inc/obscure.h File Reference

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Functions
long	incCounterFile (char *fileName)
int	digitsBaseTwo (unsigned long x)
int	digitsBaseTen (int x)
void	sprintLongWithCommas (char *s, long long l)
void	printLongWithCommas (FILE *f, long long l)
void	writeGulp (char *file, char *buf, int size)
void	readInGulp (char *fileName, char **retBuf, size_t *retSize)
void	readAllWords (char *fileName, char ***retWords, int *retWordCount, char **retBuf)
int	countWordsInFile (char *fileName)
slName *	readAllLines (char *fileName)
void	copyFile (char *source, char *dest)
void	copyOpenFile (FILE *inFh, FILE *outFh)
void	cpFile (int s, int d)
void *	intToPt (int i)
int	ptToInt (void *pt)
void *	sizetToPt (size_t i)
size_t	ptToSizet (void *pt)
boolean	parseQuotedString (char *in, char *out, char **retNext)
char *	nextQuotedWord (char **pLine)
char *	makeQuotedString (char *in, char quoteChar)
char *	makeEscapedString (char *in, char toEscape)
void	escCopy (char *in, char *out, char toEscape, char escape)
slName *	stringToSlNames (char *string)
slName *	commaSepToSlNames (char *commaSep)
slName *	charSepToSlNames (char *string, char c)
hash *	hashVarLine (char *line, int lineIx)
hash *	hashWordsInFile (char *fileName, int hashSize)
hash *	hashNameIntFile (char *fileName)
hash *	hashTwoColumnFile (char *fileName)
void	shuffleArrayOfPointers (void *pointerArray, int arraySize, int shuffleCount)
void	shuffleList (void *pList, int shuffleCount)
char *	stripCommas (char *position)
void	dotForUserInit (int dotMod)
void	dotForUser ()
void	spaceToUnderbar (char *s)

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Function Documentation

struct slName* charSepToSlNames	(	char *	string,
		char	c
	)			[read]

Definition at line 456 of file obscure.c.

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

Referenced by commaSepToSlNames().

{
struct slName *list = NULL, *el;
char *s, *e;

s = string;
while (s != NULL && s[0] != 0)
    {
    e = strchr(s, c);
    if (e == NULL)
        {
        el = slNameNew(s);
        slAddHead(&list, el);
        break;
        }
    else
        {
        el = slNameNewN(s, e - s);
        slAddHead(&list, el);
        s = e+1;
        }
    }
slReverse(&list);
return list;
}

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struct slName* commaSepToSlNames

(

char *

commaSep

)

[read]

Definition at line 486 of file obscure.c.

References charSepToSlNames().

Referenced by spacedColumnFromSizeCommaList().

{
return charSepToSlNames(commaSep, ',');
}

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void copyFile	(	char *	source,
		char *	dest
	)

Definition at line 185 of file obscure.c.

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

{
int bufSize = 64*1024;
char *buf = needMem(bufSize);
int bytesRead;
int s, d;

s = open(source, O_RDONLY);
if (s < 0)
    errAbort("Couldn't open %s. %s\n", source, strerror(errno));
d = creat(dest, 0777);
if (d < 0)
    {
    close(s);
    errAbort("Couldn't open %s. %s\n", dest, strerror(errno));
    }
while ((bytesRead = read(s, buf, bufSize)) > 0)
    {
    if (write(d, buf, bytesRead) < 0)
        errAbort("Write error on %s. %s\n", dest, strerror(errno));
    }
close(s);
if (close(d) != 0)
    errnoAbort("close failed");
freeMem(buf);
}

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void copyOpenFile	(	FILE *	inFh,
		FILE *	outFh
	)

Definition at line 213 of file obscure.c.

References errnoAbort().

{
int c;
while ((c = fgetc(inFh)) != EOF)
    fputc(c, outFh);
if (ferror(inFh))
    errnoAbort("file read failed");
if (ferror(outFh))
    errnoAbort("file write failed");
}

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int countWordsInFile

(

char *

fileName

)

Definition at line 113 of file obscure.c.

References chopByWhite(), lineFileClose(), lineFileNext(), lineFileOpen(), and TRUE.

{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *line;
int wordCount = 0;
while (lineFileNext(lf, &line, NULL))
    wordCount += chopByWhite(line, NULL, 0);
lineFileClose(&lf);
return wordCount;
}

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void cpFile	(	int	s,
		int	d
	)

Definition at line 225 of file obscure.c.

References freeMem(), and needMem().

{
int bufSize = 64*1024, readSize;
char *buf = needMem(bufSize);

for (;;)
    {
    readSize = read(s, buf, bufSize);
    if (readSize > 0)
        write(d, buf, readSize);
    if (readSize <= 0)
        break;
    }
freeMem(buf);
}

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int digitsBaseTen

(

int

x

)

Definition at line 53 of file obscure.c.

Referenced by axtPrintTraditional(), calcDigitCount(), mafWrite(), and maxDigits().

{
int digCount = 1;
if (x < 0)
    {
    digCount = 2;
    x = -x;
    }
while (x >= 10)
    {
    digCount += 1;
    x /= 10;
    }
return digCount;
}

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int digitsBaseTwo

(

unsigned long

x

)

Definition at line 41 of file obscure.c.

Referenced by dnaSeqHash(), ffCalcCdnaGapPenalty(), leftNextMatch(), rightNextMatch(), and twoBitOpen().

{
int digits = 0;
while (x)
    {
    digits += 1;
    x >>= 1;
    }
return digits;
}

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void dotForUser

(

)

Definition at line 602 of file obscure.c.

References _dotForUserMod.

{
static int dot = -10;
/* Check to see if dot has been initialized. */
if(dot == - 10)
    dot = _dotForUserMod;

if (--dot <= 0)
    {
    putc('.', stderr);
    fflush(stderr);
    dot = _dotForUserMod;
    }
}

void dotForUserInit

(

int

dotMod

)

Definition at line 595 of file obscure.c.

References _dotForUserMod.

{
assert(dotMod > 0);
_dotForUserMod = dotMod;
}

void escCopy	(	char *	in,
		char *	out,
		char	toEscape,
		char	escape
	)

Definition at line 342 of file obscure.c.

Referenced by makeEscapedString(), and makeQuotedString().

{
char c;
for (;;)
    {
    c = *in++;
    if (c == toEscape)
        *out++ = escape;
    *out++ = c;
    if (c == 0)
        break;
    }
}

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struct hash* hashNameIntFile

(

char *

fileName

)

[read]

Definition at line 140 of file obscure.c.

References hashAddInt(), hashNew, lineFileClose(), lineFileNeedNum(), lineFileOpen(), lineFileRow, and TRUE.

{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[2];
struct hash *hash = hashNew(16);
while (lineFileRow(lf, row))
    hashAddInt(hash, row[0], lineFileNeedNum(lf, row, 1));
lineFileClose(&lf);
return hash;
}

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struct hash* hashTwoColumnFile

(

char *

fileName

)

[read]

Definition at line 153 of file obscure.c.

References hashAdd(), hashNew, lineFileClose(), lineFileOpen(), lineFileRow, hash::lm, lmCloneString(), name, and TRUE.

{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[2];
struct hash *hash = hashNew(16);
while (lineFileRow(lf, row))
    {
    char *name = row[0];
    char *value = lmCloneString(hash->lm, row[1]);
    hashAdd(hash, name, value);
    }
lineFileClose(&lf);
return hash;
}

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struct hash* hashVarLine	(	char *	line,
		int	lineIx
	)			[read]

Definition at line 381 of file obscure.c.

References cloneString(), errAbort(), freez(), hashAdd(), newHash(), parseQuotedString(), skipLeadingSpaces(), and skipToSpaces().

                                            :
 *   var1=val1 var2='quoted val2' var3="another val" */
{
char *dupe = cloneString(line);
char *s = dupe, c;
char *var, *val;
struct hash *hash = newHash(8);

for (;;)
    {
    if ((var = skipLeadingSpaces(s)) == NULL)
        break;

    if ((c = *var) == 0)
        break;
    if (!isalpha(c))
        errAbort("line %d of custom input: variable needs to start with letter '%s'", lineIx, var);
    val = strchr(var, '=');
    if (val == NULL)
        {
        errAbort("line %d of var %s in custom input: %s \n missing = in var/val pair", lineIx, var, line);
        }
    *val++ = 0;
    c = *val;
    if (c == '\'' || c == '"')
        {
        if (!parseQuotedString(val, val, &s))
            errAbort("line %d of input: missing closing %c", lineIx, c);
        }
    else
        {
        s = skipToSpaces(val);
        if (s != NULL) *s++ = 0;
        }
    hashAdd(hash, var, cloneString(val));
    }
freez(&dupe);
return hash;
}

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struct hash* hashWordsInFile	(	char *	fileName,
		int	hashSize
	)			[read]

Definition at line 125 of file obscure.c.

References hashAdd(), lineFileClose(), lineFileNext(), lineFileOpen(), newHash(), nextWord(), and TRUE.

{
struct hash *hash = newHash(hashSize);
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *line, *word;
while (lineFileNext(lf, &line, NULL))
    {
    while ((word = nextWord(&line)) != NULL)
        hashAdd(hash, word, NULL);
    }
lineFileClose(&lf);
return hash;
}

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long incCounterFile

(

char *

fileName

)

Definition at line 17 of file obscure.c.

References errnoAbort().

Referenced by _makeTempName().

{
long val = 0;
FILE *f = fopen(fileName, "r+b");
if (f != NULL)
    {
    fread(&val, sizeof(val), 1, f);
    rewind(f);
    }
else
    {
    f = fopen(fileName, "wb");
    }
++val;
if (f != NULL)
    {
    fwrite(&val, sizeof(val), 1, f);
    if (fclose(f) != 0)
        errnoAbort("fclose failed");
    }
return val;
}

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void* intToPt

(

int

i

)

Definition at line 242 of file obscure.c.

{
char *pt = NULL;
return pt+i;
}

char* makeEscapedString	(	char *	in,
		char	toEscape
	)

Definition at line 358 of file obscure.c.

References countChars(), escCopy(), and needMem().

{
int newSize = strlen(in) + countChars(in, toEscape);
char *out = needMem(newSize+1);
escCopy(in, out, toEscape, '\\');
return out;
}

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char* makeQuotedString	(	char *	in,
		char	quoteChar
	)

Definition at line 369 of file obscure.c.

References countChars(), escCopy(), and needMem().

{
int newSize = 2 + strlen(in) + countChars(in, quoteChar);
char *out = needMem(newSize+1);
out[0] = quoteChar;
escCopy(in, out+1, quoteChar, '\\');
out[newSize-1] = quoteChar;
return out;
}

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char* nextQuotedWord

(

char **

pLine

)

Definition at line 319 of file obscure.c.

References nextWord(), parseQuotedString(), and skipLeadingSpaces().

{
char *line, c;
line = skipLeadingSpaces(*pLine);
if (line == NULL || line[0] == 0)
    return NULL;
c = *line;
if (c == '"' || c == '\'')
    {
    if (!parseQuotedString(line, line, pLine))
        return NULL;
    return line;
    }
else
    {
    return nextWord(pLine);
    }
}

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boolean parseQuotedString	(	char *	in,
		char *	out,
		char **	retNext
	)

Definition at line 274 of file obscure.c.

References FALSE, TRUE, and warn().

Referenced by apacheAccessLogParse(), hashVarLine(), htmlTagScan(), needQuotedString(), nextQuotedWord(), readQuotedString(), and stringToSlNames().

{
char c, *s = in;
int quoteChar = *s++;
boolean escaped = FALSE;

for (;;)
   {
   c = *s++;
   if (c == 0)
       {
       warn("Unmatched %c", quoteChar);
       return FALSE;
       }
   if (escaped)
       {
       if (c == '\\' || c == quoteChar)
          *out++ = c;
       else
          {
          *out++ = '\\';
          *out++ = c;
          }
       escaped = FALSE;
       }
   else
       {
       if (c == '\\')
           escaped = TRUE;
       else if (c == quoteChar)
           break;
       else
           *out++ = c;
       }
   }
*out = 0;
if (retNext != NULL)
    *retNext = s;
return TRUE;
}

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void printLongWithCommas	(	FILE *	f,
		long long	l
	)

Definition at line 525 of file obscure.c.

References sprintLongWithCommas().

{
char ascii[32];
sprintLongWithCommas(ascii, l);
fprintf(f, "%s", ascii);
}

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int ptToInt

(

void *

pt

)

Definition at line 250 of file obscure.c.

Referenced by hashIntSum(), hashIntVal(), and hashIntValDefault().

{
char *a = NULL, *b = pt;
return b - a;
}

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size_t ptToSizet

(

void *

pt

)

Definition at line 266 of file obscure.c.

{
char *a = NULL, *b = pt;
return b - a;
}

struct slName* readAllLines

(

char *

fileName

)

[read]

Definition at line 169 of file obscure.c.

References lineFileNext(), lineFileOpen(), newSlName(), slAddHead, slReverse(), and TRUE.

{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct slName *list = NULL, *el;
char *line;

while (lineFileNext(lf, &line, NULL))
     {
     el = newSlName(line);
     slAddHead(&list, el);
     }
slReverse(&list);
return list;
}

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void readAllWords	(	char *	fileName,
		char ***	retWords,
		int *	retWordCount,
		char **	retBuf
	)

Definition at line 92 of file obscure.c.

References chopByWhite(), needMem(), and readInGulp().

Referenced by gfClientFileArray().

{
int wordCount;
char *buf = NULL;
char **words = NULL;
size_t bufSize;

readInGulp(fileName, &buf, &bufSize);
wordCount = chopByWhite(buf, NULL, 0);
if (wordCount != 0)
    {
    words = needMem(wordCount * sizeof(words[0]));
    chopByWhite(buf, words, wordCount);
    }
*retWords = words;
*retWordCount = wordCount;
*retBuf = buf;
}

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void readInGulp	(	char *	fileName,
		char **	retBuf,
		size_t *	retSize
	)

Definition at line 78 of file obscure.c.

References fileSize(), mustOpen(), mustRead(), and needLargeMem().

Referenced by axtScoreSchemeProteinRead(), htmlIncludeFile(), htmlPageGet(), and readAllWords().

{
size_t size = (size_t)fileSize(fileName);
char *buf;
FILE *f = mustOpen(fileName, "rb");
*retBuf = buf = needLargeMem(size+1);
mustRead(f, buf, size);
buf[size] = 0;      /* Just in case it needs zero termination. */
fclose(f);
if (retSize != NULL)
    *retSize = size;
}

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void shuffleArrayOfPointers	(	void *	pointerArray,
		int	arraySize,
		int	shuffleCount
	)

Definition at line 533 of file obscure.c.

Referenced by shuffleList().

{
void **array = pointerArray, *pt;
int i, randIx;

for (i=0; i<arraySize; ++i)
    {
    randIx = rand() % arraySize;
    pt = array[i];
    array[i] = array[randIx];
    array[randIx] = pt;
    }
}

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void shuffleList	(	void *	pList,
		int	shuffleCount
	)

Definition at line 548 of file obscure.c.

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

                                    :
 *     randomizeList(&list)
 * where list is a pointer to a structure that
 * begins with a next field. */
{
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;
    for (i=0; i<4; ++i)
        shuffleArrayOfPointers(array, count, shuffleCount);
    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* sizetToPt

(

size_t

i

)

Definition at line 258 of file obscure.c.

{
char *pt = NULL;
return pt+i;
}

void spaceToUnderbar

(

char *

s

)

Definition at line 618 of file obscure.c.

{
char c;
while ((c = *s) != 0)
    {
    if (isspace(c))
        *s = '_';
    ++s;
    }
}

void sprintLongWithCommas	(	char *	s,
		long long	l
	)

Definition at line 493 of file obscure.c.

Referenced by carefulAlloc(), ncbiBlastOut(), printLongWithCommas(), and wuBlastOut().

{
long long billions, millions, thousands;
if (l >= 1000000000)
    {
    billions = l/1000000000;
    l -= billions * 1000000000;
    millions = l/1000000;
    l -= millions * 1000000;
    thousands = l/1000;
    l -= thousands * 1000;
    sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
    }
else if (l >= 1000000)
    {
    millions = l/1000000;
    l -= millions * (long long)1000000;
    thousands = l/1000;
    l -= thousands * 1000;
    sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
    }
else if (l >= 1000)
    {
    thousands = l/1000;
    l -= thousands * 1000;
    sprintf(s, "%lld,%03lld", thousands, l);
    }
else
    sprintf(s, "%lld", l);
}

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struct slName* stringToSlNames

(

char *

string

)

[read]

Definition at line 422 of file obscure.c.

References cloneString(), errAbort(), freeMem(), name, parseQuotedString(), skipLeadingSpaces(), skipToSpaces(), slAddHead, slNameNew, and slReverse().

{
struct slName *list = NULL, *name;
char *dupe = cloneString(string);
char c, *s = dupe, *e;

for (;;)
    {
    if ((s = skipLeadingSpaces(s)) == NULL)
        break;
    if ((c = *s) == 0)
        break;
    if (c == '\'' || c == '"')
        {
        if (!parseQuotedString(s, s, &e))
            errAbort("missing closing %c in %s", c, string);
        }
    else
        {
        e = skipToSpaces(s);
        if (e != NULL) *e++ = 0;
        }
    name = slNameNew(s);
    slAddHead(&list, name);
    s = e;
    }
freeMem(dupe);
slReverse(&list);
return list;
}

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char* stripCommas

(

char *

position

)

Definition at line 580 of file obscure.c.

References cloneString().

{
char *newPos = cloneString(position);
char *nPtr = newPos;

if (position == NULL)
    return NULL;
while((*nPtr = *position++))
    if (*nPtr != ',')
        nPtr++;

return newPos;
}

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void writeGulp	(	char *	file,
		char *	buf,
		int	size
	)

Definition at line 70 of file obscure.c.

References carefulClose(), mustOpen(), and mustWrite().

{
FILE *f = mustOpen(file, "w");
mustWrite(f, buf, size);
carefulClose(&f);
}

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