/*
 * Copyright (c) 2003-2012 Fred Hutchinson Cancer Research Center
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package org.fhcrc.cpl.viewer.feature.extraction.strategy;

import org.apache.log4j.Logger;
import org.fhcrc.cpl.toolbox.proteomics.MSRun;
import org.fhcrc.cpl.viewer.feature.extraction.*;
import org.fhcrc.cpl.toolbox.datastructure.FloatRange;

/**
 * Adapted from FeatureStrategyPeakClusters, created by Matt Bellew
 */
public class FeatureStrategyPeakClusters extends BaseFeatureStrategyModular
{
    private static Logger _log = Logger.getLogger(FeatureStrategyPeakClusters.class);

    public FeatureStrategyPeakClusters()
    {
    }

    /**
     * Plug in the peak combiner and peak extractor
     * @param run
     * @param startScan
     * @param scanCount
     * @param maxCharge
     * @param mzRange
     */
    public void init(MSRun run, int startScan,
                     int scanCount, int maxCharge,
                     FloatRange mzRange, boolean plotStatistics)
    {
        super.init(run, startScan, scanCount, maxCharge, mzRange, plotStatistics);

        WaveletPeakExtractor waveletPeakExtractor = new WaveletPeakExtractor();
        setPeakExtractor(waveletPeakExtractor);

        DefaultPeakCombiner peakCombiner = new DefaultPeakCombiner();
        peakCombiner.setKeepStatistics(plotStatistics);

        peakCombiner.setMaxCharge(_maxCharge);
        setPeakCombiner(peakCombiner);
    }

    public void plotStatistics()
    {
        if (_keepStatistics)
            ((DefaultPeakCombiner) peakCombiner).plotStatistics();
    }
}