Set apairs according to a seed position.

@param l
@param i
@param j
165975
public void  apairs_from_seed(int l,int i, int j){
		aligpath = new IndexPair[l];
		idx1 = new int[l];
		idx2 = new int[l];
		for (int x = 0 ; x < l ; x++) {
			idx1[x]=i+x;
			idx2[x]=j+x;
			aligpath[x] = new IndexPair((short)(i+x),(short)(j+x));
		}
	}
553369
@Override
	public void setNullAt(int i) {
		assertIndexIsValid(i);
		SegmentsUtil.bitSet(segments, offset, i + 8);
		SegmentsUtil.setLong(segments, getFieldOffset(i), 0);
	}
412685
synchronized public void setSeed(final long seed)
        {
        // Due to a bug in java.util.Random clear up to 1.2, we're
        // doing our own Gaussian variable.
        __haveNextNextGaussian = false;

        mt = new int[N];
        
        mag01 = new int[2];
        mag01[0] = 0x0;
        mag01[1] = MATRIX_A;

        mt[0]= (int)(seed & 0xffffffff);
        for (mti=1; mti<N; mti++) 
            {
            mt[mti] = 
                (1812433253 * (mt[mti-1] ^ (mt[mti-1] >>> 30)) + mti); 
            /* See Knuth TAOCP Vol2. 3rd Ed. P.106 for multiplier. */
            /* In the previous versions, MSBs of the seed affect   */
            /* only MSBs of the array mt[].                        */
            /* 2002/01/09 modified by Makoto Matsumoto             */
            mt[mti] &= 0xffffffff;
            /* for >32 bit machines */
            }
        }
1221741
public void setPosition (float x, float y, float z)
    {
        if (_px != x || _py != y || _pz != z) {
            AL10.alSource3f(_id, AL10.AL_POSITION, _px = x, _py = y, _pz = z);
        }
    }
1173208
public void swapColumns(int i, int j) {
        if (i != j) {
            Vector ii = getColumn(i);
            Vector jj = getColumn(j);

            setColumn(i, jj);
            setColumn(j, ii);
        }
    }
1365794
public void setPosition(float x, float y, float z) {
        if (isActive()) {
            mIODevice.setPosition(x, y, z);
        }
    }
1117301
public void swap(int i, int j) {
    checkBounds(i);
    checkBounds(j);

    if (i == j)
      return;

    copier.copy(tmp, offset(i));
    unsafe.copyMemory(null, offset(j), null, offset(i), elementSpacing);
    unsafe.copyMemory(tmp, firstFieldOffset, null, offset(j), elementSize);
  }
680715
public Stream<IntPair> adjacent4Points(final int i, final int j) {
        final IntPair up = i == 0 ? null : IntPair.of(i - 1, j);
        final IntPair right = j == cols - 1 ? null : IntPair.of(i, j + 1);
        final IntPair down = i == rows - 1 ? null : IntPair.of(i + 1, j);
        final IntPair left = j == 0 ? null : IntPair.of(i, j - 1);

        return Stream.of(up, right, down, left);
    }
706741
public void set(int i, int j, DoubleMatrix B)
    {
        int m = B.rows();
        int n = B.columns();
        for (int ii = 0; ii < m; ii++)
        {
            for (int jj = 0; jj < n; jj++)
            {
                set(i+ii, j+jj, B.get(ii, jj));
            }
        }
    }
76610
public void setColumn(int j, Vector column) {
        if (rows != column.length()) {
            fail("Wrong vector length: " + column.length() + ". Should be: " + rows + ".");
        }

        for (int i = 0; i < column.length(); i++) {
            set(i, j, column.get(i));
        }
    }
944200
public int get(int i, int j) {
        if (i < 0 || i >= size()) {
            throw new IllegalArgumentException("Invalid index: i = " + i);
        }

        int[] x = get(i).x;
        if (x.length == 0) {
            return 0;
        }
        
        int low = 0;
        int high = x.length - 1;
        int mid = (low + high) / 2;
        
        while (j != x[mid] && low <= high) {
            mid = (low + high) / 2;
            if (j < x[mid]) 
                high = mid - 1;
            else
                low = mid + 1;
        }
        
        if (j == x[mid]) {
            return 1;
        } else {
            return 0;
        }
    }
1373707
public Stream<IntPair> adjacent8Points(final int i, final int j) {
        final IntPair up = i == 0 ? null : IntPair.of(i - 1, j);
        final IntPair right = j == cols - 1 ? null : IntPair.of(i, j + 1);
        final IntPair down = i == rows - 1 ? null : IntPair.of(i + 1, j);
        final IntPair left = j == 0 ? null : IntPair.of(i, j - 1);

        final IntPair leftUp = i > 0 && j > 0 ? IntPair.of(i - 1, j - 1) : null;
        final IntPair rightUp = i > 0 && j < cols - 1 ? IntPair.of(i - 1, j + 1) : null;
        final IntPair rightDown = i < rows - 1 && j < cols - 1 ? IntPair.of(j + 1, j + 1) : null;
        final IntPair leftDown = i < rows - 1 && j > 0 ? IntPair.of(i + 1, j - 1) : null;

        return Stream.of(leftUp, up, rightUp, right, rightDown, down, leftDown, left);
    }
1327699
public void updateAt(int i, int j, MatrixFunction function) {
        set(i, j, function.evaluate(i, j, get(i, j)));
    }
254435
public void setPosition (float x, float y, float z)
    {
        if (_source != null) {
            _source.setPosition(x, y, z);
        }
        _px = x;
        _py = y;
        _pz = z;
    }
1285233
public void set(int i, int j, T v)
    {
        consumer.set(i, j, v);
    }
1013048
public void add(int i, int j, double v)
    {
        consumer.set(i, j, supplier.get(i, j) + v);
    }
1307938
public synchronized void setValue(int i, int value) {

        if (i < 0 || i >= count) {
            throw new IndexOutOfBoundsException();
        }

        if (sortOnValues) {
            sorted = false;
        }

        values[i] = value;
    }