blat: lib/bits.c File Reference

Bits* bitAlloc ( int bitCount )

Definition at line 51 of file bits.c.

Referenced by maskFromUpperCaseSeq(), and nibInput().

00053 {
00054 int byteCount = ((bitCount+7)>>3);
00055 return needLargeZeroedMem(byteCount);
00056 }

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

Definition at line 218 of file bits.c.

00220 {
00221 int byteCount = ((bitCount+7)>>3);
00222 while (--byteCount >= 0)
00223     {
00224     *a = (*a & *b++);
00225     a++;
00226     }
00227 }

void bitClear	(	Bits *	b,
		int	bitCount
	)

Definition at line 190 of file bits.c.

References zeroBytes().

00192 {
00193 int byteCount = ((bitCount+7)>>3);
00194 zeroBytes(b, byteCount);
00195 }

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void bitClearOne	(	Bits *	b,
		int	bitIx
	)

Definition at line 87 of file bits.c.

References oneBit.

00089 {
00090 b[bitIx>>3] &= ~oneBit[bitIx&7];
00091 }

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

Definition at line 197 of file bits.c.

References leftMask, and rightMask.

00199 {
00200 int endIx = (startIx + bitCount - 1);
00201 int startByte = (startIx>>3);
00202 int endByte = (endIx>>3);
00203 int startBits = (startIx&7);
00204 int endBits = (endIx&7);
00205 int i;
00206 
00207 if (startByte == endByte)
00208     {
00209     b[startByte] &= ~(leftMask[startBits] & rightMask[endBits]);
00210     return;
00211     }
00212 b[startByte] &= ~leftMask[startBits];
00213 for (i = startByte+1; i<endByte; ++i)
00214     b[i] = 0x00;
00215 b[endByte] &= ~rightMask[endBits];
00216 }

Bits* bitClone	(	Bits *	orig,
		int	bitCount
	)

Definition at line 66 of file bits.c.

References needLargeZeroedMem().

Referenced by cloneDnaSeq().

00068 {
00069 int byteCount = ((bitCount+7)>>3);
00070 Bits* bits = needLargeZeroedMem(byteCount);
00071 memcpy(bits, orig, byteCount);
00072 return bits;
00073 }

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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().

00123 {
00124 int endIx = (startIx + bitCount - 1);
00125 int startByte = (startIx>>3);
00126 int endByte = (endIx>>3);
00127 int startBits = (startIx&7);
00128 int endBits = (endIx&7);
00129 int i;
00130 int count = 0;
00131 
00132 if (!inittedBitsInByte)
00133     bitsInByteInit();
00134 if (startByte == endByte)
00135     return bitsInByte[b[startByte] & leftMask[startBits] & rightMask[endBits]];
00136 count = bitsInByte[b[startByte] & leftMask[startBits]];
00137 for (i = startByte+1; i<endByte; ++i)
00138     count += bitsInByte[b[i]];
00139 count += bitsInByte[b[endByte] & rightMask[endBits]];
00140 return count;
00141 }

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int bitFind	(	Bits *	b,
		int	startIx,
		boolean	val,
		int	bitCount
	)

Definition at line 143 of file bits.c.

References bitReadOne().

Referenced by bitFindClear(), and bitFindSet().

00145 {
00146 unsigned char notByteVal = val ? 0 : 0xff;
00147 int iBit = startIx;
00148 int endByte = ((bitCount-1)>>3);
00149 int iByte;
00150 
00151 /* scan initial byte */
00152 while (((iBit & 7) != 0) && (iBit < bitCount))
00153     {
00154     if (bitReadOne(b, iBit) == val)
00155         return iBit;
00156     iBit++;
00157     }
00158 
00159 /* scan byte at a time, if not already in last byte */
00160 iByte = (iBit >> 3);
00161 if (iByte < endByte)
00162     {
00163     while ((iByte < endByte) && (b[iByte] == notByteVal))
00164         iByte++;
00165     iBit = iByte << 3;
00166     }
00167 
00168 /* scan last byte */
00169 while (iBit < bitCount)
00170     {
00171     if (bitReadOne(b, iBit) == val)
00172         return iBit;
00173     iBit++;
00174     }
00175  return bitCount;  /* not found */
00176 }

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

Definition at line 184 of file bits.c.

References bitFind(), and FALSE.

00186 {
00187 return bitFind(b, startIx, FALSE, bitCount);
00188 }

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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().

00180 {
00181 return bitFind(b, startIx, TRUE, bitCount);
00182 }

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void bitFree ( Bits ** pB )

Definition at line 75 of file bits.c.

References freez().

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

00077 {
00078 freez(pB);
00079 }

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void bitNot	(	Bits *	a,
		int	bitCount
	)

Definition at line 250 of file bits.c.

00252 {
00253 int byteCount = ((bitCount+7)>>3);
00254 while (--byteCount >= 0)
00255     {
00256     *a = ~*a;
00257     a++;
00258     }
00259 }

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

Definition at line 229 of file bits.c.

00231 {
00232 int byteCount = ((bitCount+7)>>3);
00233 while (--byteCount >= 0)
00234     {
00235     *a = (*a | *b++);
00236     a++;
00237     }
00238 }

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

Definition at line 261 of file bits.c.

References bitReadOne().

00264 {
00265 int i;
00266 for (i = startIx; i < bitCount; i++)
00267     {
00268     if (bitReadOne(a, i))
00269         fputc('1', out);
00270     else
00271         fputc('0', out);
00272     }
00273 fputc('\n', out);
00274 }

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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().

00117 {
00118 return (b[bitIx>>3] & oneBit[bitIx&7]) != 0;
00119 }

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

Definition at line 58 of file bits.c.

References needLargeZeroedMemResize().

00060 {
00061 int byteCount = ((bitCount+7)>>3);
00062 int newByteCount = ((newBitCount+7)>>3);
00063 return needLargeZeroedMemResize(b, byteCount, newByteCount);
00064 }

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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().

00083 {
00084 b[bitIx>>3] |= oneBit[bitIx&7];
00085 }

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

Definition at line 93 of file bits.c.

References leftMask, and rightMask.

00095 {
00096 int endIx = (startIx + bitCount - 1);
00097 int startByte = (startIx>>3);
00098 int endByte = (endIx>>3);
00099 int startBits = (startIx&7);
00100 int endBits = (endIx&7);
00101 int i;
00102 
00103 if (startByte == endByte)
00104     {
00105     b[startByte] |= (leftMask[startBits] & rightMask[endBits]);
00106     return;
00107     }
00108 b[startByte] |= leftMask[startBits];
00109 for (i = startByte+1; i<endByte; ++i)
00110     b[i] = 0xff;
00111 b[endByte] |= rightMask[endBits];
00112 }

void bitsInByteInit ( )

Definition at line 19 of file bits.c.

References bitsInByte, inittedBitsInByte, and TRUE.

Referenced by bitCountRange().

00021 {
00022 int i;
00023 
00024 if (!inittedBitsInByte)
00025     {
00026     inittedBitsInByte = TRUE;
00027     for (i=0; i<256; ++i)
00028         {
00029         int count = 0;
00030         if (i&1)
00031             count = 1;
00032         if (i&2)
00033             ++count;
00034         if (i&4)
00035             ++count;
00036         if (i&8)
00037             ++count;
00038         if (i&0x10)
00039             ++count;
00040         if (i&0x20)
00041             ++count;
00042         if (i&0x40)
00043             ++count;
00044         if (i&0x80)
00045             ++count;
00046         bitsInByte[i] = count;
00047         }
00048     }
00049 }

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

Definition at line 240 of file bits.c.

00241 {
00242 int byteCount = ((bitCount+7)>>3);
00243 while (--byteCount >= 0)
00244     {
00245     *a = (*a ^ *b++);
00246     a++;
00247     }
00248 }

int bitsInByte[256]

Definition at line 15 of file bits.c.

Referenced by bitCountRange(), and bitsInByteInit().

boolean inittedBitsInByte = FALSE [static]

Definition at line 17 of file bits.c.

Referenced by bitCountRange(), and bitsInByteInit().

Bits leftMask[8] = {0xFF, 0x7F, 0x3F, 0x1F, 0xF, 0x7, 0x3, 0x1,} [static]

Definition at line 13 of file bits.c.

Referenced by bitClearRange(), bitCountRange(), and bitSetRange().

Bits oneBit[8] = { 0x80, 0x40, 0x20, 0x10, 0x8, 0x4, 0x2, 0x1} [static]

Definition at line 12 of file bits.c.

Referenced by bitClearOne(), bitReadOne(), and bitSetOne().

char const rcsid[] = "$Id: bits.c,v 1.19 2006/02/28 05:40:46 markd Exp $" [static]

Definition at line 9 of file bits.c.

Bits rightMask[8] = {0x80, 0xC0, 0xE0, 0xF0, 0xF8, 0xFC, 0xFE, 0xFF,} [static]

Definition at line 14 of file bits.c.

Referenced by bitClearRange(), bitCountRange(), and bitSetRange().


Functions
void	bitsInByteInit ()
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	bitFind (Bits *b, int startIx, boolean val, 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)
Variables
static char const	rcsid [] = "$Id: bits.c,v 1.19 2006/02/28 05:40:46 markd Exp $"
static Bits	oneBit [8] = { 0x80, 0x40, 0x20, 0x10, 0x8, 0x4, 0x2, 0x1}
static Bits	leftMask [8] = {0xFF, 0x7F, 0x3F, 0x1F, 0xF, 0x7, 0x3, 0x1,}
static Bits	rightMask [8] = {0x80, 0xC0, 0xE0, 0xF0, 0xF8, 0xFC, 0xFE, 0xFF,}
int	bitsInByte [256]
static boolean	inittedBitsInByte = FALSE

lib/bits.c File Reference

Functions

Variables

Function Documentation

Variable Documentation