ubic.basecode.io.reader.HistogramReader.java Source code

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Here is the source code for ubic.basecode.io.reader.HistogramReader.java

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/*
 * The baseCode project
 * 
 * Copyright (c) 2008-2019 University of British Columbia
 * 
 * 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 ubic.basecode.io.reader;

import hep.aida.ref.Histogram1D;

import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.Reader;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;

import org.apache.commons.lang3.StringUtils;

/**
 * Reads histograms stored in flat files
 * 
 * @author raymond
 */
public class HistogramReader {
    protected BufferedReader in;
    private String title;

    public HistogramReader(Reader in, String title) {
        this.in = new BufferedReader(in);
        this.title = title;
    }

    public HistogramReader(String fileName) throws FileNotFoundException {
        this.in = new BufferedReader(new FileReader(fileName));
    }

    /**
     * @return
     * @throws IOException
     */
    public Histogram1D read1D() throws IOException {
        int numHeaderLines = 1; // ignore the column header
        Map<Double, Integer> binCountMap = new HashMap<Double, Integer>();
        double min = Double.POSITIVE_INFINITY;
        double max = Double.NEGATIVE_INFINITY;
        while (in.ready()) {
            String line = in.readLine();
            if (StringUtils.isBlank(line))
                continue;
            if (line.startsWith("#") || numHeaderLines-- > 0)
                continue;
            String fields[] = line.split("\t");
            Double bin = Double.valueOf(fields[0]);
            Integer count = Integer.valueOf(fields[1]);
            binCountMap.put(bin, count);
            if (bin < min) {
                min = bin;
            } else if (bin > max) {
                max = bin;
            }
        }
        int numBins = binCountMap.keySet().size();

        Histogram1D hist = new Histogram1D(title, numBins, min, max);
        for (Entry<Double, Integer> element : binCountMap.entrySet()) {
            Entry<Double, Integer> entry = element;
            Double bin = entry.getKey();
            Integer count = entry.getValue();
            hist.fill(bin.doubleValue(), count.doubleValue());
        }
        return hist;
    }
}