lib/common.c File Reference

#include "common.h"
#include "errabort.h"
#include "portable.h"
#include "linefile.h"

Include dependency graph for common.c:

Go to the source code of this file.

Functions
void *	cloneMem (void *pt, size_t size)
char *	cloneStringZ (char *s, int size)
char *	cloneString (char *s)
char *	cloneLongString (char *s)
void	zeroBytes (void *vpt, int count)
void	reverseBytes (char *bytes, long length)
void	reverseInts (int *a, int length)
void	reverseUnsigned (unsigned *a, int length)
void	reverseDoubles (double *a, int length)
void	reverseStrings (char **a, int length)
void	swapBytes (char *a, char *b, int length)
int	slCount (void *list)
void *	slElementFromIx (void *list, int ix)
int	slIxFromElement (void *list, void *el)
void *	slLastEl (void *list)
void	slAddTail (void *listPt, void *node)
void	slSafeAddHead (void *listPt, void *node)
void *	slPopHead (void *vListPt)
void *	slPopTail (void *vListPt)
void *	slCat (void *va, void *vb)
void	slReverse (void *listPt)
void	slFreeList (void *listPt)
void	slSort (void *pList, int(*compare)(const void *elem1, const void *elem2))
void	slUniqify (void *pList, int(*compare)(const void *elem1, const void *elem2), void(*free)())
boolean	slRemoveEl (void *vpList, void *vToRemove)
slInt *	slIntNew (int x)
int	slIntCmp (const void *va, const void *vb)
int	slIntCmpRev (const void *va, const void *vb)
static int	doubleCmp (const void *va, const void *vb)
void	doubleSort (int count, double *array)
double	doubleMedian (int count, double *array)
slDouble *	slDoubleNew (double x)
int	slDoubleCmp (const void *va, const void *vb)
double	slDoubleMedian (struct slDouble *list)
static int	intCmp (const void *va, const void *vb)
void	intSort (int count, int *array)
int	intMedian (int count, int *array)
slName *	newSlName (char *name)
slName *	slNameNewN (char *name, int size)
int	slNameCmpCase (const void *va, const void *vb)
void	slNameSortCase (struct slName **pList)
int	slNameCmp (const void *va, const void *vb)
void	slNameSort (struct slName **pList)
boolean	slNameInList (struct slName *list, char *string)
void *	slNameFind (void *list, char *string)
int	slNameFindIx (struct slName *list, char *string)
char *	slNameStore (struct slName **pList, char *string)
slName *	slNameAddHead (struct slName **pList, char *name)
slName *	slNameAddTail (struct slName **pList, char *name)
slName *	slNameCloneList (struct slName *list)
slName *	slNameListFromString (char *s, char delimiter)
slName *	slNameLoadReal (char *fileName)
slRef *	refOnList (struct slRef *refList, void *val)
slRef *	slRefNew (void *val)
void	refAdd (struct slRef **pRefList, void *val)
void	refAddUnique (struct slRef **pRefList, void *val)
slRef *	refListFromSlList (void *list)
slPair *	slPairNew (char *name, void *val)
void	slPairAdd (struct slPair **pList, char *name, void *val)
void	slPairFree (struct slPair **pEl)
void	slPairFreeList (struct slPair **pList)
void	slPairFreeVals (struct slPair *list)
void	slPairFreeValsAndList (struct slPair **pList)
slPair *	slPairFind (struct slPair *list, char *name)
void *	slPairFindVal (struct slPair *list, char *name)
void	gentleFree (void *pt)
int	differentWord (char *s1, char *s2)
int	differentStringNullOk (char *a, char *b)
boolean	startsWith (char *start, char *string)
boolean	startsWithWord (char *firstWord, char *line)
char *	rStringIn (char *needle, char *haystack)
char *	stringBetween (char *start, char *end, char *haystack)
boolean	endsWith (char *string, char *end)
char	lastChar (char *s)
char *	memMatch (char *needle, int nLen, char *haystack, int hLen)
void	toUpperN (char *s, int n)
void	toLowerN (char *s, int n)
void	toggleCase (char *s, int size)
void	touppers (char *s)
char *	replaceChars (char *string, char *old, char *new)
void	tolowers (char *s)
void	subChar (char *s, char oldChar, char newChar)
void	stripChar (char *s, char c)
void	stripString (char *s, char *strip)
int	countChars (char *s, char c)
int	countCharsN (char *s, char c, int size)
int	countLeadingChars (char *s, char c)
int	countSame (char *a, char *b)
int	chopString (char *in, char *sep, char *outArray[], int outSize)
int	chopByWhite (char *in, char *outArray[], int outSize)
int	chopByChar (char *in, char chopper, char *outArray[], int outSize)
char *	skipLeadingSpaces (char *s)
char *	skipToSpaces (char *s)
void	eraseTrailingSpaces (char *s)
void	eraseWhiteSpace (char *s)
char *	trimSpaces (char *s)
void	spaceOut (FILE *f, int count)
void	starOut (FILE *f, int count)
boolean	hasWhiteSpace (char *s)
char *	firstWordInLine (char *line)
char *	lastWordInLine (char *line)
char *	nextWord (char **pLine)
char *	nextTabWord (char **pLine)
int	stringArrayIx (char *string, char *array[], int arraySize)
int	ptArrayIx (void *pt, void *array, int arraySize)
FILE *	mustOpen (char *fileName, char *mode)
void	mustWrite (FILE *file, void *buf, size_t size)
void	mustRead (FILE *file, void *buf, size_t size)
void	writeString (FILE *f, char *s)
char *	readString (FILE *f)
char *	mustReadString (FILE *f)
boolean	fastReadString (FILE *f, char buf[256])
void	writeBits64 (FILE *f, bits64 x)
bits64	readBits64 (FILE *f)
char *	addSuffix (char *head, char *suffix)
void	chopSuffix (char *s)
void	chopSuffixAt (char *s, char c)
char *	chopPrefixAt (char *s, char c)
char *	chopPrefix (char *s)
boolean	carefulCloseWarn (FILE **pFile)
void	carefulClose (FILE **pFile)
char *	firstWordInFile (char *fileName, char *wordBuf, int wordBufSize)
int	roundingScale (int a, int p, int q)
int	intAbs (int a)
int	rangeIntersection (int start1, int end1, int start2, int end2)
int	positiveRangeIntersection (int start1, int end1, int start2, int end2)
bits32	byteSwap32 (bits32 a)
void	removeReturns (char *dest, char *src)
char *	readLine (FILE *fh)
boolean	fileExists (char *fileName)
char *	containsStringNoCase (char *haystack, char *needle)
char *	strstrNoCase (char *haystack, char *needle)
int	vasafef (char *buffer, int bufSize, char *format, va_list args)
int	safef (char *buffer, int bufSize, char *format,...)
void	safecpy (char *buf, size_t bufSize, const char *src)
void	safencpy (char *buf, size_t bufSize, const char *src, size_t n)
void	safecat (char *buf, size_t bufSize, const char *src)
void	safencat (char *buf, size_t bufSize, const char *src, size_t n)
char *	naForNull (char *s)
char *	naForEmpty (char *s)
char *	emptyForNull (char *s)
char *	nullIfAllSpace (char *s)
char *	trueFalseString (boolean b)
void	uglyTime (char *label,...)
void	makeDirs (char *path)
char *	skipNumeric (char *s)
char *	skipToNumeric (char *s)
char *	splitOffNonNumeric (char *s)
char *	splitOffNumber (char *db)
Variables
static char const	rcsid [] = "$Id: common.c,v 1.108 2007/03/30 00:12:11 markd Exp $"
char	crLfChopper [] = "\n\r"
char	whiteSpaceChopper [] = " \t\n\r"
static char *	naStr = "n/a"
static char *	emptyStr = ""

---

Function Documentation

char* addSuffix	(	char *	head,
		char *	suffix
	)

Definition at line 1613 of file common.c.

References needMem().

Referenced by convertEpsToPdf().

{
char *ret = NULL;
int size = strlen(head) + strlen(suffix) +1;
ret = needMem(sizeof(char)*size);
snprintf(ret, size, "%s%s", head, suffix);
return ret;
}

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bits32 byteSwap32

(

bits32

a

)

Definition at line 1739 of file common.c.

References bits32, and UBYTE.

Referenced by nibOpenVerify(), oocMaskCounts(), readBits32(), readBlockCoords(), twoBitOutNBeds(), and twoBitSeqSizeNoNs().

{
union {bits32 whole; UBYTE bytes[4];} u,v;
u.whole = a;
v.bytes[0] = u.bytes[3];
v.bytes[1] = u.bytes[2];
v.bytes[2] = u.bytes[1];
v.bytes[3] = u.bytes[0];
return v.whole;
}

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void carefulClose

(

FILE **

pFile

)

Definition at line 1683 of file common.c.

References carefulCloseWarn(), and noWarnAbort().

Referenced by appendMimeVar(), bigBlat(), dnaMotifToLogoPs(), dnaMotifToLogoPsW(), doBlat(), doDetailLine(), fofClose(), freeWormCdnaIterator(), gfMakeOoc(), gfPcrOutputWriteAll(), hashHisto(), loadNt4(), mafWriteAll(), nibGetSize(), nibInfoFree(), nibOutput(), parseMultiParts(), psClose(), searchOneIndex(), twoBitClose(), wormCdnaUncache(), wormUncacheSomeGdf(), writeGulp(), and xapParseFile().

{
if (!carefulCloseWarn(pFile))
    noWarnAbort();
}

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boolean carefulCloseWarn

(

FILE **

pFile

)

Definition at line 1661 of file common.c.

References errnoWarn(), FALSE, and TRUE.

Referenced by carefulClose().

{
FILE *f;
boolean ok = TRUE;
if ((pFile != NULL) && ((f = *pFile) != NULL))
    {
    if (f != stdin && f != stdout)
        {
        if (fclose(f) != 0)
            {
            errnoWarn("fclose failed");
            ok = FALSE;
            }
        }
    *pFile = NULL;
    }
return ok;
}

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int chopByChar	(	char *	in,
		char	chopper,
		char *	outArray[],
		int	outSize
	)

Definition at line 1248 of file common.c.

Referenced by lineFileChopCharNext(), lineFileChopNextTab(), nextBlock(), tabRowByChar(), and trixParseHitList().

{
int i;
char c;
if (*in == 0)
    return 0;
for (i=0; (i<outSize) || (outArray==NULL); ++i)
    {
    if (outArray != NULL)
        outArray[i] = in;
    for (;;)
        {
        if ((c = *in++) == 0)
            return i+1;
        else if (c == chopper)
            {
            if (outArray != NULL)
                in[-1] = 0;
            break;
            }
        }
    }
return i;
}

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int chopByWhite	(	char *	in,
		char *	outArray[],
		int	outSize
	)

Definition at line 1209 of file common.c.

Referenced by countWordsInFile(), faReadMixedNext(), lineFileChopNext(), mafNextWithPos(), readAllWords(), and tabRowByWhite().

{
int recordCount = 0;
char c;
for (;;)
    {
    if (outArray != NULL && recordCount >= outSize)
        break;

    /* Skip initial separators. */
    while (isspace(*in)) ++in;
    if (*in == 0)
        break;
    
    /* Store start of word and look for end of word. */    
    if (outArray != NULL)
        outArray[recordCount] = in;
    recordCount += 1;
    for (;;)
        {
        if ((c = *in) == 0)
            break;
        if (isspace(c))
            break;
        ++in;
        }
    if (*in == 0)
        break;
 
    /* Tag end of word with zero. */
    if (outArray != NULL)
        *in = 0;
    /* And skip over the zero. */
    in += 1;
    }
return recordCount;
}

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char* chopPrefix

(

char *

s

)

Definition at line 1650 of file common.c.

References chopPrefixAt().

{
return chopPrefixAt(s, '.');
}

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char* chopPrefixAt	(	char *	s,
		char	c
	)

Definition at line 1641 of file common.c.

Referenced by chopPrefix().

{
char *e = strchr(s, c);
if (e == NULL) return s;
*e++ = 0;
return e;
}

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int chopString	(	char *	in,
		char *	sep,
		char *	outArray[],
		int	outSize
	)

Definition at line 1184 of file common.c.

Referenced by axtScoreSchemeFromBlastzMatrix(), axtScoreSchemeReadLf(), kvtParseAdd(), netParseSubnet(), parseElement(), parsePasvPort(), parseRestOfCdnaInfo(), twoBitSpecNew(), wormGeneToOrfNames(), wormIsGeneName(), wormParseChromRange(), xaReadNext(), and xStitch().

{
int recordCount = 0;

for (;;)
    {
    if (outArray != NULL && recordCount >= outSize)
        break;
    /* Skip initial separators. */
    in += strspn(in, sep);
    if (*in == 0)
        break;
    if (outArray != NULL)
        outArray[recordCount] = in;
    recordCount += 1;
    in += strcspn(in, sep);
    if (*in == 0)
        break;
    if (outArray != NULL)
        *in = 0;
    in += 1;
    }
return recordCount;
}

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void chopSuffix

(

char *

s

)

Definition at line 1624 of file common.c.

Referenced by convertEpsToPdf(), and getHost().

{
char *e = strrchr(s, '.');
if (e != NULL)
    *e = 0;
}

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void chopSuffixAt	(	char *	s,
		char	c
	)

Definition at line 1632 of file common.c.

{
char *e = strrchr(s, c);
if (e != NULL)
    *e = 0;
}

char* cloneLongString

(

char *

s

)

Definition at line 40 of file common.c.

References cloneMem().

Referenced by htmlPageParse().

{
size_t size = strlen(s);
return cloneMem(s, size+1);
}

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void* cloneMem	(	void *	pt,
		size_t	size
	)

Definition at line 14 of file common.c.

References needLargeMem().

Referenced by axtReadWithPos(), cloneLongString(), faReadAllMixableInLf(), ffShNeedle(), nextBlock(), and stringBetween().

{
void *newPt = needLargeMem(size);
memcpy(newPt, pt, size);
return newPt;
}

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char* cloneString

(

char *

s

)

Definition at line 31 of file common.c.

References cloneStringZ().

Referenced by allocNt4(), apacheAccessLogParse(), asParseColArraySpec(), asParseColDef(), asParseTableDef(), asParseText(), axtAffine2Level(), axtFromBlocks(), axtReadWithPos(), axtScoreSchemeReadLf(), blastFileNextGapped(), blastFileOpenVerify(), bundleIntoTargets(), cgiEncode(), cgiEncodeFull(), cgiFromFile(), cgiParseMultipart(), cgiVarSet(), chainReadChainLine(), chainSubsetOnQ(), chainToPsl(), checkTagIsInside(), cloneDnaSeq(), clumpToExactRange(), clumpToHspRange(), convertEpsToPdf(), dnaLoadNextFromStack(), dnaLoadOpen(), dnaLoadSingle(), doBlat(), doDetailLine(), emblRecord(), expandRelativePath(), faReadAllMixableInLf(), faReadMixedNext(), faReadNamedSeq(), findMultipleWordHits(), fofOpen(), formParseVars(), forwardMergeTwo(), gapCalcFromString(), getDirs(), getFileNameFromHdrSig(), getLineMB(), getMimeHeaderFieldVal(), getMimeHeaderMainVal(), getQueryInput(), getWormGeneExonDna(), gfClientFileArray(), gffFileNew(), gffHasGtfGroup(), gfIndexNibsAndTwoBits(), gfPcrGetRanges(), gfPcrInputLoad(), gfQuerySeqTrans(), gfQuerySeqTransTrans(), gfRangeLoad(), gfRangesBundle(), gfWebConfigRead(), hashVarLine(), hpfNext(), htmlCookieFileRead(), htmlExpandUrl(), htmlFormVarSet(), htmlHeaderRead(), htmlPageParse(), htmlPageParseNoHead(), htmlTagScan(), initialEntityHash(), lineFileAttach(), lineFileOnString(), lineFileParseHttpHeader(), loadHashT3Ranges(), mafFromAxt(), mafMayOpen(), mafNextWithPos(), mafSubsetE(), mafWrite(), main(), mergeContigs(), netHttpGetMultiple(), netUrlHead(), newDnaSeq(), nextSeqFromMem(), nibInfoNew(), nibInput(), nibStreamOpen(), nibTwoCacheNew(), oligoDg(), oligoTm(), outputFa(), parseAttribute(), parseCookie(), parseCookies(), parseDatabaseLines(), parseElement(), parseEntity(), parseFileSeq(), parseGtfEnd(), parseIdent(), parseMultiParts(), parseQueryLines(), parseSeqSpec(), pcrLocalStrand(), peelChains(), phhmTraceToAxt(), plProcNew(), pscmSetHint(), pslFromFakeFfAli(), pslGetCreateSql(), pslLoad(), pslNew(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslTblNew(), pslTrimToQueryRange(), pslTrimToTargetRange(), pslxFileOpen(), pslxFileOpenWithMetaConfig(), qaStatusOnPage(), qaStatusSoftError(), quotedPrintableDecode(), raFromString(), readPartHeaderMB(), repeatMaskOutLoad(), saveAxtBundle(), searchOneIndex(), seqClumpToRangeList(), shaNewNode(), slPairNew(), spacedColumnFromSample(), splitOffNumber(), sqlByteArrayToString(), sqlCharArrayToString(), sqlDoubleArrayToString(), sqlFloatArrayToString(), sqlLongLongArrayToString(), sqlShortArrayToString(), sqlSignedArrayToString(), sqlStringArrayToString(), sqlStringComma(), sqlStringDynamicArray(), sqlUbyteArrayToString(), sqlUnsignedArrayToString(), sqlUshortArrayToString(), stringToSlNames(), stripCommas(), subTextNew(), tabRowGuessFixedOffsets(), transIndexBothStrands(), translateSeqN(), trixParseHitList(), trixSearchWordResults(), twoBitFromDnaSeq(), twoBitFromFile(), twoBitIsRange(), twoBitOpen(), twoBitReadSeqFragExt(), twoBitSpecNew(), twoBitSpecNewFile(), vgOpenGif(), wormCdnaInfo(), wormGeneFirstOrfName(), wormInfoForGene(), xAliLoad(), xapNew(), xapParseAny(), xapStartTag(), xaReadNext(), xpNew(), and xStitch().

{
if (s == NULL)
    return NULL;
else
    return cloneStringZ(s, strlen(s));
}

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char* cloneStringZ	(	char *	s,
		int	size
	)

Definition at line 22 of file common.c.

References needMem().

Referenced by cloneString(), faReadNamedSeq(), formParseVars(), htmlExpandUrl(), htmlStatusParse(), mafFromAxt(), mafSubsetE(), newGdfGene(), outputFa(), parseFileSeq(), pcrLocalStrand(), qaStringBetween(), splitOffNonNumeric(), and xStitch().

{
char *d = needMem(size+1);
memcpy(d, s, size);
d[size] = 0;
return d;
}

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char* containsStringNoCase	(	char *	haystack,
		char *	needle
	)

Definition at line 1828 of file common.c.

References strstrNoCase().

{
return strstrNoCase(haystack, needle);
}

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int countChars	(	char *	s,
		char	c
	)

Definition at line 1127 of file common.c.

Referenced by expandRelativePath(), gfPcrMakePrimer(), isGtfGroup(), makeEscapedString(), makeQuotedString(), projectString(), and tabRowByChar().

{
char a;
int count = 0;
while ((a = *s++) != 0)
    if (a == c)
        ++count;
return count;
}

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int countCharsN	(	char *	s,
		char	c,
		int	size
	)

Definition at line 1138 of file common.c.

{
int i;
int count = 0;
for (i=0; i<size; ++i)
    if (s[i] == c)
        ++count;
return count;
}

int countLeadingChars	(	char *	s,
		char	c
	)

Definition at line 1149 of file common.c.

{
int count = 0;
while (*s++ == c)
   ++count;
return count;
}

int countSame	(	char *	a,
		char *	b
	)

Definition at line 1158 of file common.c.

Referenced by cmpSeqName().

{
char c;
int i;
int count = 0;
for (i=0; ; ++i)
   {
   c = a[i];
   if (b[i] != c)
       break;
   if (c == 0)
       break;
   ++count;
   }
return count;
}

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int differentStringNullOk	(	char *	a,
		char *	b
	)

Definition at line 856 of file common.c.

References FALSE.

{
if (a == b)
    return FALSE;
else if (a == NULL)
    return -1;
else if (b == NULL)
    return 1;
else
    return strcmp(a,b) != 0;
}

int differentWord	(	char *	s1,
		char *	s2
	)

Definition at line 839 of file common.c.

Referenced by gffFindGeneIgnoreCase(), gffReadGenes(), rbTreeCmpWord(), stringArrayIx(), and warnAboutDupes().

{
char c1, c2;
for (;;)
    {
    c1 = toupper(*s1++);
    c2 = toupper(*s2++);
    if (c1 != c2) /* Takes care of end of string in one but not the other too */
        return c2-c1;
    if (c1 == 0)  /* Take care of end of string in both. */
        return 0;
    }
}

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static int doubleCmp	(	const void *	va,
		const void *	vb
	)			[static]

Definition at line 421 of file common.c.

Referenced by doubleSort().

{
const double *a = va;
const double *b = vb;
double diff = *a - *b;
if (diff < 0)
    return -1;
else if (diff > 0)
    return 1;
else
    return 0;
}

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double doubleMedian	(	int	count,
		double *	array
	)

Definition at line 442 of file common.c.

References doubleSort().

Referenced by slDoubleMedian().

{
double median;
doubleSort(count, array);
if ((count&1) == 1)
    median = array[count>>1];
else
    {
    count >>= 1;
    median = (array[count] + array[count-1]) * 0.5;
    }
return median;
}

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void doubleSort	(	int	count,
		double *	array
	)

Definition at line 435 of file common.c.

References doubleCmp().

Referenced by doubleMedian().

{
if (count > 1)
qsort(array, count, sizeof(array[0]), doubleCmp);
}

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char* emptyForNull

(

char *

s

)

Definition at line 1973 of file common.c.

{
if (s == NULL)
   s = emptyStr;
return s;
}

boolean endsWith	(	char *	string,
		char *	end
	)

Definition at line 937 of file common.c.

References FALSE, and sameString.

Referenced by getDecompressor(), netLineFileMayOpen(), netLineFileMayOpenCatchError(), nibIsFile(), nibIsRange(), sendFtpCommand(), setupWss(), textOutInit(), twoBitIsFile(), and twoBitSpecNew().

{
int sLen, eLen, offset;
sLen = strlen(string);
eLen = strlen(end);
offset = sLen - eLen;
if (offset < 0)
    return FALSE;
return sameString(string+offset, end);
}

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void eraseTrailingSpaces

(

char *

s

)

Definition at line 1311 of file common.c.

Referenced by htmlTagScan(), and trimSpaces().

{
int len = strlen(s);
int i;
char c;

for (i=len-1; i>=0; --i)
    {
    c = s[i];
    if (isspace(c))
        s[i] = 0;
    else
        break;
    }
}

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void eraseWhiteSpace

(

char *

s

)

Definition at line 1329 of file common.c.

Referenced by base64Validate(), and phyloParseString().

{
char *in, *out;
char c;

in = out = s;
for (;;)
    {
    c = *in++;
    if (c == 0) 
        break;
    if (!isspace(c))
        *out++ = c;
    }
*out++ = 0;
}

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boolean fastReadString	(	FILE *	f,
		char	buf[256]
	)

Definition at line 1570 of file common.c.

References FALSE, mustRead(), readOne, TRUE, and UBYTE.

Referenced by twoBitOpen().

{
UBYTE bLen;
int len;
if (!readOne(f, bLen))
    return FALSE;
if ((len = bLen)> 0)
    mustRead(f, buf, len);
buf[len] = 0;
return TRUE;
} 

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boolean fileExists

(

char *

fileName

)

Definition at line 1814 of file common.c.

References fileSize(), sameString, and TRUE.

Referenced by htmlIncludeFile(), htmlPageGet(), mysqlHost(), and rTempName().

{
/* To make piping easier stdin and stdout always exist. */
if (sameString(fileName, "stdin")) return TRUE;
if (sameString(fileName, "stdout")) return TRUE;

return fileSize(fileName) != -1;
}

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char* firstWordInFile	(	char *	fileName,
		char *	wordBuf,
		int	wordBufSize
	)

Definition at line 1691 of file common.c.

References mustOpen(), and trimSpaces().

Referenced by getDirs(), and mysqlHost().

{
FILE *f = mustOpen(fileName, "r");
fgets(wordBuf, wordBufSize, f);
fclose(f);
return trimSpaces(wordBuf);
}

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char* firstWordInLine

(

char *

line

)

Definition at line 1381 of file common.c.

References skipLeadingSpaces(), and skipToSpaces().

Referenced by faMixedSpeedReadNext().

{
char *e;
line = skipLeadingSpaces(line);
if ((e = skipToSpaces(line)) != NULL)
    *e = 0;
return line;
}

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void gentleFree

(

void *

pt

)

Definition at line 834 of file common.c.

References freeMem().

Referenced by gif_compress_data().

{
if (pt != NULL) freeMem((char*)pt);
}

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boolean hasWhiteSpace

(

char *

s

)

Definition at line 1371 of file common.c.

References FALSE, and TRUE.

{
char c;
while ((c = *s++) != 0)
    if (isspace(c))
        return TRUE;
return FALSE;
}

int intAbs

(

int

a

)

Definition at line 1714 of file common.c.

Referenced by cdaCoalesceOne().

{
return (a >= 0 ? a : -a);
}

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static int intCmp	(	const void *	va,
		const void *	vb
	)			[static]

Definition at line 497 of file common.c.

Referenced by intSort().

{
const int *a = va;
const int *b = vb;
int diff = *a - *b;
if (diff < 0)
    return -1;
else if (diff > 0)
    return 1;
else
    return 0;
}

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int intMedian	(	int	count,
		int *	array
	)

Definition at line 518 of file common.c.

References intSort().

{
int median;
intSort(count, array);
if ((count&1) == 1)
    median = array[count>>1];
else
    {
    count >>= 1;
    median = (array[count] + array[count-1]) * 0.5;
    }
return median;
}

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void intSort	(	int	count,
		int *	array
	)

Definition at line 511 of file common.c.

References intCmp().

Referenced by intMedian().

{
if (count > 1)
qsort(array, count, sizeof(array[0]), intCmp);
}

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char lastChar

(

char *

s

)

Definition at line 949 of file common.c.

Referenced by htmlExpandUrl(), quotedPCollapse(), and quotedPrintableEncode().

{
if (s == NULL || s[0] == 0)
    return 0;
return s[strlen(s)-1];
}

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char* lastWordInLine

(

char *

line

)

Definition at line 1392 of file common.c.

References skipLeadingSpaces(), and skipToSpaces().

{
char *s = line;
char *word = NULL, *wordEnd = NULL;
for (;;)
    {
    s = skipLeadingSpaces(s);
    if (s == NULL || s[0] == 0)
        break;
    word = s;
    s = wordEnd = skipToSpaces(s);
    if (s == NULL)
        break;
    }
if (wordEnd != NULL)
    *wordEnd = 0;
return word;
}

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void makeDirs

(

char *

path

)

Definition at line 2014 of file common.c.

References makeDir(), and PATH_LEN.

{
char pathBuf[PATH_LEN];
char* next = pathBuf;

strcpy(pathBuf, path);
if (*next == '/')
    next++;

while((*next != '\0')
      && (next = strchr(next, '/')) != NULL)
    {
    *next = '\0';
    makeDir(pathBuf);
    *next = '/';
    next++;
    }
makeDir(pathBuf);
}

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char* memMatch	(	char *	needle,
		int	nLen,
		char *	haystack,
		int	hLen
	)

Definition at line 957 of file common.c.

Referenced by countOccurrences(), getChunkMB(), jiggleSmallExons(), pcrLocalStrand(), and setEopMB().

{
char c = *needle++;
nLen -= 1;
hLen -= nLen;
while (--hLen >= 0)
    {   
    if (*haystack++ == c && memcmp(needle, haystack, nLen) == 0)
        {
        return haystack-1;
        }
    }
return NULL;
}

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FILE* mustOpen	(	char *	fileName,
		char *	mode
	)

Definition at line 1482 of file common.c.

References errAbort(), errno, and sameString.

Referenced by appendMimeVar(), blat(), cdaCreate(), cdaOpenVerify(), codonLoadBias(), dnaMotifToLogoPs(), dnaMotifToLogoPsW(), doBlat(), doDetailLine(), elFromRec(), faWrite(), faWriteAll(), firstWordInFile(), flyCdnaSeq(), fofMake(), fofOpen(), fofRecToPos(), gfClient(), gfClientFileArray(), gfMakeOoc(), gfPcrOutputWriteAll(), hashHisto(), jpegSize(), logOpenFile(), mafWriteAll(), mgLoadGif(), mgSaveGif(), nibOutput(), nibStreamOpen(), nt4OpenVerify(), oocMaskCounts(), parseMultiParts(), pslWriteAll(), psOpen(), readInGulp(), saveNt4(), scanChromOffsetFile(), twoBitOpen(), verboseSetLogFile(), wormCacheSomeGdf(), wormCdaAlisInRange(), wormCdnaCache(), wormGeneForOrf(), wormGeneRange(), wormInfoForGene(), wormSearchAllCdna(), writeGulp(), xaIxOpenVerify(), xaOpenVerify(), xapOpen(), xapParseFile(), xenAlignBig(), xenAlignWorm(), and xStitch().

{
FILE *f;

if (sameString(fileName, "stdin"))
    return stdin;
if (sameString(fileName, "stdout"))
    return stdout;
if ((f = fopen(fileName, mode)) == NULL)
    {
    char *modeName = "";
    if (mode)
        {
        if (mode[0] == 'r')
            modeName = " to read";
        else if (mode[0] == 'w')
            modeName = " to write";
        else if (mode[0] == 'a')
            modeName = " to append";
        }
    errAbort("Can't open %s%s: %s", fileName, modeName, strerror(errno));
    }
return f;
}

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void mustRead	(	FILE *	file,
		void *	buf,
		size_t	size
	)

Definition at line 1518 of file common.c.

References errAbort().

Referenced by cdaLoadString(), fastReadString(), fofBatchFind(), fofFetch(), fofFetchString(), fofFindFirst(), fofOpen(), fofSearch(), gdfReadOneGene(), loadNt4(), nt4LoadPart(), readBits64(), readInGulp(), readString(), scanChromOffsetFile(), twoBitFromFile(), twoBitReadSeqFragExt(), and xaReadNext().

{
if (size != 0 && fread(buf, size, 1, file) != 1)
    errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
}

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char* mustReadString

(

FILE *

f

)

Definition at line 1560 of file common.c.

References errAbort(), and readString().

{
char *s = readString(f);
if (s == NULL)
    errAbort("Couldn't read string");
return s;
}

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void mustWrite	(	FILE *	file,
		void *	buf,
		size_t	size
	)

Definition at line 1508 of file common.c.

References errAbort().

Referenced by axtWrite(), bandExt(), cdaWriteString(), dumpNearCrossover(), fofMake(), kvtWriteAll(), makeIndex(), parseMultiParts(), savePslx(), twoBitWriteOne(), writeBits64(), writeContig(), writeGulp(), writeSeqWithBreaks(), writeString(), and xenShowAli().

{
if (size != 0 && fwrite(buf, size, 1, file) != 1)
    {
    errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
    }
}

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char* naForEmpty

(

char *

s

)

Definition at line 1965 of file common.c.

{
if (s == NULL || s[0] == 0)
    s = naStr;
return s;
}

char* naForNull

(

char *

s

)

Definition at line 1957 of file common.c.

Referenced by htmlFormVarPrint().

{
if (s == NULL) 
   s = naStr;
return s;
}

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struct slName* newSlName

(

char *

name

)

[read]

Definition at line 535 of file common.c.

References AllocVar, and needMem().

Referenced by cgiStringList(), listDir(), parseMultiOption(), readAllLines(), slNameStore(), wormGeneToOrfNames(), and xStitch().

{
struct slName *sn;
if (name != NULL)
    {
    int len = strlen(name);
    sn = needMem(sizeof(*sn)+len);
    strcpy(sn->name, name);
    return sn;
    }
else
    {
    AllocVar(sn);
    }
return sn;
}

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char* nextTabWord

(

char **

pLine

)

Definition at line 1431 of file common.c.

{
char *s = *pLine;
char *e;
if (s == NULL || *s == '\n' || *s == 0)
    {
    *pLine = NULL;
    return NULL;
    }
e = strchr(s, '\t');
if (e == NULL)
    {
    e = strchr(s, '\n');
    if (e != NULL)
        *e = 0;
    *pLine = NULL;
    }
else
    {
    *e++ = 0;
    *pLine = e;
    }
return s;
}

char* nextWord

(

char **

pLine

)

Definition at line 1414 of file common.c.

References skipLeadingSpaces(), and skipToSpaces().

Referenced by apacheAccessLogParse(), checkTagIsInside(), emblLineGroup(), findTileSize(), getHitsFromServer(), gfPcrGetRanges(), gfWebConfigRead(), hashWordsInFile(), hpfNext(), htmlCookieFileRead(), htmlHeaderRead(), lineFileParseHttpHeader(), lineFileSlurpHttpBody(), mafMayOpen(), mafNextWithPos(), needNextWord(), netSkipHttpHeaderLines(), netSkipHttpHeaderLinesCatch(), netUrlHead(), nextQuotedWord(), parseGtfEnd(), raFoldInOneRetName(), raFromString(), raNextRecord(), readTaggedNumLine(), spacedColumnFromSample(), startServer(), trixParseHitList(), and trixSearchWordResults().

{
char *s = *pLine, *e;
if (s == NULL || s[0] == 0)
    return NULL;
s = skipLeadingSpaces(s);
if (s[0] == 0)
    return NULL;
e = skipToSpaces(s);
if (e != NULL)
    *e++ = 0;
*pLine = e;
return s;
}

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char* nullIfAllSpace

(

char *

s

)

Definition at line 1981 of file common.c.

References skipLeadingSpaces().

{
s = skipLeadingSpaces(s);
if (s != NULL)
    if (s[0] == 0)
        s = NULL;
return s;
}

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int positiveRangeIntersection	(	int	start1,
		int	end1,
		int	start2,
		int	end2
	)

Definition at line 1729 of file common.c.

References rangeIntersection().

Referenced by addOverlap().

{
int ret = rangeIntersection(start1,end1,start2,end2);
if (ret < 0)
    ret = 0;
return ret;
}

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int ptArrayIx	(	void *	pt,
		void *	array,
		int	arraySize
	)

Definition at line 1467 of file common.c.

Referenced by aliLines().

{
int i;
void **a = array;
for (i=0; i<arraySize; ++i)
    {
    if (pt == a[i])
        return i;
    }
return -1;
}

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int rangeIntersection	(	int	start1,
		int	end1,
		int	start2,
		int	end2
	)

Definition at line 1720 of file common.c.

References max, and min.

Referenced by binKeeperAnyOverlap(), binKeeperFind(), binKeeperFindLowest(), binKeeperReplaceVal(), positiveRangeIntersection(), pslTrimToQueryRange(), pslTrimToTargetRange(), and rBoxJoin().

{
int s = max(start1,start2);
int e = min(end1,end2);
return e-s;
}

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bits64 readBits64

(

FILE *

f

)

Definition at line 1597 of file common.c.

References bits64, mustRead(), and UBYTE.

{
int i;
UBYTE buf[8];
bits64 x = 0;
mustRead(f, buf, 8);
for (i=0; i<8; ++i)
    {
    x <<= 8;
    x |= buf[i];
    }
return x;
}

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char* readLine

(

FILE *

fh

)

Definition at line 1779 of file common.c.

References errAbort(), freeMem(), and needMem().

{
int bufCapacity = 256;
int bufSize = 0;
char* buf = needMem(bufCapacity);
int ch;

/* loop until EOF of EOLN */
while (((ch = getc(fh)) != EOF) && (ch != '\n'))
    {
    /* expand if almost full, always keep one extra char for
     * zero termination */
    if (bufSize >= bufCapacity-2)
        {
        bufCapacity *= 2;
        buf = realloc(buf, bufCapacity);
        if (buf == NULL)
            {
            errAbort("Out of memory in readline - request size %d bytes", bufCapacity);
            }
        }
    buf[bufSize++] = ch;
    }

/* only return EOF if no data was read */
if ((ch == EOF) && (bufSize == 0))
    {
    freeMem(buf);
    return NULL;
    }
buf[bufSize] = '\0';
return buf;
}

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char* readString

(

FILE *

f

)

Definition at line 1543 of file common.c.

References mustRead(), needMem(), readOne, and UBYTE.

Referenced by mustReadString().

{
UBYTE bLen;
int len;
char *s;

if (!readOne(f, bLen))
    return NULL;
len = bLen;
s = needMem(len+1);
if (len > 0)
    mustRead(f, s, len);
return s;
}

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void refAdd	(	struct slRef **	pRefList,
		void *	val
	)

Definition at line 725 of file common.c.

References AllocVar, slAddHead, and slRef::val.

Referenced by addRef(), findOrMakeVar(), loadHashT3Ranges(), and refAddUnique().

{
struct slRef *ref;
AllocVar(ref);
ref->val = val;
slAddHead(pRefList, ref);
}

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void refAddUnique	(	struct slRef **	pRefList,
		void *	val
	)

Definition at line 734 of file common.c.

References refAdd(), and refOnList().

{
if (refOnList(*pRefList, val) == NULL)
    {
    refAdd(pRefList, val);
    }
}

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struct slRef* refListFromSlList

(

void *

list

)

[read]

Definition at line 743 of file common.c.

References slList::next, slAddHead, slRefNew(), and slReverse().

{
struct slList *el;
struct slRef *refList = NULL, *ref;
for (el= list; el != NULL; el = el->next)
    {
    ref = slRefNew(el);
    slAddHead(&refList, ref);
    }
slReverse(&refList);
return refList;
}

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struct slRef* refOnList	(	struct slRef *	refList,
		void *	val
	)			[read]

Definition at line 706 of file common.c.

References slRef::next, and slRef::val.

Referenced by refAddUnique().

{
struct slRef *ref;
for (ref = refList; ref != NULL; ref = ref->next)
    if (ref->val == val)
        return ref;
return NULL;
}

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void removeReturns	(	char *	dest,
		char *	src
	)

Definition at line 1751 of file common.c.

{
int i = 0;
int j = 0;

/* until the end of the string */
for (;;)
    {
    /* skip the returns */
    while(src[j] == '\r')
        j++;

    /* copy the characters */
    dest[i] = src[j];

    /* check to see if done */
    if(src[j] == '\0')
        break;

    /* advance the counters */
    i++;
    j++;
    }
}

char* replaceChars	(	char *	string,
		char *	old,
		char *	new
	)

Definition at line 1018 of file common.c.

References max, and needMem().

Referenced by netParseUrl().

{
int numTimes = 0;
int oldLen = strlen(old);
int newLen = strlen(new);
int strLen = 0;
char *result = NULL;
char *ptr = strstr(string, old);
char *resultPtr = NULL;

while(NULL != ptr)
    {
    numTimes++;
    ptr += oldLen;
    ptr = strstr(ptr, old);
    }
strLen = max(strlen(string) + (numTimes * (newLen - oldLen)), strlen(string));
result = needMem(strLen + 1);

ptr = strstr(string, old);
resultPtr = result;
while(NULL != ptr)
    {
    strLen = ptr - string;
    strcpy(resultPtr, string);
    string = ptr + oldLen;

    resultPtr += strLen;
    strcpy(resultPtr, new);
    resultPtr += newLen;
    ptr = strstr(string, old);
    }

strcpy(resultPtr, string);
return result;
}

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void reverseBytes	(	char *	bytes,
		long	length
	)

Definition at line 57 of file common.c.

Referenced by axtAffine2Level(), bandExt(), mafFlipStrand(), reverseComplement(), and reverseFold().

{
long halfLen = (length>>1);
char *end = bytes+length;
char c;
while (--halfLen >= 0)
    {
    c = *bytes;
    *bytes++ = *--end;
    *end = c;
    }
}

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void reverseDoubles	(	double *	a,
		int	length
	)

Definition at line 98 of file common.c.

{
int halfLen = (length>>1);
double *end = a+length;
double c;
while (--halfLen >= 0)
    {
    c = *a;
    *a++ = *--end;
    *end = c;
    }
}

void reverseInts	(	int *	a,
		int	length
	)

Definition at line 70 of file common.c.

Referenced by pslShowAlignmentStranded2().

{
int halfLen = (length>>1);
int *end = a+length;
int c;
while (--halfLen >= 0)
    {
    c = *a;
    *a++ = *--end;
    *end = c;
    }
}

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void reverseStrings	(	char **	a,
		int	length
	)

Definition at line 112 of file common.c.

{
int halfLen = (length>>1);
char **end = a+length;
char *c;
while (--halfLen >= 0)
    {
    c = *a;
    *a++ = *--end;
    *end = c;
    }
}

void reverseUnsigned	(	unsigned *	a,
		int	length
	)

Definition at line 84 of file common.c.

Referenced by pslRc(), pslRcBoth(), and swapRCBlocks().

{
int halfLen = (length>>1);
unsigned *end = a+length;
unsigned c;
while (--halfLen >= 0)
    {
    c = *a;
    *a++ = *--end;
    *end = c;
    }
}

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int roundingScale	(	int	a,
		int	p,
		int	q
	)

Definition at line 1700 of file common.c.

References round.

Referenced by cdaAliFromFfAli(), cdaCoalesceOne(), cdaShowAlignmentTrack(), and savePslx().

{
if (a > 100000 || p > 100000)
    {
    double x = a;
    x *= p;
    x /= q;
    return round(x);
    }
else
    return (a*p + q/2)/q;
}

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char* rStringIn	(	char *	needle,
		char *	haystack
	)

Definition at line 903 of file common.c.

{
int nSize = strlen(needle);
char *pos;
for (pos = haystack + strlen(haystack) - nSize; pos >= haystack; pos -= 1)
    {
    if (memcmp(needle, pos, nSize) == 0)
        return pos;
    }
return NULL;
}

void safecat	(	char *	buf,
		size_t	bufSize,
		const char *	src
	)

Definition at line 1930 of file common.c.

References errAbort().

{
size_t blen = strlen(buf);
size_t slen = strlen(src);
if (blen+slen > bufSize-1)
    errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
strcat(buf, src);
}

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void safecpy	(	char *	buf,
		size_t	bufSize,
		const char *	src
	)

Definition at line 1908 of file common.c.

References errAbort().

{
size_t slen = strlen(src);
if (slen > bufSize-1)
    errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
strcpy(buf, src);
}

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int safef	(	char *	buffer,
		int	bufSize,
		char *	format,
			...
	)

Definition at line 1896 of file common.c.

References vasafef().

Referenced by cgiBooleanDefined(), cgiEncode(), cgiEncodeFull(), cgiFromCommandLine(), cgiMakeCheckBoxWithMsg(), cgiMakeClearButton(), cgiMakeHiddenBoolean(), cgiParseMultipart(), chainLookup(), chainReadUsedSwapLf(), checkNest(), checkTagIsInside(), convertEpsToPdf(), envUpdate(), evalToDouble(), fofOpen(), getFileNameFromHdrSig(), getTargetName(), gfiExpandAndLoadCached(), gfIndexNibsAndTwoBits(), gfIndexTransNibsAndTwoBits(), gfPcrGetRanges(), gifLabelVerticalText(), hashLookupUpperCase(), htmlFormCgiVars(), htmlIncludeWebFile(), mafFromAxt(), mkdirTrashDirectory(), ncbiPrintE(), netGetOpenFtp(), netHttpConnect(), netHttpGet(), nibInfoFromCache(), nibLdPartMasked(), nibOpenVerify(), nibTwoLoadOne(), parseMultiParts(), pcrQuery(), pslGetCreateSql(), pslTransMap(), readSeqFrag(), rTempName(), semiUniqName(), trixOpen(), and twoBitReadSeqFragExt().

{
int sz;
va_list args;
va_start(args, format);
sz = vasafef(buffer, bufSize, format, args);
va_end(args);
return sz;
}

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void safencat	(	char *	buf,
		size_t	bufSize,
		const char *	src,
		size_t	n
	)

Definition at line 1940 of file common.c.

References errAbort().

{
size_t blen = strlen(buf);
if (blen+n > bufSize-1)
    errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
size_t slen = strlen(src);
if (slen > n)
    slen = n;
strncat(buf, src, n);
buf[blen+slen] = '\0';
}

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void safencpy	(	char *	buf,
		size_t	bufSize,
		const char *	src,
		size_t	n
	)

Definition at line 1917 of file common.c.

References errAbort().

{
if (n > bufSize-1)
    errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
size_t slen = strlen(src);
if (slen > n)
    slen = n;
strncpy(buf, src, n);
buf[slen] = '\0';
}

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char* skipLeadingSpaces

(

char *

s

)

Definition at line 1278 of file common.c.

Referenced by axtScoreSchemeFromProteinText(), bfSkipBlankLines(), cgiInt(), cgiOptionalInt(), eatComment(), emblLineGroup(), faMixedSpeedReadNext(), firstWordInLine(), hashVarLine(), hpfNext(), htmlCookieFileRead(), htmlHeaderRead(), htmlStatusParse(), htmlTagScan(), lastWordInLine(), lineFileNextReal(), netSkipHttpHeaderLines(), netSkipHttpHeaderLinesCatch(), netUrlHead(), nextQuotedWord(), nextSeqFromMem(), nextWord(), nullIfAllSpace(), parseAttribute(), parseCookie(), parseEntity(), parseGtfEnd(), parseQueryLines(), raFoldInOneRetName(), raFromString(), raNextRecord(), stringToSlNames(), tabRowGuessFixedOffsets(), tokenizerNext(), and trimSpaces().

{
char c;
if (s == NULL) return NULL;
for (;;)
    {
    c = *s;
    if (!isspace(c))
        return s;
    ++s;
    }
}

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char* skipNumeric

(

char *

s

)

Definition at line 2035 of file common.c.

{
while (isdigit(*s))
   ++s;
return s;
}

char* skipToNumeric

(

char *

s

)

Definition at line 2043 of file common.c.

Referenced by splitOffNonNumeric(), and splitOffNumber().

{
while (*s != 0 && !isdigit(*s))
    ++s;
return s;
}

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char* skipToSpaces

(

char *

s

)

Definition at line 1293 of file common.c.

Referenced by firstWordInLine(), hashVarLine(), htmlStatusParse(), lastWordInLine(), nextSeqFromMem(), nextWord(), stringToSlNames(), and tabRowGuessFixedOffsets().

{
char c;
if (s == NULL)
    return NULL;
for (;;)
    {
    c = *s;
    if (c == 0)
        return NULL;
    if (isspace(c))
        return s;
    ++s;
    }
}

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void slAddTail	(	void *	listPt,
		void *	node
	)

Definition at line 200 of file common.c.

References slList::next.

Referenced by asParseTokens(), dgFindPath(), gffReadGenes(), gfRangesBundle(), gfWebConfigRead(), hpfNext(), htmlFormVarAddValue(), htmlHeaderRead(), htmlTagScan(), loadHashT3Ranges(), parseAttribute(), parseMultiOption(), pipelineNew(), slNameAddTail(), spaceSaverAddOverflow(), wormGeneToOrfNames(), and wormGetSomeGdfGeneList().

{
struct slList **ppt = (struct slList **)listPt;
struct slList *n = (struct slList *)node;

while (*ppt != NULL)
    {
    ppt = &((*ppt)->next);
    }
n->next = NULL; 
*ppt = n;
}

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void* slCat	(	void *	va,
		void *	vb
	)

Definition at line 265 of file common.c.

References slList::next.

Referenced by addToBigBundleList(), boxLump(), clumpHits(), gfAlignTrans(), gfAlignTransTrans(), gfClientSeqList(), gfTransTransFindBundles(), mergeClusters(), and xenAlignWorm().

                :
 *   struct slName *a = getNames("a");
 *   struct slName *b = getNames("b");
 *   struct slName *ab = slCat(a,b)
 */
{
struct slList *a = va;
struct slList *b = vb;
struct slList *end;
if (a == NULL)
    return b;
for (end = a; end->next != NULL; end = end->next)
    ;
end->next = b;
return a;
}

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int slCount

(

void *

list

)

List managing routines.

Definition at line 144 of file common.c.

References slList::next.

Referenced by bigBlat(), blat(), boxLump(), chainToPsl(), dlCount(), dnaSeqHash(), dumpBuns(), fofMake(), gffDupeGeneAndSurrounds(), gffPrintInfo(), gfHitSortDiagonal(), gfLargeIndexSeq(), gfQuerySeqTrans(), gfQuerySeqTransTrans(), gfSmallIndexSeq(), hpfNext(), kdTreeMake(), mafColMinMaxScore(), makeIndex(), phhmTraceToAxt(), rBoxJoin(), shuffleList(), slDoubleMedian(), slSort(), spacedColumnFromSizeCommaList(), tabRowByFixedOffsets(), twoBitWriteHeader(), wuBlastOut(), and xenAlignWorm().

{
struct slList *pt = (struct slList *)list;
int len = 0;

while (pt != NULL)
    {
    len += 1;
    pt = pt->next;
    }
return len;
}

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int slDoubleCmp	(	const void *	va,
		const void *	vb
	)

Definition at line 467 of file common.c.

References slDouble::val.

{
const struct slDouble *a = *((struct slDouble **)va);
const struct slDouble *b = *((struct slDouble **)vb);
double diff = a->val - b->val;
if (diff < 0)
    return -1;
else if (diff > 0)
    return 1;
else
    return 0;
}

double slDoubleMedian

(

struct slDouble *

list

)

Definition at line 481 of file common.c.

References AllocArray, doubleMedian(), errAbort(), freeMem(), slDouble::next, and slCount().

{
int i,count = slCount(list);
struct slDouble *el;
double *array, median;
if (count == 0)
    errAbort("Can't take median of empty list");
AllocArray(array,count);
for (i=0, el=list; i<count; ++i, el=el->next)
    array[i] = el->val;
median = doubleMedian(count, array);
freeMem(array);
return median;
}

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struct slDouble* slDoubleNew

(

double

x

)

[read]

Definition at line 458 of file common.c.

References AllocVar, and slDouble::val.

{
struct slDouble *a;
AllocVar(a);
a->val = x;
return a;
}

void* slElementFromIx	(	void *	list,
		int	ix
	)

Definition at line 157 of file common.c.

References slList::next.

{
struct slList *pt = (struct slList *)list;
int i;
for (i=0;i<ix;i++)
    {
    if (pt == NULL) return NULL;
    pt = pt->next;
    }
return pt;
}

void slFreeList

(

void *

listPt

)

Definition at line 305 of file common.c.

References freeMem(), and slList::next.

Referenced by axtAffine(), binKeeperFree(), boxClumpFree(), chainFree(), connectedComponents(), dgNodeFree(), doubleExp(), ffFreeAli(), gfAlignTrans(), gfAlignTransTrans(), gffFileFree(), gffGroupFree(), gfxPolyFree(), hashElFreeList(), hpfModelFree(), hpfNext(), htmlFormVarFree(), lmCleanup(), mergeAdd(), pcrClumps(), psOneColumn(), psPolyFree(), saveAliToPermanentMem(), spacedColumnFromSizeCommaList(), spaceSaverFree(), ssFindBundles(), ssStitch(), tabRowByFixedGuess(), targetHitsFree(), validateCgiUrls(), wormChromPartExonsUpper(), wormGdfGenesInRange(), wormGeneFirstOrfName(), wormGeneRange(), xenAlignBig(), xenAlignWorm(), and xStitch().

{
struct slList **ppt = (struct slList**)listPt;
struct slList *next = *ppt;
struct slList *el;

while (next != NULL)
    {
    el = next;
    next = el->next;
    freeMem((char*)el);
    }
*ppt = NULL;
}

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int slIntCmp	(	const void *	va,
		const void *	vb
	)

Definition at line 405 of file common.c.

References slInt::val.

{
const struct slInt *a = *((struct slInt **)va);
const struct slInt *b = *((struct slInt **)vb);
return a->val - b->val;
}

int slIntCmpRev	(	const void *	va,
		const void *	vb
	)

Definition at line 413 of file common.c.

References slInt::val.

{
const struct slInt *a = *((struct slInt **)va);
const struct slInt *b = *((struct slInt **)vb);
return b->val - a->val;
}

struct slInt* slIntNew

(

int

x

)

[read]

Definition at line 396 of file common.c.

References AllocVar, and slInt::val.

{
struct slInt *a;
AllocVar(a);
a->val = x;
return a;
}

int slIxFromElement	(	void *	list,
		void *	el
	)

Definition at line 171 of file common.c.

References slList::next.

{
struct slList *pt;
int ix = 0;

for (pt = list, ix=0; pt != NULL; pt = pt->next, ++ix)
    if (el == (void*)pt)
        return ix;
return -1;
}

void* slLastEl

(

void *

list

)

Definition at line 183 of file common.c.

References slList::next.

Referenced by chainCalcBounds().

{
struct slList *next, *el;
if ((el = list) == NULL)
    return NULL;
while ((next = el->next) != NULL)
    el = next;
return el;
}

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struct slName* slNameAddHead	(	struct slName **	pList,
		char *	name
	)			[read]

Definition at line 638 of file common.c.

References slAddHead, and slNameNew.

{
struct slName *el = slNameNew(name);
slAddHead(pList, el);
return el;
}

struct slName* slNameAddTail	(	struct slName **	pList,
		char *	name
	)			[read]

Definition at line 646 of file common.c.

References slAddTail(), and slNameNew.

{
struct slName *el = slNameNew(name);
slAddTail(pList, el);
return el;
}

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struct slName* slNameCloneList

(

struct slName *

list

)

[read]

Definition at line 655 of file common.c.

References slName::name, slName::next, slAddHead, slNameNew, and slReverse().

{
struct slName *el, *newEl, *newList = NULL;
for (el = list; el != NULL; el = el->next)
    {
    newEl = slNameNew(el->name);
    slAddHead(&newList, newEl);
    }
slReverse(&newList);
return newList;
}

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int slNameCmp	(	const void *	va,
		const void *	vb
	)

Definition at line 575 of file common.c.

References slName::name.

Referenced by slNameSort().

{
const struct slName *a = *((struct slName **)va);
const struct slName *b = *((struct slName **)vb);
return strcmp(a->name, b->name);
}

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int slNameCmpCase	(	const void *	va,
		const void *	vb
	)

Definition at line 561 of file common.c.

References slName::name.

Referenced by slNameSortCase().

{
const struct slName *a = *((struct slName **)va);
const struct slName *b = *((struct slName **)vb);
return strcasecmp(a->name, b->name);
}

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void* slNameFind	(	void *	list,
		char *	string
	)

Definition at line 599 of file common.c.

References slName::name, slName::next, and sameWord.

{
struct slName *el;
for (el = list; el != NULL; el = el->next)
    if (sameWord(string, el->name))
        return el;
return NULL;
}

int slNameFindIx	(	struct slName *	list,
		char *	string
	)

Definition at line 610 of file common.c.

References slName::name, slName::next, and sameString.

{
struct slName *el;
int ix = 0;
for (el = list; el != NULL; el = el->next, ix++)
    if (sameString(string, el->name))
        return ix;
return -1;
}

boolean slNameInList	(	struct slName *	list,
		char *	string
	)

Definition at line 589 of file common.c.

References FALSE, slName::name, slName::next, sameWord, and TRUE.

Referenced by kvtWriteAll().

{
struct slName *el;
for (el = list; el != NULL; el = el->next)
    if (sameWord(string, el->name))
        return TRUE;
return FALSE;
}

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struct slName* slNameListFromString	(	char *	s,
		char	delimiter
	)			[read]

Definition at line 668 of file common.c.

References slAddHead, slNameNew, slNameNewN(), and slReverse().

{
char *e;
struct slName *list = NULL, *el;
while (s != NULL && s[0] != 0)
    {
    e = strchr(s, delimiter);
    if (e == NULL)
        el = slNameNew(s);
    else
        {
        el = slNameNewN(s, e-s);
        e += 1;
        }
    slAddHead(&list, el);
    s = e;
    }
slReverse(&list);
return list;
}

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struct slName* slNameLoadReal

(

char *

fileName

)

[read]

Definition at line 692 of file common.c.

References lineFileClose(), lineFileNextReal(), lineFileOpen(), slNameNew, slReverse(), slSafeAddHead(), and TRUE.

{
struct slName *lines = NULL;
char *line;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
while (lineFileNextReal(lf, &line))
    slSafeAddHead(&lines, slNameNew(line));
lineFileClose(&lf);
slReverse(&lines);
return lines;
}

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struct slName* slNameNewN	(	char *	name,
		int	size
	)			[read]

Definition at line 553 of file common.c.

References needMem().

Referenced by charSepToSlNames(), and slNameListFromString().

{
struct slName *sn = needMem(sizeof(*sn) + size);
memcpy(sn->name, name, size);
return sn;
}

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void slNameSort

(

struct slName **

pList

)

Definition at line 583 of file common.c.

References slNameCmp(), and slSort().

Referenced by listDir().

{
slSort(pList, slNameCmp);
}

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void slNameSortCase

(

struct slName **

pList

)

Definition at line 569 of file common.c.

References slNameCmpCase(), and slSort().

{
slSort(pList, slNameCmpCase);
}

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char* slNameStore	(	struct slName **	pList,
		char *	string
	)

Definition at line 623 of file common.c.

References slName::name, newSlName(), slName::next, sameString, and slAddHead.

{
struct slName *el;
for (el = *pList; el != NULL; el = el->next)
    {
    if (sameString(string, el->name))
        return el->name;
    }
el = newSlName(string);
slAddHead(pList, el);
return el->name;
}

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void slPairAdd	(	struct slPair **	pList,
		char *	name,
		void *	val
	)

Definition at line 768 of file common.c.

References slAddHead, and slPairNew().

{
struct slPair *el = slPairNew(name, val);
slAddHead(pList, el);
}

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struct slPair* slPairFind	(	struct slPair *	list,
		char *	name
	)			[read]

Definition at line 814 of file common.c.

References slPair::name, slPair::next, and sameString.

Referenced by slPairFindVal().

{
struct slPair *el;
for (el = list; el != NULL; el = el->next)
    if (sameString(name, el->name))
        break;
return el;
}

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void* slPairFindVal	(	struct slPair *	list,
		char *	name
	)

Definition at line 824 of file common.c.

References slPairFind(), and slPair::val.

{
struct slPair *el = slPairFind(list, name);
if (el == NULL)
    return NULL;
return el->val;
}

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void slPairFree

(

struct slPair **

pEl

)

Definition at line 775 of file common.c.

References freeMem(), freez(), and slPair::name.

Referenced by slPairFreeList().

{
struct slPair *el = *pEl;
if (el != NULL)
    {
    freeMem(el->name);
    freez(pEl);
    }
}

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void slPairFreeList

(

struct slPair **

pList

)

Definition at line 786 of file common.c.

References slPair::next, and slPairFree().

Referenced by slPairFreeValsAndList().

{
struct slPair *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    slPairFree(&el);
    }
*pList = NULL;
}

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void slPairFreeVals

(

struct slPair *

list

)

Definition at line 799 of file common.c.

References freez(), slPair::next, and slPair::val.

Referenced by slPairFreeValsAndList().

{
struct slPair *el;
for (el = list; el != NULL; el = el->next)
    freez(&el->val);
}

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void slPairFreeValsAndList

(

struct slPair **

pList

)

Definition at line 807 of file common.c.

References slPairFreeList(), and slPairFreeVals().

{
slPairFreeVals(*pList);
slPairFreeList(pList);
}

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struct slPair* slPairNew	(	char *	name,
		void *	val
	)			[read]

Definition at line 758 of file common.c.

References AllocVar, cloneString(), slPair::name, and slPair::val.

Referenced by slPairAdd().

{
struct slPair *el;
AllocVar(el);
el->name = cloneString(name);
el->val = val;
return el;
}

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void* slPopHead

(

void *

vListPt

)

Definition at line 229 of file common.c.

References slList::next.

Referenced by slUniqify(), and twoBitSpecFree().

{
struct slList **listPt = (struct slList **)vListPt;
struct slList *el = *listPt;
if (el != NULL)
    {
    *listPt = el->next;
    el->next = NULL;
    }
return el;
}

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void* slPopTail

(

void *

vListPt

)

Definition at line 242 of file common.c.

References slList::next.

{
struct slList **listPt = (struct slList **)vListPt;
struct slList *el = *listPt;
if (el != NULL)
    {
    for (;;)
        {
        if (el->next == NULL)
            {
            *listPt = NULL;
            break;
            }
        listPt = &el->next;
        el = el->next;
        }
    }
return el;
}

struct slRef* slRefNew

(

void *

val

)

[read]

Definition at line 716 of file common.c.

References AllocVar, and slRef::val.

Referenced by refListFromSlList().

{
struct slRef *ref;
AllocVar(ref);
ref->val = val;
return ref;
}

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boolean slRemoveEl	(	void *	vpList,
		void *	vToRemove
	)

Definition at line 371 of file common.c.

References FALSE, slList::next, slAddHead, slReverse(), and TRUE.

Referenced by cgiVarExclude(), hashRemove(), and mafMoveComponentToTop().

                                                 :
 *    slRemove(&list, el);  
 * Returns TRUE if element in list.  */
{
struct slList **pList = vpList;
struct slList *toRemove = vToRemove;
struct slList *el, *next, *newList = NULL;
boolean didRemove = FALSE;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    if (el != toRemove)
        {
        slAddHead(&newList, el);
        }
    else
        didRemove = TRUE;
    }
slReverse(&newList);
*pList = newList;
return didRemove;
}

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void slReverse

(

void *

listPt

)

Definition at line 284 of file common.c.

References slList::next.

Referenced by aliLines(), asParseColSymSpec(), asParseTableDef(), blastFileNextGapped(), blastFileNextQuery(), blastFileReadAll(), cgiParseInputAbort(), cgiParseMultipart(), chainMergeAbutting(), chainReadBlocks(), chainSubsetOnQ(), chainSwap(), chainToAxt(), charSepToSlNames(), clumpHits(), clumpNear(), crudeAliFind(), dgConstrainedPriorityOrder(), dnaLoadAll(), dtdParse(), faReadAllMixableInLf(), faSeqListFromMemText(), faSeqListFromMemTextRaw(), fastMapClumpsToBundles(), ffAliSort(), findMultipleWordHits(), fixDirectionAndOffsets(), formParseVars(), getHitsFromServer(), gfAlignSomeClumps(), gfAlignTrans(), gfAlignTransTrans(), gfClumpsToBundles(), gffFileAdd(), gffGroupLines(), gfFindAlignAaTrans(), gfHitSortDiagonal(), gfPcrGetRanges(), gfPcrInputLoadAll(), gfPcrViaNet(), gfQuerySeq(), gfQuerySeqTrans(), gfQuerySeqTransTrans(), gfTransTransFindBundles(), htmlCookieFileRead(), htmlPageScanAttribute(), htmlTagScan(), kxTokenizeFancy(), mafNextWithPos(), mafReadAll(), mafSubsetE(), makeOffsetList(), mergeHits(), parseCookies(), parseElement(), parseMultiParts(), pslLoadAll(), rangeTreeAllOverlapping(), rangeTreeList(), rbTreeItems(), rbTreeItemsInRange(), readAllLines(), refListFromSlList(), removeNegativeBlocks(), saveAxtBundle(), scanChromOffsetFile(), seqClumpToRangeList(), seqListToTrans3List(), shuffleList(), slNameCloneList(), slNameListFromString(), slNameLoadReal(), slRemoveEl(), slSort(), slUniqify(), spacedColumnFromSample(), spacedColumnFromWidthArray(), spaceSaverFinish(), ssGraphMake(), ssStitch(), stringToSlNames(), tabRowByFixedOffsets(), tabRowByWhite(), tabRowGuessFixedOffsets(), targetClump(), trixParseHitList(), trixSearch(), twoBitFromFile(), twoBitLoadAll(), twoBitOpen(), twoBitSeqNames(), twoBitSpecNew(), twoBitSpecNewFile(), wormCdaAlisInRange(), wormGdfGenesInRange(), wormGetSomeGdfGeneList(), xAliLoadAll(), and xaRdRange().

        :
 *    slReverse(&list);
 */
{
struct slList **ppt = (struct slList **)listPt;
struct slList *newList = NULL;
struct slList *el, *next;

next = *ppt;
while (next != NULL)
    {
    el = next;
    next = el->next;
    el->next = newList;
    newList = el;
    }
*ppt = newList;
}

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void slSafeAddHead	(	void *	listPt,
		void *	node
	)

Definition at line 219 of file common.c.

References slList::next.

Referenced by asParseColSymSpec(), slNameLoadReal(), twoBitLoadAll(), twoBitSpecNew(), and twoBitSpecNewFile().

{
struct slList **ppt = (struct slList **)listPt;
struct slList *n = (struct slList *)node;

n->next = *ppt; 
*ppt = n; 
}

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void slSort	(	void *	pList,
		int(*)(const void *elem1, const void *elem2)	compare
	)

Definition at line 321 of file common.c.

References freeMem(), needLargeMem(), slList::next, slCount(), and slReverse().

{
struct slList **pL = (struct slList **)pList;
struct slList *list = *pL;
int count;
count = slCount(list);
if (count > 1)
    {
    struct slList *el;
    struct slList **array;
    int i;
    array = needLargeMem(count * sizeof(*array));
    for (el = list, i=0; el != NULL; el = el->next, i++)
        array[i] = el;
    qsort(array, count, sizeof(array[0]), compare);
    list = NULL;
    for (i=0; i<count; ++i)
        {
        array[i]->next = list;
        list = array[i];
        }
    freeMem(array);
    slReverse(&list);
    *pL = list;       
    }
}

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void slUniqify	(	void *	pList,
		int(*)(const void *elem1, const void *elem2)	compare,
		void(*)()	free
	)

Definition at line 349 of file common.c.

References slAddHead, slPopHead(), slReverse(), and slSort().

{
struct slList **pSlList = (struct slList **)pList;
struct slList *oldList = *pSlList;
struct slList *newList = NULL, *el;

slSort(&oldList, compare);
while ((el = slPopHead(&oldList)) != NULL)
    {
    if ((newList == NULL) || (compare(&newList, &el) != 0))
        slAddHead(&newList, el);
    else if (free != NULL)
        free(el);
    }
slReverse(&newList);
*pSlList = newList;
}

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void spaceOut	(	FILE *	f,
		int	count
	)

Definition at line 1357 of file common.c.

Referenced by axtPrintTraditional(), and rTreeDump().

{
while (--count >= 0)
    fputc(' ', f);
}

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char* splitOffNonNumeric

(

char *

s

)

Definition at line 2051 of file common.c.

References cloneStringZ(), and skipToNumeric().

{
return cloneStringZ(s,skipToNumeric(s)-s);
}

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char* splitOffNumber

(

char *

db

)

Definition at line 2057 of file common.c.

References cloneString(), and skipToNumeric().

{
return cloneString(skipToNumeric(db));
}

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void starOut	(	FILE *	f,
		int	count
	)

Definition at line 1364 of file common.c.

{
while (--count >= 0)
    fputc('*', f);
}

boolean startsWith	(	char *	start,
		char *	string
	)

Definition at line 875 of file common.c.

References FALSE, and TRUE.

Referenced by aliLines(), bfSearchForLine(), blastFileNextGapped(), cgiParseMultipart(), codonLoadBias(), dtdParse(), emblLineGroup(), expandRelativePath(), getFileNameFromHdrSig(), getPostInput(), gffTnName(), gfPcrGetRanges(), gfQuerySeq(), gfQuerySeqTrans(), gfQuerySeqTransTrans(), hpfNext(), htmlExpandUrl(), htmlPageParse(), htmlPageValidateOrAbort(), initCgiInput(), lineFileParseHttpHeader(), lineFileSkipToLineStartingWith(), lineFileSlurpHttpBody(), mafMayFindCompPrefix(), mafMayFindCompSpecies(), mafMayOpen(), maskFromOut(), mgLoadGif(), netLineFileMayOpen(), netLineFileMayOpenCatchError(), netSkipHttpHeaderLines(), netSkipHttpHeaderLinesCatch(), netUrlHead(), netUrlOpen(), nextBlock(), nextBlockLine(), parseAnOption(), parseMultiParts(), parseSubTree(), pcrServer(), pslOutFormat(), pslxFileOpen(), pslxFileOpenWithMetaConfig(), qaCountBetween(), queryServer(), raNextRecord(), reasonablePrefix(), startServer(), stripString(), trixSearchWordResults(), and validateCgiUrl().

{
char c;
int i;

for (i=0; ;i += 1)
    {
    if ((c = start[i]) == 0)
        return TRUE;
    if (string[i] != c)
        return FALSE;
    }
}

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boolean startsWithWord	(	char *	firstWord,
		char *	line
	)

Definition at line 890 of file common.c.

References FALSE.

{
int len = strlen(firstWord);
int i;
for (i=0; i<len; ++i)
   if (firstWord[i] != line[i])
       return FALSE;
char c = line[len];
return c == 0 || isspace(c);
}

int stringArrayIx	(	char *	string,
		char *	array[],
		int	arraySize
	)

Definition at line 1457 of file common.c.

References differentWord().

Referenced by gfOutputAny().

{
int i;
for (i=0; i<arraySize; ++i)
    if (!differentWord(array[i], string))
        return i;
return -1;
}

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char* stringBetween	(	char *	start,
		char *	end,
		char *	haystack
	)

Definition at line 916 of file common.c.

References cloneMem(), and stringIn.

{
char *pos, *p;
int len;
if ((p = stringIn(start, haystack)) != NULL)
    {
    pos = p + strlen(start);
    if ((p = stringIn(end, pos)) != NULL)
        {
        len = p - pos;
        pos = cloneMem(pos, len + 1);
        pos[len] = 0;
        return pos;
        }
    }
return NULL;
}

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void stripChar	(	char *	s,
		char	c
	)

Definition at line 1086 of file common.c.

Referenced by axtScoreSchemeDnaWrite().

{
char *in = s, *out = s;
char b;

for (;;)
    {
    b = *out = *in++;
    if (b == 0)
       break;
    if (b != c)
       ++out;
    }
}

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void stripString	(	char *	s,
		char *	strip
	)

Definition at line 1102 of file common.c.

References startsWith().

{
char c, *in = s, *out = s;
int stripSize = strlen(strip);
char stripFirst = strip[0];

while ((c = *in) != 0)
    {
    c = *in;
    if (c == stripFirst)
        {
        if (startsWith(strip, in))
            {
            in += stripSize;
            continue;
            }
        }
    *out = c;
    ++out;
    ++in;
    }
*out = 0;
}

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char* strstrNoCase	(	char *	haystack,
		char *	needle
	)

Definition at line 1833 of file common.c.

References freeMem(), and needMem().

Referenced by containsStringNoCase().

{
char *haystackCopy = NULL;
char *needleCopy = NULL;
int index = 0;
int haystackLen = 0;
int needleLen = 0;
char *p, *q;

if (NULL == haystack || NULL == needle) 
    {
    return NULL;
    }

haystackLen = strlen(haystack);
needleLen = strlen(needle);

haystackCopy = (char*) needMem(haystackLen + 1);
needleCopy = (char*) needMem(needleLen + 1);

for(index = 0; index < haystackLen;  index++)
    {
    haystackCopy[index] = tolower(haystack[index]);
    }
haystackCopy[haystackLen] = 0; /* Null terminate */

for(index = 0; index < needleLen;  index++)
    {
    needleCopy[index] = tolower(needle[index]);
    }
needleCopy[needleLen] = 0; /* Null terminate */

p=strstr(haystackCopy, needleCopy);
q=haystackCopy;
 
freeMem(haystackCopy);
freeMem(needleCopy);

if(p==NULL) return NULL;

return p-q+haystack;
}

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void subChar	(	char *	s,
		char	oldChar,
		char	newChar
	)

Definition at line 1071 of file common.c.

Referenced by qaStatusOnPage(), semiUniqName(), and undosPath().

{
char c;
for (;;)
    {
    c = *s;
    if (c == 0)
        break;
    if (c == oldChar)
        *s = newChar;
    ++s;
    }
}

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void swapBytes	(	char *	a,
		char *	b,
		int	length
	)

Definition at line 127 of file common.c.

{
char c;
int i;

for (i=0; i<length; ++i)
    {
    c = a[i];
    a[i] = b[i];
    b[i] = c;
    }
}

void toggleCase	(	char *	s,
		int	size
	)

Definition at line 990 of file common.c.

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

{
char c;
int i;
for (i=0; i<size; ++i)
    {
    c = s[i];
    if (isupper(c))
        c = tolower(c);
    else if (islower(c))
        c = toupper(c);
    s[i] = c;
    }
}

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void toLowerN	(	char *	s,
		int	n
	)

Definition at line 982 of file common.c.

Referenced by bigBlat(), doBlat(), gfMakeOoc(), trixFindIndexStartLine(), and twoBitReadSeqFragExt().

{
int i;
for (i=0; i<n; ++i)
    s[i] = tolower(s[i]);
}

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void tolowers

(

char *

s

)

Definition at line 1060 of file common.c.

Referenced by bafWriteLine(), gfPcrClumps(), gfPcrOneViaNet(), netParseUrl(), outputFa(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), readPartHeaderMB(), wormFixupOrfName(), and wormGeneToOrfNames().

{
char c;
for (;;)
    {
    if ((c = *s) == 0) break;
    *s++ = tolower(c);
    }
}

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void toUpperN	(	char *	s,
		int	n
	)

Definition at line 974 of file common.c.

Referenced by bigBlat(), gdfUpcExons(), getWormGeneDna(), maskFromOut(), twoBitReadSeqFragExt(), and wormFixupOrfName().

{
int i;
for (i=0; i<n; ++i)
    s[i] = toupper(s[i]);
}

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void touppers

(

char *

s

)

Definition at line 1007 of file common.c.

Referenced by checkTagIsInside(), hashLookupUpperCase(), htmlPageValidateOrAbort(), oligoTm(), outputFa(), parseMultiParts(), rnaPair(), and wormGeneRange().

{
char c;
for (;;)
    {
    if ((c = *s) == 0) break;
    *s++ = toupper(c);
    }
}

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char* trimSpaces

(

char *

s

)

Definition at line 1346 of file common.c.

References eraseTrailingSpaces(), and skipLeadingSpaces().

Referenced by dnaLoadNextFromStack(), dnaLoadStackNew(), dtdParse(), dtdxTag(), firstWordInFile(), gfWebConfigRead(), netParseUrl(), readPartHeaderMB(), spacedColumnParseLine(), tabRowByFixedOffsets(), textOutInit(), and twoBitSpecNewFile().

{
if (s != NULL)
    {
    s = skipLeadingSpaces(s);
    eraseTrailingSpaces(s);
    }
return s;
}

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char* trueFalseString

(

boolean

b

)

Definition at line 1991 of file common.c.

{
return (b ? "true" : "false");
}

void uglyTime	(	char *	label,
			...
	)

Definition at line 1997 of file common.c.

References clock1000().

{
static long lastTime = 0;
long time = clock1000();
va_list args;
va_start(args, label);
if (label != NULL)
    {
    vfprintf(stdout, label, args);
    fprintf(stdout, ": %ld millis<BR>\n", time - lastTime);
    }
lastTime = time;
va_end(args);
}

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int vasafef	(	char *	buffer,
		int	bufSize,
		char *	format,
		va_list	args
	)

Definition at line 1885 of file common.c.

References errAbort().

Referenced by safef().

{
int sz = vsnprintf(buffer, bufSize, format, args);
/* note that some version return -1 if too small */
if ((sz < 0) || (sz >= bufSize))
    errAbort("buffer overflow, size %d, format: %s", bufSize, format);
return sz;
}

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void writeBits64	(	FILE *	f,
		bits64	x
	)

Definition at line 1584 of file common.c.

References mustWrite(), and UBYTE.

{
int i;
UBYTE buf[8];
for (i=7; i>=0; --i)
    {
    buf[i] = (UBYTE)(x&0xff);
    x >>= 8;
    }
mustWrite(f, buf, 8);
}

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void writeString	(	FILE *	f,
		char *	s
	)

Definition at line 1525 of file common.c.

References mustWrite(), UBYTE, warn(), and writeOne.

Referenced by twoBitWriteHeader().

{
UBYTE bLen;
int len = strlen(s);

if (len > 255)
    {
    warn("String too long in writeString (%d chars):\n%s", len, s);
    len = 255;
    }
bLen = len;
writeOne(f, bLen);
mustWrite(f, s, len);
}

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void zeroBytes	(	void *	vpt,
		int	count
	)

Definition at line 49 of file common.c.

Referenced by bitClear(), dnaBaseHistogram(), dnaMark0(), dnaMark1(), dnaMarkTriple(), ffShNeedle(), flyFaCommentIntoInfo(), gffClose(), gffOpen(), init_table(), initNtChars(), initNtCompTable(), initNtMixedCaseChars(), internetIpToDottedQuad(), makeIndex(), mgClearPixels(), mgFree(), mgSaveToGif(), saveNt4(), wormFaCommentIntoInfo(), and wormFreeCdnaInfo().

{
char *pt = (char*)vpt;
while (--count>=0)
    *pt++=0;
}

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---

Variable Documentation

char crLfChopper[] = "\n\r"

Definition at line 1274 of file common.c.

char* emptyStr = "" [static]

Definition at line 1955 of file common.c.

char* naStr = "n/a" [static]

Definition at line 1954 of file common.c.

char const rcsid[] = "$Id: common.c,v 1.108 2007/03/30 00:12:11 markd Exp $" [static]

Definition at line 12 of file common.c.

char whiteSpaceChopper[] = " \t\n\r"

Definition at line 1275 of file common.c.

Referenced by wormGeneToOrfNames().

---