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TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
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/*
 *  SuperByteMatrixSingleValue
 * 
 *  Created on Aug 7, 2014
 */
package net.maizegenetics.util;

import java.util.Arrays;
import java.util.Spliterator;
import static java.util.Spliterator.IMMUTABLE;
import static java.util.Spliterator.ORDERED;
import static java.util.Spliterator.SIZED;
import static java.util.Spliterator.SUBSIZED;
import java.util.function.Consumer;
import java.util.stream.Stream;
import java.util.stream.StreamSupport;

/**
 *
 * @author Terry Casstevens
 */
public class SuperByteMatrixSingleValue implements SuperByteMatrix {

    private byte myData;
    private final int myNumRows;
    private final int myNumColumns;

    SuperByteMatrixSingleValue(int rows, int columns, byte value) {
        myNumRows = rows;
        myNumColumns = columns;
        myData = value;
    }

    @Override
    public byte get(int row, int column) {
        return myData;
    }

    @Override
    public byte[] getAllColumns(int row) {

        if ((row < 0) || (row >= myNumRows)) {
            throw new IndexOutOfBoundsException("SuperByteMatrixSingleValue: getAllColumns: row: " + row);
        }

        byte[] result = new byte[myNumColumns];
        Arrays.fill(result, myData);
        return result;

    }

    @Override
    public byte[] getColumnRange(int row, int start, int end) {

        if ((row < 0) || (row >= myNumRows)) {
            throw new IndexOutOfBoundsException("SuperByteMatrixSingleValue: getColumnRange: row: " + row);
        }

        if ((start < 0) || (start >= myNumColumns)) {
            throw new IndexOutOfBoundsException("SuperByteMatrixSingleValue: getColumnRange: start: " + start);
        }

        if ((end < 0) || (end >= myNumColumns)) {
            throw new IndexOutOfBoundsException("SuperByteMatrixSingleValue: getColumnRange: end: " + end);
        }

        if (end < start) {
            throw new IllegalArgumentException("SuperByteMatrixSingleValue: getColumnRange: end: " + end + " less than start: " + start);
        }

        int numElements = end - start;
        byte[] result = new byte[numElements];
        Arrays.fill(result, myData);
        return result;

    }

    @Override
    public byte[] getAllRows(int column) {

        if ((column < 0) || (column >= myNumColumns)) {
            throw new IndexOutOfBoundsException("SuperByteMatrixSingleValue: getAllRows: column: " + column);
        }

        byte[] result = new byte[myNumRows];
        for (int i = 0; i < myNumRows; i++) {
            result[i] = myData;
        }
        return result;

    }

    @Override
    public int getNumRows() {
        return myNumRows;
    }

    @Override
    public int getNumColumns() {
        return myNumColumns;
    }

    @Override
    public boolean isColumnInnerLoop() {
        return true;
    }

    @Override
    public void setHetsTo(byte value) {
        if (((myData >>> 4) & 0xf) != (myData & 0xf)) {
            myData = value;
        }
    }

    @Override
    public void set(int row, int column, byte value) {
        throw new UnsupportedOperationException("Not supported yet.");
    }

    @Override
    public void arraycopy(int row, byte[] src, int startColumn) {
        throw new UnsupportedOperationException("Not supported yet.");
    }

    @Override
    public void setAll(byte value) {
        myData = value;
    }

    @Override
    public void reorderRows(int[] newIndices) {
        // nothing to do
    }

    @Override
    public void reorderColumns(int[] newIndices) {
        // nothing to do
    }

    @Override
    public Stream stream() {
        return StreamSupport.stream(spliterator(), true);
    }

    @Override
    public Stream stream(int row) {
        long start = (long) row * (long) myNumColumns;
        return StreamSupport.stream(new SuperByteMatrixSingleValueSpliterator<>(start, start + (long) myNumColumns), true);
    }

    public Spliterator spliterator() {
        return new SuperByteMatrixSingleValueSpliterator<>(0, (long) myNumRows * (long) myNumColumns);
    }

    class SuperByteMatrixSingleValueSpliterator implements Spliterator {

        private long myCurrentIndex;
        private final long myFence;

        SuperByteMatrixSingleValueSpliterator(long currentIndex, long fence) {
            myCurrentIndex = currentIndex;
            myFence = fence;
        }

        @Override
        public void forEachRemaining(Consumer action) {
            for (; myCurrentIndex < myFence; myCurrentIndex++) {
                action.accept(myData);
            }
        }

        @Override
        public boolean tryAdvance(Consumer action) {
            if (myCurrentIndex < myFence) {
                action.accept(myData);
                myCurrentIndex++;
                return true;
            } else {
                return false;
            }
        }

        @Override
        public Spliterator trySplit() {
            long lo = myCurrentIndex;
            long mid = (lo + myFence) >>> 1;
            if (lo < mid) {
                myCurrentIndex = mid;
                return new SuperByteMatrixSingleValueSpliterator<>(lo, mid);
            } else {
                return null;
            }
        }

        @Override
        public long estimateSize() {
            return myFence - myCurrentIndex;
        }

        @Override
        public int characteristics() {
            return ORDERED | SIZED | IMMUTABLE | SUBSIZED;
        }
    }

}