inc/bits.h File Reference

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Typedefs
typedef unsigned char	Bits
Functions
Bits *	bitAlloc (int bitCount)
Bits *	bitRealloc (Bits *b, int bitCount, int newBitCount)
Bits *	bitClone (Bits *orig, int bitCount)
void	bitFree (Bits **pB)
void	bitSetOne (Bits *b, int bitIx)
void	bitClearOne (Bits *b, int bitIx)
void	bitSetRange (Bits *b, int startIx, int bitCount)
boolean	bitReadOne (Bits *b, int bitIx)
int	bitCountRange (Bits *b, int startIx, int bitCount)
int	bitFindSet (Bits *b, int startIx, int bitCount)
int	bitFindClear (Bits *b, int startIx, int bitCount)
void	bitClear (Bits *b, int bitCount)
void	bitClearRange (Bits *b, int startIx, int bitCount)
void	bitAnd (Bits *a, Bits *b, int bitCount)
void	bitOr (Bits *a, Bits *b, int bitCount)
void	bitXor (Bits *a, Bits *b, int bitCount)
void	bitNot (Bits *a, int bitCount)
void	bitPrint (Bits *a, int startIx, int bitCount, FILE *out)
void	bitsInByteInit ()
Variables
int	bitsInByte [256]

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Typedef Documentation

typedef unsigned char Bits

Definition at line 9 of file bits.h.

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Function Documentation

Bits* bitAlloc

(

int

bitCount

)

Definition at line 51 of file bits.c.

References needLargeZeroedMem().

Referenced by maskFromUpperCaseSeq(), and nibInput().

{
int byteCount = ((bitCount+7)>>3);
return needLargeZeroedMem(byteCount);
}

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void bitAnd	(	Bits *	a,
		Bits *	b,
		int	bitCount
	)

Definition at line 218 of file bits.c.

{
int byteCount = ((bitCount+7)>>3);
while (--byteCount >= 0)
    {
    *a = (*a & *b++);
    a++;
    }
}

void bitClear	(	Bits *	b,
		int	bitCount
	)

Definition at line 190 of file bits.c.

References zeroBytes().

{
int byteCount = ((bitCount+7)>>3);
zeroBytes(b, byteCount);
}

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void bitClearOne	(	Bits *	b,
		int	bitIx
	)

Definition at line 87 of file bits.c.

References oneBit.

{
b[bitIx>>3] &= ~oneBit[bitIx&7];
}

void bitClearRange	(	Bits *	b,
		int	startIx,
		int	bitCount
	)

Definition at line 197 of file bits.c.

References leftMask, and rightMask.

{
int endIx = (startIx + bitCount - 1);
int startByte = (startIx>>3);
int endByte = (endIx>>3);
int startBits = (startIx&7);
int endBits = (endIx&7);
int i;

if (startByte == endByte)
    {
    b[startByte] &= ~(leftMask[startBits] & rightMask[endBits]);
    return;
    }
b[startByte] &= ~leftMask[startBits];
for (i = startByte+1; i<endByte; ++i)
    b[i] = 0x00;
b[endByte] &= ~rightMask[endBits];
}

Bits* bitClone	(	Bits *	orig,
		int	bitCount
	)

Definition at line 66 of file bits.c.

References needLargeZeroedMem().

Referenced by cloneDnaSeq().

{
int byteCount = ((bitCount+7)>>3);
Bits* bits = needLargeZeroedMem(byteCount);
memcpy(bits, orig, byteCount);
return bits;
}

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int bitCountRange	(	Bits *	b,
		int	startIx,
		int	bitCount
	)

Definition at line 121 of file bits.c.

References bitsInByte, bitsInByteInit(), inittedBitsInByte, leftMask, and rightMask.

Referenced by gfFastFindDnaHits(), gfSegmentedFindHits(), gfSegmentedFindNearHits(), gfStraightFindHits(), and gfStraightFindNearHits().

{
int endIx = (startIx + bitCount - 1);
int startByte = (startIx>>3);
int endByte = (endIx>>3);
int startBits = (startIx&7);
int endBits = (endIx&7);
int i;
int count = 0;

if (!inittedBitsInByte)
    bitsInByteInit();
if (startByte == endByte)
    return bitsInByte[b[startByte] & leftMask[startBits] & rightMask[endBits]];
count = bitsInByte[b[startByte] & leftMask[startBits]];
for (i = startByte+1; i<endByte; ++i)
    count += bitsInByte[b[i]];
count += bitsInByte[b[endByte] & rightMask[endBits]];
return count;
}

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int bitFindClear	(	Bits *	b,
		int	startIx,
		int	bitCount
	)

Definition at line 184 of file bits.c.

References bitFind(), and FALSE.

{
return bitFind(b, startIx, FALSE, bitCount);
}

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int bitFindSet	(	Bits *	b,
		int	startIx,
		int	bitCount
	)

Definition at line 178 of file bits.c.

References bitFind(), and TRUE.

Referenced by drawAfterOnOff().

{
return bitFind(b, startIx, TRUE, bitCount);
}

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void bitFree

(

Bits **

pB

)

Definition at line 75 of file bits.c.

References freez().

Referenced by freeDnaSeq(), genoFindFree(), and searchOneMaskTrim().

{
freez(pB);
}

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void bitNot	(	Bits *	a,
		int	bitCount
	)

Definition at line 250 of file bits.c.

{
int byteCount = ((bitCount+7)>>3);
while (--byteCount >= 0)
    {
    *a = ~*a;
    a++;
    }
}

void bitOr	(	Bits *	a,
		Bits *	b,
		int	bitCount
	)

Definition at line 229 of file bits.c.

{
int byteCount = ((bitCount+7)>>3);
while (--byteCount >= 0)
    {
    *a = (*a | *b++);
    a++;
    }
}

void bitPrint	(	Bits *	a,
		int	startIx,
		int	bitCount,
		FILE *	out
	)

Definition at line 261 of file bits.c.

References bitReadOne().

{
int i;
for (i = startIx; i < bitCount; i++)
    {
    if (bitReadOne(a, i))
        fputc('1', out);
    else
        fputc('0', out);
    }
fputc('\n', out);
}

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boolean bitReadOne	(	Bits *	b,
		int	bitIx
	)

Definition at line 115 of file bits.c.

References oneBit.

Referenced by bitFind(), bitPrint(), chainReadUsedSwapLf(), nibOutput(), and savePslx().

{
return (b[bitIx>>3] & oneBit[bitIx&7]) != 0;
}

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Bits* bitRealloc	(	Bits *	b,
		int	bitCount,
		int	newBitCount
	)

Definition at line 58 of file bits.c.

References needLargeZeroedMemResize().

{
int byteCount = ((bitCount+7)>>3);
int newByteCount = ((newBitCount+7)>>3);
return needLargeZeroedMemResize(b, byteCount, newByteCount);
}

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void bitSetOne	(	Bits *	b,
		int	bitIx
	)

Definition at line 81 of file bits.c.

References oneBit.

Referenced by maskFromUpperCaseSeq(), and nibInput().

{
b[bitIx>>3] |= oneBit[bitIx&7];
}

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void bitSetRange	(	Bits *	b,
		int	startIx,
		int	bitCount
	)

Definition at line 93 of file bits.c.

References leftMask, and rightMask.

{
int endIx = (startIx + bitCount - 1);
int startByte = (startIx>>3);
int endByte = (endIx>>3);
int startBits = (startIx&7);
int endBits = (endIx&7);
int i;

if (startByte == endByte)
    {
    b[startByte] |= (leftMask[startBits] & rightMask[endBits]);
    return;
    }
b[startByte] |= leftMask[startBits];
for (i = startByte+1; i<endByte; ++i)
    b[i] = 0xff;
b[endByte] |= rightMask[endBits];
}

void bitsInByteInit

(

)

Definition at line 19 of file bits.c.

References bitsInByte, inittedBitsInByte, and TRUE.

Referenced by bitCountRange().

{
int i;

if (!inittedBitsInByte)
    {
    inittedBitsInByte = TRUE;
    for (i=0; i<256; ++i)
        {
        int count = 0;
        if (i&1)
            count = 1;
        if (i&2)
            ++count;
        if (i&4)
            ++count;
        if (i&8)
            ++count;
        if (i&0x10)
            ++count;
        if (i&0x20)
            ++count;
        if (i&0x40)
            ++count;
        if (i&0x80)
            ++count;
        bitsInByte[i] = count;
        }
    }
}

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void bitXor	(	Bits *	a,
		Bits *	b,
		int	bitCount
	)

Definition at line 240 of file bits.c.

{
int byteCount = ((bitCount+7)>>3);
while (--byteCount >= 0)
    {
    *a = (*a ^ *b++);
    a++;
    }
}

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Variable Documentation

int bitsInByte[256]

Definition at line 15 of file bits.c.

Referenced by bitCountRange(), and bitsInByteInit().

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