edu.berkeley.compbio.phyloutils.NASTDistanceMapper.java Source code

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Here is the source code for edu.berkeley.compbio.phyloutils.NASTDistanceMapper.java

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/*
 * Copyright (c) 2006-2013  David Soergel  <dev@davidsoergel.com>
 * Licensed under the Apache License, Version 2.0
 * http://www.apache.org/licenses/LICENSE-2.0
 */

package edu.berkeley.compbio.phyloutils;

import com.davidsoergel.dsutils.DSArrayUtils;
import com.davidsoergel.dsutils.file.StringListDoubleMapReader;
import org.apache.commons.collections15.map.MultiKeyMap;

import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.Map;

/**
 * Estimate the phylogenetic distance on one of Morgan Price's FastTree + GreenGenes trees between a NAST-aligned
 * fragment pair
 *
 * @author <a href="mailto:dev@davidsoergel.com">David Soergel</a>
 * @version $Id$
 */
public class NASTDistanceMapper {
    int[] positions;
    int[] widths;
    MultiKeyMap<Integer, Double> slopeTable = new MultiKeyMap<Integer, Double>();
    //** make configurable
    final String filename = "nast.constraints.10k..4.slopes.txt";

    public NASTDistanceMapper() throws IOException {
        Map<String, List<Double>> map = StringListDoubleMapReader.read(filename);

        positions = DSArrayUtils.castToInt(map.get("Positions").toArray(DSArrayUtils.EMPTY_DOUBLE_OBJECT_ARRAY));
        widths = DSArrayUtils.castToInt(map.get("NonGapWidths").toArray(DSArrayUtils.EMPTY_DOUBLE_OBJECT_ARRAY));

        List<Double> rowMajorSlopes = map.get("Slopes");
        int numPositions = positions.length;

        for (int widthIndex = 0; widthIndex < widths.length; widthIndex++) {
            for (int positionIndex = 0; positionIndex < positions.length; positionIndex++) {
                // see GreenGenesFragmentDistanceCorrelationGrid:145
                //int gridIndex = widthQuantizedIndex * positions.length + positionIndex;

                int slopeIndex = widthIndex * numPositions + positionIndex;
                //slopeTable.put(widths[widthIndex], positions[positionIndex], rowMajorSlopes.get(slopeIndex));
                slopeTable.put(widthIndex, positionIndex, rowMajorSlopes.get(slopeIndex));
            }
        }
    }

    public double map(final int position, final int width, final double dnadist) {
        // find the floor of the position and width among the known entries

        int widthQuantizedIndex = Arrays.binarySearch(widths, width);
        if (widthQuantizedIndex < 0) {
            //BAD test me
            widthQuantizedIndex = -(widthQuantizedIndex + 1) - 1;
        }

        int positionQuantizedIndex = Arrays.binarySearch(positions, position);
        if (positionQuantizedIndex < 0) {
            //BAD test me
            positionQuantizedIndex = -(positionQuantizedIndex + 1) - 1;
        }

        double slope = slopeTable.get(widthQuantizedIndex, positionQuantizedIndex);
        return dnadist * slope;
    }
}