inc/dnautil.h File Reference

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Defines
#define	T_BASE_VAL   0
#define	U_BASE_VAL   0
#define	C_BASE_VAL   1
#define	A_BASE_VAL   2
#define	G_BASE_VAL   3
#define	N_BASE_VAL   4
#define	MASKED_BASE_BIT   8
Typedefs
typedef char	DNA
typedef char	AA
typedef char	BIOPOL
typedef char	Codon
Enumerations
enum	dnaCase { dnaUpper, dnaLower, dnaMixed }
Functions
void	dnaUtilOpen ()
void	complement (DNA *dna, long length)
void	reverseComplement (DNA *dna, long length)
long	reverseOffset (long offset, long arraySize)
void	reverseIntRange (int *pStart, int *pEnd, int size)
void	reverseUnsignedRange (unsigned *pStart, unsigned *pEnd, int size)
void	toRna (DNA *dna)
AA	lookupCodon (DNA *dna)
boolean	isStopCodon (DNA *dna)
boolean	isKozak (char *dna, int dnaSize, int pos)
boolean	isReallyStopCodon (char *dna, boolean selenocysteine)
AA	lookupMitoCodon (DNA *dna)
Codon	codonVal (DNA *start)
DNA *	valToCodon (int val)
void	dnaTranslateSome (DNA *dna, char *out, int outSize)
char *	skipIgnoringDash (char *a, int size, bool skipTrailingDash)
int	countNonDash (char *a, int size)
int	nextPowerOfFour (long x)
long	dnaFilteredSize (char *rawDna)
long	aaFilteredSize (char *rawDna)
void	dnaFilter (char *in, DNA *out)
void	aaFilter (char *in, DNA *out)
void	dnaFilterToN (char *in, DNA *out)
void	upperToN (char *s, int size)
void	lowerToN (char *s, int size)
void	dnaBaseHistogram (DNA *dna, int dnaSize, int histogram[4])
void	dnaMixedCaseFilter (char *in, DNA *out)
bits32	packDna16 (DNA *in)
bits16	packDna8 (DNA *in)
UBYTE	packDna4 (DNA *in)
void	unpackDna (bits32 *tiles, int tileCount, DNA *out)
void	unpackDna4 (UBYTE *tiles, int byteCount, DNA *out)
void	unalignedUnpackDna (bits32 *tiles, int start, int size, DNA *unpacked)
int	intronOrientationMinSize (DNA *iStart, DNA *iEnd, int minIntronSize)
int	intronOrientation (DNA *iStart, DNA *iEnd)
int	dnaScore2 (DNA a, DNA b)
int	dnaScoreMatch (DNA *a, DNA *b, int size)
int	aaScore2 (AA a, AA b)
int	aaScoreMatch (AA *a, AA *b, int size)
int	dnaOrAaScoreMatch (char *a, char *b, int size, int matchScore, int mismatchScore, char ignore)
void	writeSeqWithBreaks (FILE *f, char *letters, int letterCount, int maxPerLine)
int	tailPolyASizeLoose (DNA *dna, int size)
int	headPolyTSizeLoose (DNA *dna, int size)
int	maskTailPolyA (DNA *dna, int size)
int	maskHeadPolyT (DNA *dna, int size)
boolean	isDna (char *poly, int size)
boolean	isAllDna (char *poly, int size)
Variables
DNA	ntChars [256]
AA	aaChars [256]
int	ntVal [256]
int	aaVal [256]
int	ntValLower [256]
int	ntValUpper [256]
int	ntValNoN [256]
int	ntVal5 [256]
DNA	valToNt []
DNA	ntMixedCaseChars [256]
DNA	ntCompTable [256]
int	ntValMasked [256]
DNA	valToNtMasked [256]

---

Define Documentation

#define A_BASE_VAL   2

Definition at line 26 of file dnautil.h.

Referenced by initNtLookup(), initNtVal(), isKozak(), makeMatchTable(), and makeWobbleMatchTable().

#define C_BASE_VAL   1

Definition at line 25 of file dnautil.h.

Referenced by calcGcRatio(), initNtLookup(), initNtVal(), makeMatchTable(), and makeWobbleMatchTable().

#define G_BASE_VAL   3

Definition at line 27 of file dnautil.h.

Referenced by calcGcRatio(), initNtLookup(), initNtVal(), isKozak(), makeMatchTable(), and makeWobbleMatchTable().

#define MASKED_BASE_BIT   8

Definition at line 69 of file dnautil.h.

Referenced by initNtVal(), nibInput(), and nibOutput().

#define N_BASE_VAL   4

Definition at line 28 of file dnautil.h.

Referenced by initNtVal().

#define T_BASE_VAL   0

Definition at line 23 of file dnautil.h.

Referenced by initNtLookup(), initNtVal(), makeMatchTable(), and makeWobbleMatchTable().

#define U_BASE_VAL   0

Definition at line 24 of file dnautil.h.

Referenced by initNtVal().

---

Typedef Documentation

typedef char AA

Definition at line 31 of file dnautil.h.

typedef char BIOPOL

Definition at line 32 of file dnautil.h.

typedef char Codon

Definition at line 98 of file dnautil.h.

typedef char DNA

Definition at line 30 of file dnautil.h.

---

Enumeration Type Documentation

enum dnaCase

Enumerator:

dnaUpper
dnaLower
dnaMixed

Definition at line 92 of file dnautil.h.

{dnaUpper,dnaLower,dnaMixed,};

---

Function Documentation

void aaFilter	(	char *	in,
		DNA *	out
	)

Definition at line 599 of file dnautil.c.

References aaChars, and dnaOrAaFilter().

Referenced by startServer().

{
dnaOrAaFilter(in, out, aaChars);
}

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long aaFilteredSize

(

char *

rawDna

)

Definition at line 593 of file dnautil.c.

References aaChars, and dnaOrAaFilteredSize().

Referenced by startServer().

{
return dnaOrAaFilteredSize(raw, aaChars);
}

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int aaScore2	(	AA	a,
		AA	b
	)

Definition at line 801 of file dnautil.c.

Referenced by clumpToHspRange(), and findCrossover().

{
if (a == 'X' || b == 'X') return 0;
if (a == b) return 2;
else return -1;
}

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int aaScoreMatch	(	AA *	a,
		AA *	b,
		int	size
	)

Definition at line 809 of file dnautil.c.

References dnaOrAaScoreMatch().

Referenced by ffScoreSomething(), findCrossover(), and scoreAli().

{
return dnaOrAaScoreMatch(a, b, size, 2, -1, 'X');
}

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Codon codonVal

(

DNA *

start

)

Definition at line 289 of file dnautil.c.

References ntVal.

{
int v1,v2,v3;

if ((v1 = ntVal[(int)start[0]]) < 0)
    return -1;
if ((v2 = ntVal[(int)start[1]]) < 0)
    return -1;
if ((v3 = ntVal[(int)start[2]]) < 0)
    return -1;
return ((v1<<4) + (v2<<2) + v3);
}

void complement	(	DNA *	dna,
		long	length
	)

Definition at line 431 of file dnautil.c.

References initNtCompTable(), inittedCompTable, and ntCompTable.

Referenced by reverseComplement().

{
int i;

if (!inittedCompTable) initNtCompTable();
for (i=0; i<length; ++i)
    {
    *dna = ntCompTable[(int)*dna];
    ++dna;
    }
}

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int countNonDash	(	char *	a,
		int	size
	)

Definition at line 511 of file dnautil.c.

Referenced by axtCheck(), axtSubsetOnT(), axtTransPosToQ(), and mafSubsetE().

{
int count = 0;
int i;
for (i=0; i<size; ++i)
    if (a[i] != '-') 
        ++count;
return count;
}

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void dnaBaseHistogram	(	DNA *	dna,
		int	dnaSize,
		int	histogram[4]
	)

Definition at line 632 of file dnautil.c.

References ntVal, and zeroBytes().

Referenced by dnaMark0(), and makeFreqTable().

{
int val;
zeroBytes(histogram, 4*sizeof(int));
while (--dnaSize >= 0)
    {
    if ((val = ntVal[(int)*dna++]) >= 0)
        ++histogram[val];
    }
}

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void dnaFilter	(	char *	in,
		DNA *	out
	)

Definition at line 568 of file dnautil.c.

References dnaOrAaFilter(), and ntChars.

Referenced by gfPcrMakePrimer(), and startServer().

{
dnaOrAaFilter(in, out, ntChars);
}

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long dnaFilteredSize

(

char *

rawDna

)

Definition at line 562 of file dnautil.c.

References dnaOrAaFilteredSize(), and ntChars.

Referenced by gfPcrMakePrimer(), and startServer().

{
return dnaOrAaFilteredSize(rawDna, ntChars);
}

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void dnaFilterToN	(	char *	in,
		DNA *	out
	)

Definition at line 574 of file dnautil.c.

References initNtChars(), and ntChars.

Referenced by doBlat().

{
DNA c;
initNtChars();
while ((c = *in++) != 0)
    {
    if ((c = ntChars[(int)c]) != 0) *out++ = c;
    else *out++ = 'n';
    }
*out++ = 0;
}

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void dnaMixedCaseFilter	(	char *	in,
		DNA *	out
	)

Definition at line 587 of file dnautil.c.

References dnaOrAaFilter(), and ntMixedCaseChars.

{
dnaOrAaFilter(in, out, ntMixedCaseChars);
}

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int dnaOrAaScoreMatch	(	char *	a,
		char *	b,
		int	size,
		int	matchScore,
		int	mismatchScore,
		char	ignore
	)

Definition at line 773 of file dnautil.c.

Referenced by aaScoreMatch(), bioScoreMatch(), and dnaScoreMatch().

{
int i;
int score = 0;
for (i=0; i<size; ++i)
    {
    char aa = a[i];
    char bb = b[i];
    if (aa == ignore || bb == ignore)
        continue;
    if (aa == bb)
        score += matchScore;
    else
        score += mismatchScore;
    }
return score;
}

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int dnaScore2	(	DNA	a,
		DNA	b
	)

Definition at line 765 of file dnautil.c.

Referenced by clumpToHspRange(), and findCrossover().

{
if (a == 'n' || b == 'n') return 0;
if (a == b) return 1;
else return -1;
}

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int dnaScoreMatch	(	DNA *	a,
		DNA *	b,
		int	size
	)

Definition at line 793 of file dnautil.c.

References dnaOrAaScoreMatch().

Referenced by cdaAliFromFfAli(), expandLeft(), expandRight(), ffScoreSomeAlis(), ffScoreSomething(), findCrossover(), rangeScore(), reconsiderAlignedGaps(), and scoreAli().

{
return dnaOrAaScoreMatch(a, b, size, 1, -1, 'n');
}

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void dnaTranslateSome	(	DNA *	dna,
		char *	out,
		int	outSize
	)

Definition at line 311 of file dnautil.c.

References lookupCodon().

{
int i;
int dnaSize;
int protSize = 0;

outSize -= 1;  /* Room for terminal zero */
dnaSize = strlen(dna);
for (i=0; i<dnaSize-2; i+=3)
    {
    if (protSize >= outSize)
        break;
    if ((out[protSize++] = lookupCodon(dna+i)) == 0)
        break;
    }
out[protSize] = 0;
}

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void dnaUtilOpen

(

)

Definition at line 1068 of file dnautil.c.

References checkSizeTypes(), FALSE, initAaVal(), initNtChars(), initNtCompTable(), initNtMixedCaseChars(), initNtVal(), and TRUE.

Referenced by axtScoreSym(), axtScoreSymFilterRepeats(), dnaOrAaFilter(), dnaOrAaFilteredSize(), faFastReadNext(), faMixedSpeedReadNext(), faReadMixedNext(), faToDna(), faToProtein(), ffFind(), gffOpen(), htmShell(), htmShellWithHead(), isAllDna(), isDna(), main(), nextSeqFromMem(), nibOpenVerify(), nibStreamOpen(), twoBitReadSeqFragExt(), and unalignedUnpackDna().

{
static boolean opened = FALSE;
if (!opened)
    {
    checkSizeTypes();
    initNtVal();
    initAaVal();
    initNtChars();
    initNtMixedCaseChars();
    initNtCompTable();
    opened = TRUE;
    }
}

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int headPolyTSizeLoose	(	DNA *	dna,
		int	size
	)

Definition at line 960 of file dnautil.c.

References FALSE, findHeadPolyTMaybeMask(), and TRUE.

{
return findHeadPolyTMaybeMask(dna, size, FALSE, TRUE);
}

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int intronOrientation	(	DNA *	iStart,
		DNA *	iEnd
	)

Definition at line 757 of file dnautil.c.

References intronOrientationMinSize().

Referenced by ffIntronOrientation(), ffOneIntronOrientation(), pslHasIntron(), pslWeightedIntronOrientation(), and tradeMismatchToCloseSpliceGap().

{
return intronOrientationMinSize(iStart, iEnd, 32);
}

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int intronOrientationMinSize	(	DNA *	iStart,
		DNA *	iEnd,
		int	minIntronSize
	)

Definition at line 738 of file dnautil.c.

Referenced by intronOrientation().

{
if (iEnd - iStart < minIntronSize)
    return 0;
if (iStart[0] == 'g' && iStart[1] == 't' && iEnd[-2] == 'a' && iEnd[-1] == 'g')
    {
    return 1;
    }
else if (iStart[0] == 'c' && iStart[1] == 't' && iEnd[-2] == 'a' && iEnd[-1] == 'c')
    {
    return -1;
    }
else
    return 0;
}

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boolean isAllDna	(	char *	poly,
		int	size
	)

Definition at line 991 of file dnautil.c.

References dnaUtilOpen(), FALSE, ntChars, and TRUE.

{
int i;

if (size <= 1)
    return FALSE;
dnaUtilOpen();
for (i=0; i<size-1; ++i)
    {
    if (ntChars[(int)poly[i]] == 0) 
        return FALSE;
    }
return TRUE;
}

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boolean isDna	(	char *	poly,
		int	size
	)

Definition at line 976 of file dnautil.c.

References dnaUtilOpen(), ntChars, and round.

Referenced by faReadAllIntoHash(), and seqIsDna().

{
int i;
int dnaCount = 0;

dnaUtilOpen();
for (i=0; i<size; ++i)
    {
    if (ntChars[(int)poly[i]]) 
        dnaCount += 1;
    }
return (dnaCount >= round(0.9 * size));
}

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boolean isKozak	(	char *	dna,
		int	dnaSize,
		int	pos
	)

Definition at line 226 of file dnautil.c.

References A_BASE_VAL, FALSE, G_BASE_VAL, lookupCodon(), ntVal, and TRUE.

{
if (lookupCodon(dna+pos) != 'M')
   {
   return FALSE;
   }
if (pos + 3 < dnaSize)
    {
    if (ntVal[(int)dna[pos+3]] == G_BASE_VAL)
        return TRUE;
    }
if (pos >= 3)
    {
    int c = ntVal[(int)dna[pos-3]];
    if (c == A_BASE_VAL || c == G_BASE_VAL)
        return TRUE;
    }
return FALSE;
}

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boolean isReallyStopCodon	(	char *	dna,
		boolean	selenocysteine
	)

Definition at line 248 of file dnautil.c.

References lookupCodon(), and lookupMitoCodon().

{
if (selenocysteine)
    {
    /* Luckily the mitochondria *also* replaces TGA with 
     * something else, even though it isn't selenocysteine */
    return lookupMitoCodon(dna) == 0;
    }
else
    {
    return lookupCodon(dna) == 0;
    }
}

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boolean isStopCodon

(

DNA *

dna

)

Definition at line 220 of file dnautil.c.

References lookupCodon().

{
return lookupCodon(dna) == 0;
}

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AA lookupCodon

(

DNA *

dna

)

Definition at line 200 of file dnautil.c.

References codonTable, initNtVal(), inittedNtVal, ntVal, and codonTable::protCode.

Referenced by bafWriteLine(), dnaTranslateSome(), isKozak(), isReallyStopCodon(), isStopCodon(), pslShowAlignmentStranded(), and translateSeqN().

{
int ix;
int i;
char c;

if (!inittedNtVal)
    initNtVal();
ix = 0;
for (i=0; i<3; ++i)
    {
    int bv = ntVal[(int)dna[i]];
    if (bv<0)
        return 'X';
    ix = (ix<<2) + bv;
    }
c = codonTable[ix].protCode;
return c;
}

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AA lookupMitoCodon

(

DNA *

dna

)

Definition at line 268 of file dnautil.c.

References codonTable, initNtVal(), inittedNtVal, codonTable::mitoCode, and ntVal.

Referenced by isReallyStopCodon().

{
int ix;
int i;
char c;

if (!inittedNtVal)
    initNtVal();
ix = 0;
for (i=0; i<3; ++i)
    {
    int bv = ntVal[(int)dna[i]];
    if (bv<0)
        return 'X';
    ix = (ix<<2) + bv;
    }
c = codonTable[ix].mitoCode;
c = toupper(c);
return c;
}

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void lowerToN	(	char *	s,
		int	size
	)

Definition at line 618 of file dnautil.c.

{
char c;
int i;
for (i=0; i<size; ++i)
    {
    c = s[i];
    if (islower(c))
        s[i] = 'N';
    }
}

int maskHeadPolyT	(	DNA *	dna,
		int	size
	)

Definition at line 969 of file dnautil.c.

References FALSE, findHeadPolyTMaybeMask(), and TRUE.

Referenced by trimSeq().

{
return findHeadPolyTMaybeMask(dna, size, TRUE, FALSE);
}

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int maskTailPolyA	(	DNA *	dna,
		int	size
	)

Definition at line 896 of file dnautil.c.

References FALSE, findTailPolyAMaybeMask(), and TRUE.

Referenced by trimSeq().

{
return findTailPolyAMaybeMask(dna, size, TRUE, FALSE);
}

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int nextPowerOfFour

(

long

x

)

Definition at line 522 of file dnautil.c.

Referenced by findBestAli(), and rwFindTilesBetween().

{
int count = 1;
while (x > 4)
    {
    count += 1;
    x >>= 2;
    }
return count;
}

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bits32 packDna16

(

DNA *

in

)

Definition at line 645 of file dnautil.c.

References bits32, and ntValNoN.

Referenced by makeGoodTile(), newNt4(), and saveNt4().

{
bits32 out = 0;
int count = 16;
int bVal;
while (--count >= 0)
    {
    bVal = ntValNoN[(int)*in++];
    out <<= 2;
    out += bVal;
    }
return out;
}

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UBYTE packDna4

(

DNA *

in

)

Definition at line 675 of file dnautil.c.

References ntValNoN, and UBYTE.

Referenced by twoBitFromDnaSeq().

{
UBYTE out = 0;
int count = 4;
int bVal;
while (--count >= 0)
    {
    bVal = ntValNoN[(int)*in++];
    out <<= 2;
    out += bVal;
    }
return out;
}

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bits16 packDna8

(

DNA *

in

)

Definition at line 660 of file dnautil.c.

References bits16, and ntValNoN.

Referenced by makeGoodTile().

{
bits16 out = 0;
int count = 8;
int bVal;
while (--count >= 0)
    {
    bVal = ntValNoN[(int)*in++];
    out <<= 2;
    out += bVal;
    }
return out;
}

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void reverseComplement	(	DNA *	dna,
		long	length
	)

Definition at line 445 of file dnautil.c.

References complement(), and reverseBytes().

Referenced by axtSwap(), bigBlat(), cdaAliFromFfAli(), crudeAliFind(), dnaMotifBestStrand(), doBlat(), ffFindAndScore(), fixDirectionAndOffsets(), getWormGeneDna(), getWormGeneExonDna(), gfClient(), gfiExpandAndLoadCached(), gfMakeOoc(), gfPcrClumps(), mafFlipStrand(), outputBed(), outputFa(), outputPsl(), pcrLocalStrand(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), rcSeqs(), scoreNoninsertingExtensions(), searchOne(), transCountBothStrands(), transIndexBothStrands(), transTripleSearch(), xenAlignBig(), and xenAlignWorm().

{
reverseBytes(dna, length);
complement(dna, length);
}

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void reverseIntRange	(	int *	pStart,
		int *	pEnd,
		int	size
	)

Definition at line 460 of file dnautil.c.

Referenced by axtSwap(), chainSwap(), gfiExpandAndLoadCached(), mafFlipStrand(), mafNeedSubset(), mafSubsetE(), nextBlock(), printAxtTargetBlastTab(), pslFromAlign(), pslFromFakeFfAli(), pslHasIntron(), pslRangeTreeOverlap(), pslRcBoth(), pslRecalcBounds(), pslTrimToQueryRange(), pslTrimToTargetRange(), setPslBounds(), and tabBlastOut().

{
int temp;
temp = *pStart;
*pStart = size - *pEnd;
*pEnd = size - temp;
}

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long reverseOffset	(	long	offset,
		long	arraySize
	)

Definition at line 453 of file dnautil.c.

Referenced by cdaRcOne(), fixDirectionAndOffsets(), gdfRcGene(), and rcQueryOffsetsAroundSeg().

{
return arraySize-1 - offset;
}

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void reverseUnsignedRange	(	unsigned *	pStart,
		unsigned *	pEnd,
		int	size
	)

Definition at line 470 of file dnautil.c.

{
unsigned temp;
temp = *pStart;
*pStart = size - *pEnd;
*pEnd = size - temp;
}

char* skipIgnoringDash	(	char *	a,
		int	size,
		bool	skipTrailingDash
	)

Definition at line 496 of file dnautil.c.

Referenced by axtSubsetOnT(), axtTransPosToQ(), and mafSubsetE().

{
while (size > 0)
    {
    if (*a++ != '-')
        --size;
    }
if (skipTrailingDash)
    while (*a == '-')
       ++a;
return a;
}

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int tailPolyASizeLoose	(	DNA *	dna,
		int	size
	)

Definition at line 888 of file dnautil.c.

References FALSE, findTailPolyAMaybeMask(), and TRUE.

{
return findTailPolyAMaybeMask(dna, size, FALSE, TRUE);
}

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void toRna

(

DNA *

dna

)

Definition at line 480 of file dnautil.c.

{
DNA c;
for (;;)
    {
    c = *dna;
    if (c == 't')
        *dna = 'u';
    else if (c == 'T')
        *dna = 'U';
    else if (c == 0)
        break;
    ++dna;
    }
}

void unalignedUnpackDna	(	bits32 *	tiles,
		int	start,
		int	size,
		DNA *	unpacked
	)

Definition at line 169 of file nt4.c.

References bits32, dnaUtilOpen(), unpackDna(), unpackLeftSide(), unpackMidWord(), and unpackRightSide().

Referenced by nt4LoadPart(), and nt4Unpack().

{
DNA *pt = unpacked;
int sizeLeft = size;
int firstBases, middleBases;
bits32 *startTile, *endTile;

dnaUtilOpen();

/* See if all data is in a single word. */
startTile = tiles + (start>>4);
endTile = tiles + ((start + size - 1)>>4);
if (startTile == endTile)
    {
    unpackMidWord(*startTile, start&0xf, size, unpacked);
    return;
    }

/* Skip over initial stuff. */
tiles = startTile;

/* See if just have one tile to 
 * Unpack the right hand side of the first tile. */
firstBases = (16 - (start&0xf));
unpackRightSide(*tiles, firstBases, pt);
pt += firstBases;
sizeLeft -= firstBases;
tiles += 1;

/* Unpack all of the middle tiles. */
middleBases = (sizeLeft&0x7ffffff0);
unpackDna(tiles, middleBases>>4, pt);
pt += middleBases;
sizeLeft -= middleBases;
tiles += (middleBases>>4);

/* Unpack the left side of last tile. */
if (sizeLeft > 0)
    unpackLeftSide(*tiles, sizeLeft, pt);
pt += sizeLeft;

/* Add trailing zero to make it a DNA string. */
assert(pt == unpacked+size);
*pt = 0;
}

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void unpackDna	(	bits32 *	tiles,
		int	tileCount,
		DNA *	out
	)

Definition at line 690 of file dnautil.c.

References bits32, and valToNt.

Referenced by unalignedUnpackDna().

{
int i, j;
bits32 tile;

for (i=0; i<tileCount; ++i)
    {
    tile = tiles[i];
    for (j=15; j>=0; --j)
        {
        out[j] = valToNt[tile & 0x3];
        tile >>= 2;
        }
    out += 16;
    }
}

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void unpackDna4	(	UBYTE *	tiles,
		int	byteCount,
		DNA *	out
	)

Definition at line 708 of file dnautil.c.

References UBYTE, and valToNt.

{
int i, j;
UBYTE tile;

for (i=0; i<byteCount; ++i)
    {
    tile = tiles[i];
    for (j=3; j>=0; --j)
        {
        out[j] = valToNt[tile & 0x3];
        tile >>= 2;
        }
    out += 4;
    }
}

void upperToN	(	char *	s,
		int	size
	)

Definition at line 605 of file dnautil.c.

Referenced by bigBlat(), maskNucSeqList(), readMaskedNib(), and readMaskedTwoBit().

{
char c;
int i;
for (i=0; i<size; ++i)
    {
    c = s[i];
    if (isupper(c))
        s[i] = 'n';
    }
}

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DNA* valToCodon

(

int

val

)

Definition at line 304 of file dnautil.c.

References codonTable::codon, and codonTable.

{
assert(val >= 0 && val < 64);
return codonTable[val].codon;
}

void writeSeqWithBreaks	(	FILE *	f,
		char *	letters,
		int	letterCount,
		int	maxPerLine
	)

Definition at line 815 of file dnautil.c.

References mustWrite().

Referenced by faWriteNext().

{
int lettersLeft = letterCount;
int lineSize;
while (lettersLeft > 0)
    {
    lineSize = lettersLeft;
    if (lineSize > maxPerLine)
        lineSize = maxPerLine;
    mustWrite(f, letters, lineSize);
    fputc('\n', f);
    letters += lineSize;
    lettersLeft -= lineSize;
    }
}

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Variable Documentation

AA aaChars[256]

Definition at line 1014 of file dnautil.c.

Referenced by aaFilter(), aaFilteredSize(), faToProtein(), initAaVal(), and nextSeqFromMem().

int aaVal[256]

Definition at line 1011 of file dnautil.c.

Referenced by gfPepTile(), gfSegmentedFindNearHits(), gfStraightFindNearHits(), and initAaVal().

DNA ntChars[256]

Definition at line 333 of file dnautil.c.

Referenced by dnaFilter(), dnaFilteredSize(), dnaFilterToN(), faFastReadNext(), faReadMixedNext(), faToDna(), gffReadDna(), initNtChars(), isAllDna(), isDna(), and nextSeqFromMem().

DNA ntCompTable[256]

Definition at line 380 of file dnautil.c.

Referenced by complement(), and initNtCompTable().

DNA ntMixedCaseChars[256]

Definition at line 353 of file dnautil.c.

Referenced by dnaMixedCaseFilter(), and initNtMixedCaseChars().

int ntVal[256]

Definition at line 121 of file dnautil.c.

Referenced by badPcrPrimerSeq(), calcGcRatio(), codonFindFrame(), codonVal(), dnaBaseHistogram(), dnaMark1(), dnaMarkTriple(), dnaMatchEntropy(), ffHashFuncN(), fillInMatchEtc(), findImprobableOligo(), gfSegmentedFindNearHits(), gfStraightFindNearHits(), initNtVal(), isKozak(), lookupCodon(), lookupMitoCodon(), makeGoodTile(), oligoProb(), and unN().

int ntVal5[256]

Definition at line 124 of file dnautil.c.

Referenced by initNtVal(), nibOutput(), and nibStreamOne().

int ntValLower[256]

Definition at line 122 of file dnautil.c.

Referenced by initNtVal().

int ntValMasked[256]

Definition at line 129 of file dnautil.c.

Referenced by initNtVal(), and nibOutput().

int ntValNoN[256]

Definition at line 125 of file dnautil.c.

Referenced by addToPatSpace(), countPatSpace(), gfFastFindDnaHits(), initNtVal(), packDna16(), packDna4(), packDna8(), and patSpaceFindOne().

int ntValUpper[256]

Definition at line 123 of file dnautil.c.

Referenced by initNtVal().

DNA valToNt[]

Definition at line 126 of file dnautil.c.

Referenced by initNtVal(), makeMatchTable(), nibInput(), twoBitReadSeqFragExt(), unpackDna(), unpackDna4(), unpackLeftSide(), unpackMidWord(), and unpackRightSide().

DNA valToNtMasked[256]

Definition at line 130 of file dnautil.c.

Referenced by initNtVal(), and nibInput().

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