org.rcsb.cif.binary.encoding.RunLengthEncoding Maven / Gradle / Ivy

package org.rcsb.cif.binary.encoding;

import org.rcsb.cif.binary.data.Int32Array;
import org.rcsb.cif.binary.data.IntArray;

import java.util.ArrayDeque;
import java.util.Deque;
import java.util.LinkedHashMap;
import java.util.Map;

/**
 * Represents each integer value in the input as a pair of (value, number of repeats) and stores the result
 * sequentially as {@link Int32Array}. Additionally, stores the size of the original array to make decoding
 * easier.
 *
 *  * RunLength {
 *     kind = "RunLength"
 *     srcType: int[]
 *     srcSize: number
 * }
 * Example
 * [1, 1, 1, 2, 3, 3]
 * ---RunLength--->
 * { srcSize = 6 } [1, 3, 2, 1, 3, 2]
 * 
 */
public class RunLengthEncoding implements Encoding {
    private int srcType;
    private int srcSize;

    public RunLengthEncoding() {

    }

    public RunLengthEncoding(int srcType, int srcSize) {
        this.srcType = srcType;
        this.srcSize = srcSize;
    }

    @Override
    public Map getMapRepresentation() {
        Map map = new LinkedHashMap<>();
        map.put("kind", "RunLength");
        map.put("srcType", srcType);
        map.put("srcSize", srcSize);
        return map;
    }

    @Override
    public IntArray decode(Int32Array data) {
        int[] input = data.getData();
        if (input.length == 0) {
            return data;
        }

        int dataOffset = 0;
        IntArray output = IntArray.create(srcType, srcSize);

        output.setEncoding(data.getEncoding());
        int[] outputArray = output.getData();

        for (int i = 0; i < data.length(); i += 2) {
            int value = input[i];  // value to be repeated
            int length = input[i + 1];  // number of repeats
            for (int j = 0; j < length; ++j) {
                outputArray[dataOffset++] = value;
            }
        }

        return output;
    }

    @Override
    public Int32Array encode(IntArray data) {
        int[] input = data.getData();
        if (input.length == 0) {
            Deque> enc = new ArrayDeque<>(data.getEncoding());
            this.srcType = 3;
            this.srcSize = 0;
            enc.add(this);
            return new Int32Array(new int[0], enc);
        }

        // calculate output size
        int fullLength = 2;
        for (int i = 1; i < input.length; i++) {
            if (input[i - 1] != input[i]) {
                fullLength += 2;
            }
        }

        int[] output = new int[fullLength];

        int offset = 0;
        int runLength = 1;
        for (int i = 1; i < input.length; i++) {
            if (input[i - 1] != input[i]) {
                output[offset] = input[i - 1];
                output[offset + 1] = runLength;
                runLength = 1;
                offset += 2;
            } else {
                ++runLength;
            }
        }
        output[offset] = input[input.length - 1];
        output[offset + 1] = runLength;

        Deque> enc = new ArrayDeque<>(data.getEncoding());
        this.srcType = 3;
        this.srcSize = input.length;
        enc.add(this);

        return new Int32Array(output, enc);
    }

    @Override
    public String toString() {
        return "RunLengthEncoding{" +
                "srcType=" + srcType +
                ", srcSize=" + srcSize +
                '}';
    }
}