2 of the License, or (at your option) any later
 * version.
 * 
 * MZmine 2 is distributed in the hope that it will be useful, but WITHOUT ANY
 * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
 * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with
 * MZmine 2; if not, write to the Free Software Foundation, Inc., 51 Franklin
 * St, Fifth Floor, Boston, MA 02110-1301 USA
 */

package net.sf.mzmine.modules.masslistmethods.chromatogrambuilder;

import net.sf.mzmine.main.MZmineCore;
import net.sf.mzmine.parameters.Parameter;
import net.sf.mzmine.parameters.impl.SimpleParameterSet;
import net.sf.mzmine.parameters.parametertypes.MZToleranceParameter;
import net.sf.mzmine.parameters.parametertypes.MassListParameter;
import net.sf.mzmine.parameters.parametertypes.DoubleParameter;
import net.sf.mzmine.parameters.parametertypes.RawDataFilesParameter;
import net.sf.mzmine.parameters.parametertypes.StringParameter;

public class ChromatogramBuilderParameters extends SimpleParameterSet {

    public static final RawDataFilesParameter dataFiles = new RawDataFilesParameter();

    public static final MassListParameter massList = new MassListParameter();

    public static final DoubleParameter minimumTimeSpan = new DoubleParameter(
            "Min time span",
            "Minimum time span over which the same ion must be observed in order to be recognized as a chromatogram. "
                    + "The optimal value depends on the chromatography system setup. The best way to set this parameter "
                    + "is by studying the raw data and determining what is the typical time span of chromatographic peaks.",
            MZmineCore.getConfiguration().getRTFormat());

    public static final DoubleParameter minimumHeight = new DoubleParameter(
            "Min height",
            "Minimum intensity of the highest data point in the chromatogram. If chromatogram height is below this level, it is discarded.",
            MZmineCore.getConfiguration().getIntensityFormat());

    public static final MZToleranceParameter mzTolerance = new MZToleranceParameter();

    public static final StringParameter suffix = new StringParameter("Suffix",
            "This string is added to filename as suffix", "chromatograms");

    public ChromatogramBuilderParameters() {
        super(new Parameter[] { dataFiles, massList, minimumTimeSpan,
                minimumHeight, mzTolerance, suffix });
    }

}
<commit_msg>Added parameter units<commit_after>/*
 * Copyright 2006-2012 The MZmine 2 Development Team
 * 
 * This file is part of MZmine 2.
 * 
 * MZmine 2 is free software; you can redistribute it and/or modify it under the
 * terms of the GNU General Public License as published by the Free Software
 * Foundation; either version 2 of the License, or (at your option) any later
 * version.
 * 
 * MZmine 2 is distributed in the hope that it will be useful, but WITHOUT ANY
 * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
 * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with
 * MZmine 2; if not, write to the Free Software Foundation, Inc., 51 Franklin
 * St, Fifth Floor, Boston, MA 02110-1301 USA
 */

package net.sf.mzmine.modules.masslistmethods.chromatogrambuilder;

import net.sf.mzmine.main.MZmineCore;
import net.sf.mzmine.parameters.Parameter;
import net.sf.mzmine.parameters.impl.SimpleParameterSet;
import net.sf.mzmine.parameters.parametertypes.MZToleranceParameter;
import net.sf.mzmine.parameters.parametertypes.MassListParameter;
import net.sf.mzmine.parameters.parametertypes.DoubleParameter;
import net.sf.mzmine.parameters.parametertypes.RawDataFilesParameter;
import net.sf.mzmine.parameters.parametertypes.StringParameter;

public class ChromatogramBuilderParameters extends SimpleParameterSet {

    public static final RawDataFilesParameter dataFiles = new RawDataFilesParameter();

    public static final MassListParameter massList = new MassListParameter();

    public static final DoubleParameter minimumTimeSpan = new DoubleParameter(
            "Min time span (min)",
            "Minimum time span over which the same ion must be observed in order to be recognized as a chromatogram. "
                    + "The optimal value depends on the chromatography system setup. The best way to set this parameter "
                    + "is by studying the raw data and determining what is the typical time span of chromatographic peaks.",
            MZmineCore.getConfiguration().getRTFormat());

    public static final DoubleParameter minimumHeight = new DoubleParameter(
            "Min height",
            "Minimum intensity of the highest data point in the chromatogram. If chromatogram height is below this level, it is discarded.",
            MZmineCore.getConfiguration().getIntensityFormat());

    public static final MZToleranceParameter mzTolerance = new MZToleranceParameter();

    public static final StringParameter suffix = new StringParameter("Suffix",
            "This string is added to filename as suffix", "chromatograms");

    public ChromatogramBuilderParameters() {
        super(new Parameter[] { dataFiles, massList, minimumTimeSpan,
                minimumHeight, mzTolerance, suffix });
    }

}

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