lib/common.c

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/* Commonly used routines in a wide range of applications.
 * Strings, singly-linked lists, and a little file i/o.  
 *
 * This file is copyright 2002 Jim Kent, but license is hereby
 * granted for all use - public, private or commercial. */

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

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

void *cloneMem(void *pt, size_t size)
/* Allocate a new buffer of given size, and copy pt to it. */
{
void *newPt = needLargeMem(size);
memcpy(newPt, pt, size);
return newPt;
}

char *cloneStringZ(char *s, int size)
/* Make a zero terminated copy of string in memory */
{
char *d = needMem(size+1);
memcpy(d, s, size);
d[size] = 0;
return d;
}

char *cloneString(char *s)
/* Make copy of string in dynamic memory */
{
if (s == NULL)
    return NULL;
else
    return cloneStringZ(s, strlen(s));
}

char *cloneLongString(char *s)
/* Make clone of long string. */
{
size_t size = strlen(s);
return cloneMem(s, size+1);
}


/* fill a specified area of memory with zeroes */
void zeroBytes(void *vpt, int count)
{
char *pt = (char*)vpt;
while (--count>=0)
    *pt++=0;
}

/* Reverse the order of the bytes. */
void reverseBytes(char *bytes, long length)
{
long halfLen = (length>>1);
char *end = bytes+length;
char c;
while (--halfLen >= 0)
    {
    c = *bytes;
    *bytes++ = *--end;
    *end = c;
    }
}

void reverseInts(int *a, int length)
/* Reverse the order of the integer array. */
{
int halfLen = (length>>1);
int *end = a+length;
int c;
while (--halfLen >= 0)
    {
    c = *a;
    *a++ = *--end;
    *end = c;
    }
}

void reverseUnsigned(unsigned *a, int length)
/* Reverse the order of the unsigned array. */
{
int halfLen = (length>>1);
unsigned *end = a+length;
unsigned c;
while (--halfLen >= 0)
    {
    c = *a;
    *a++ = *--end;
    *end = c;
    }
}

void reverseDoubles(double *a, int length)
/* Reverse the order of the double array. */
{
int halfLen = (length>>1);
double *end = a+length;
double c;
while (--halfLen >= 0)
    {
    c = *a;
    *a++ = *--end;
    *end = c;
    }
}

void reverseStrings(char **a, int length)
/* Reverse the order of the char* array. */
{
int halfLen = (length>>1);
char **end = a+length;
char *c;
while (--halfLen >= 0)
    {
    c = *a;
    *a++ = *--end;
    *end = c;
    }
}

/* Swap buffers a and b. */
void swapBytes(char *a, char *b, int length)
{
char c;
int i;

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


/* Count up elements in list. */
int slCount(void *list)
{
struct slList *pt = (struct slList *)list;
int len = 0;

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

void *slElementFromIx(void *list, int ix)
/* Return the ix'th element in list.  Returns NULL
 * if no such element. */
{
struct slList *pt = (struct slList *)list;
int i;
for (i=0;i<ix;i++)
    {
    if (pt == NULL) return NULL;
    pt = pt->next;
    }
return pt;
}

int slIxFromElement(void *list, void *el)
/* Return index of el in list.  Returns -1 if not on list. */
{
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)
/* Returns last element in list or NULL if none. */
{
struct slList *next, *el;
if ((el = list) == NULL)
    return NULL;
while ((next = el->next) != NULL)
    el = next;
return el;
}

/* Add new node to tail of list.
 * Usage:
 *    slAddTail(&list, node);
 * where list and nodes are both pointers to structure
 * that begin with a next pointer. 
 */
void slAddTail(void *listPt, void *node)
{
struct slList **ppt = (struct slList **)listPt;
struct slList *n = (struct slList *)node;

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

/* Add new node to start of list.
 * Usage:
 *    slAddHead(&list, node);
 * where list and nodes are both pointers to structure
 * that begin with a next pointer. 
 */
void slSafeAddHead(void *listPt, void *node)
{
struct slList **ppt = (struct slList **)listPt;
struct slList *n = (struct slList *)node;

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


void *slPopHead(void *vListPt)
/* Return head of list and remove it from list. (Fast) */
{
struct slList **listPt = (struct slList **)vListPt;
struct slList *el = *listPt;
if (el != NULL)
    {
    *listPt = el->next;
    el->next = NULL;
    }
return el;
}

void *slPopTail(void *vListPt)
/* Return tail of list and remove it from list. (Not so fast) */
{
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;
}



void *slCat(void *va, void *vb)
/* Return concatenation of lists a and b.
 * Example Usage:
 *   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;
}

void slReverse(void *listPt)
/* Reverse order of a list.
 * Usage:
 *    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;
}

void slFreeList(void *listPt)
/* Free list */
{
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;
}

void slSort(void *pList, int (*compare )(const void *elem1,  const void *elem2))
/* Sort a singly linked list with Qsort and a temporary array. */
{
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;       
    }
}

void slUniqify(void *pList, int (*compare )(const void *elem1,  const void *elem2), void (*free)())
/* Return sorted list with duplicates removed. 
 * Compare should be same type of function as slSort's compare (taking
 * pointers to pointers to elements.  Free should take a simple
 * pointer to dispose of duplicate element, and can be NULL. */
{
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;
}

boolean slRemoveEl(void *vpList, void *vToRemove)
/* Remove element from doubly linked list.  Usage:
 *    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;
}

struct slInt *slIntNew(int x)
/* Return a new int. */
{
struct slInt *a;
AllocVar(a);
a->val = x;
return a;
}

int slIntCmp(const void *va, const void *vb)
/* Compare two slInts. */
{
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)
/* Compare two slInts in reverse direction. */
{
const struct slInt *a = *((struct slInt **)va);
const struct slInt *b = *((struct slInt **)vb);
return b->val - a->val;
}

static int doubleCmp(const void *va, const void *vb)
/* Compare function to sort array of doubles. */
{
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;
}

void doubleSort(int count, double *array)
/* Sort an array of doubles. */
{
if (count > 1)
qsort(array, count, sizeof(array[0]), doubleCmp);
}

double doubleMedian(int count, double *array)
/* Return median value in array.  This will sort
 * the array as a side effect. */
{
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;
}

struct slDouble *slDoubleNew(double x)
/* Return a new double. */
{
struct slDouble *a;
AllocVar(a);
a->val = x;
return a;
}

int slDoubleCmp(const void *va, const void *vb)
/* Compare two slDoubles. */
{
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)
/* Return median value on list. */
{
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;
}

static int intCmp(const void *va, const void *vb)
/* Compare function to sort array of ints. */
{
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;
}

void intSort(int count, int *array)
/* Sort an array of ints. */
{
if (count > 1)
qsort(array, count, sizeof(array[0]), intCmp);
}

int intMedian(int count, int *array)
/* Return median value in array.  This will sort
 * the array as a side effect. */
{
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;
}


struct slName *newSlName(char *name)
/* Return a new name. */
{
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;
}

struct slName *slNameNewN(char *name, int size)
/* Return new slName of given size. */
{
struct slName *sn = needMem(sizeof(*sn) + size);
memcpy(sn->name, name, size);
return sn;
}

int slNameCmpCase(const void *va, const void *vb)
/* Compare two slNames, ignore case. */
{
const struct slName *a = *((struct slName **)va);
const struct slName *b = *((struct slName **)vb);
return strcasecmp(a->name, b->name);
}

void slNameSortCase(struct slName **pList)
/* Sort slName list, ignore case. */
{
slSort(pList, slNameCmpCase);
}

int slNameCmp(const void *va, const void *vb)
/* Compare two slNames. */
{
const struct slName *a = *((struct slName **)va);
const struct slName *b = *((struct slName **)vb);
return strcmp(a->name, b->name);
}

void slNameSort(struct slName **pList)
/* Sort slName list. */
{
slSort(pList, slNameCmp);
}

boolean slNameInList(struct slName *list, char *string)
/* Return true if string is in name list */
{
struct slName *el;
for (el = list; el != NULL; el = el->next)
    if (sameWord(string, el->name))
        return TRUE;
return FALSE;
}

void *slNameFind(void *list, char *string)
/* Return first element of slName list (or any other list starting
 * with next/name fields) that matches string. */
{
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)
/* Return index of first element of slName list (or any other 
 * list starting with next/name fields) that matches string.
 * Return -1 if not found. */
{
struct slName *el;
int ix = 0;
for (el = list; el != NULL; el = el->next, ix++)
    if (sameString(string, el->name))
        return ix;
return -1;
}

char *slNameStore(struct slName **pList, char *string)
/* Put string into list if it's not there already.  
 * Return the version of string stored in list. */
{
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;
}

struct slName *slNameAddHead(struct slName **pList, char *name)
/* Add name to start of list and return it. */
{
struct slName *el = slNameNew(name);
slAddHead(pList, el);
return el;
}

struct slName *slNameAddTail(struct slName **pList, char *name)
/* Add name to end of list (not efficient for long lists),
 * and return it. */
{
struct slName *el = slNameNew(name);
slAddTail(pList, el);
return el;
}

struct slName *slNameCloneList(struct slName *list)
/* Return clone of list. */
{
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;
}

struct slName *slNameListFromString(char *s, char delimiter)
/* Return list of slNames gotten from parsing delimited string.
 * The final delimiter is optional. a,b,c  and a,b,c, are equivalent
 * for comma-delimited lists. */
{
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;
}

struct slName *slNameLoadReal(char *fileName)
/* load file lines that are not blank or start with a '#' into a slName
 * list */
{
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;
}

struct slRef *refOnList(struct slRef *refList, void *val)
/* Return ref if val is already on list, otherwise NULL. */
{
struct slRef *ref;
for (ref = refList; ref != NULL; ref = ref->next)
    if (ref->val == val)
        return ref;
return NULL;
}

struct slRef *slRefNew(void *val)
/* Create new slRef element. */
{
struct slRef *ref;
AllocVar(ref);
ref->val = val;
return ref;
}

void refAdd(struct slRef **pRefList, void *val)
/* Add reference to list. */
{
struct slRef *ref;
AllocVar(ref);
ref->val = val;
slAddHead(pRefList, ref);
}

void refAddUnique(struct slRef **pRefList, void *val)
/* Add reference to list if not already on list. */
{
if (refOnList(*pRefList, val) == NULL)
    {
    refAdd(pRefList, val);
    }
}

struct slRef *refListFromSlList(void *list)
/* Make a reference list that mirrors a singly-linked list. */
{
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;
}


struct slPair *slPairNew(char *name, void *val)
/* Allocate new name/value pair. */
{
struct slPair *el;
AllocVar(el);
el->name = cloneString(name);
el->val = val;
return el;
}

void slPairAdd(struct slPair **pList, char *name, void *val)
/* Add new slPair to head of list. */
{
struct slPair *el = slPairNew(name, val);
slAddHead(pList, el);
}

void slPairFree(struct slPair **pEl)
/* Free up struct and name.  (Don't free up values.) */
{
struct slPair *el = *pEl;
if (el != NULL)
    {
    freeMem(el->name);
    freez(pEl);
    }
}

void slPairFreeList(struct slPair **pList)
/* Free up list.  (Don't free up values.) */
{
struct slPair *el, *next;

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

void slPairFreeVals(struct slPair *list)
/* Free up all values on list. */
{
struct slPair *el;
for (el = list; el != NULL; el = el->next)
    freez(&el->val);
}

void slPairFreeValsAndList(struct slPair **pList)
/* Free up all values on list and list itself */
{
slPairFreeVals(*pList);
slPairFreeList(pList);
}

struct slPair *slPairFind(struct slPair *list, char *name)
/* Return list element of given name, or NULL if not found. */
{
struct slPair *el;
for (el = list; el != NULL; el = el->next)
    if (sameString(name, el->name))
        break;
return el;
}

void *slPairFindVal(struct slPair *list, char *name)
/* Return value associated with name in list, or NULL if not found. */
{
struct slPair *el = slPairFind(list, name);
if (el == NULL)
    return NULL;
return el->val;
}


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

int differentWord(char *s1, char *s2)
/* strcmp ignoring case - returns zero if strings are
 * the same (ignoring case) otherwise returns difference
 * between first non-matching characters. */
{
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;
    }
}

int differentStringNullOk(char *a, char *b)
/* Returns 0 if two strings (either of which may be NULL)
 * are the same.  Otherwise it returns a positive or negative
 * number depending on the alphabetical order of the two
 * strings.
 * This is basically a strcmp that can handle NULLs in
 * the input.  If used in a sort the NULLs will end
 * up before any of the cases with data.   */
{
if (a == b)
    return FALSE;
else if (a == NULL)
    return -1;
else if (b == NULL)
    return 1;
else
    return strcmp(a,b) != 0;
}

boolean startsWith(char *start,char *string)
/* Returns TRUE if string begins with start. */
{
char c;
int i;

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

boolean startsWithWord(char *firstWord, char *line)
/* Return TRUE if first white-space-delimited word in line
 * is same as firstWord.  Comparison is case sensitive. */
{
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);
}

char *rStringIn(char *needle, char *haystack)
/* Return last position of needle in haystack, or NULL if it's not there. */
{
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;
}

char *stringBetween(char *start, char *end, char *haystack)
/* Return string between start and end strings, or NULL if
 * none found.  The first such instance is returned. 
 * String must be freed by caller. */
{
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;
}

boolean endsWith(char *string, char *end)
/* Returns TRUE if string ends with end. */
{
int sLen, eLen, offset;
sLen = strlen(string);
eLen = strlen(end);
offset = sLen - eLen;
if (offset < 0)
    return FALSE;
return sameString(string+offset, end);
}

char lastChar(char *s)
/* Return last character in string. */
{
if (s == NULL || s[0] == 0)
    return 0;
return s[strlen(s)-1];
}

char *memMatch(char *needle, int nLen, char *haystack, int hLen)
/* Returns first place where needle (of nLen chars) matches
 * haystack (of hLen chars) */
{
char c = *needle++;
nLen -= 1;
hLen -= nLen;
while (--hLen >= 0)
    {   
    if (*haystack++ == c && memcmp(needle, haystack, nLen) == 0)
        {
        return haystack-1;
        }
    }
return NULL;
}

void toUpperN(char *s, int n)
/* Convert a section of memory to upper case. */
{
int i;
for (i=0; i<n; ++i)
    s[i] = toupper(s[i]);
}

void toLowerN(char *s, int n)
/* Convert a section of memory to upper case. */
{
int i;
for (i=0; i<n; ++i)
    s[i] = tolower(s[i]);
}

void toggleCase(char *s, int size)
/* toggle upper and lower case chars in string. */
{
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;
    }
}


void touppers(char *s)
/* Convert entire string to upper case. */
{
char c;
for (;;)
    {
    if ((c = *s) == 0) break;
    *s++ = toupper(c);
    }
}

char *replaceChars(char *string, char *old, char *new)
/*
  Replaces the old with the new. The old and new string need not be of equal size
 Can take any length string.
 Return value needs to be freeMem'd.
*/
{
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;
}

void tolowers(char *s)
/* Convert entire string to lower case */
{
char c;
for (;;)
    {
    if ((c = *s) == 0) break;
    *s++ = tolower(c);
    }
}

void subChar(char *s, char oldChar, char newChar)
/* Substitute newChar for oldChar throughout string s. */
{
char c;
for (;;)
    {
    c = *s;
    if (c == 0)
        break;
    if (c == oldChar)
        *s = newChar;
    ++s;
    }
}

void stripChar(char *s, char c)
/* Remove all occurences of c from s. */
{
char *in = s, *out = s;
char b;

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

void stripString(char *s, char *strip)
/* Remove all occurences of strip from s. */
{
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;
}

int countChars(char *s, char c)
/* Return number of characters c in string s. */
{
char a;
int count = 0;
while ((a = *s++) != 0)
    if (a == c)
        ++count;
return count;
}

int countCharsN(char *s, char c, int size)
/* Return number of characters c in string s of given size. */
{
int i;
int count = 0;
for (i=0; i<size; ++i)
    if (s[i] == c)
        ++count;
return count;
}

int countLeadingChars(char *s, char c)
/* Count number of characters c at start of string. */
{
int count = 0;
while (*s++ == c)
   ++count;
return count;
}

int countSame(char *a, char *b)
/* Count number of characters that from start in a,b that are same. */
{
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;
}


/* int chopString(in, sep, outArray, outSize); */
/* This chops up the input string (cannabilizing it)
 * into an array of zero terminated strings in
 * outArray.  It returns the number of strings. 
 * If you pass in NULL for outArray, it will just
 * return the number of strings that it *would*
 * chop. */
int chopString(char *in, char *sep, char *outArray[], int outSize)
{
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;
}

int chopByWhite(char *in, char *outArray[], int outSize)
/* Like chopString, but specialized for white space separators. */
{
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;
}

int chopByChar(char *in, char chopper, char *outArray[], int outSize)
/* Chop based on a single character. */
{
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;
}

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


char *skipLeadingSpaces(char *s)
/* Return first non-white space. */
{
char c;
if (s == NULL) return NULL;
for (;;)
    {
    c = *s;
    if (!isspace(c))
        return s;
    ++s;
    }
}

/* Return first white space or NULL if none.. */
char *skipToSpaces(char *s)
{
char c;
if (s == NULL)
    return NULL;
for (;;)
    {
    c = *s;
    if (c == 0)
        return NULL;
    if (isspace(c))
        return s;
    ++s;
    }
}



void eraseTrailingSpaces(char *s)
/* Replace trailing white space with zeroes. */
{
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;
    }
}

/* Remove white space from a string */
void eraseWhiteSpace(char *s)
{
char *in, *out;
char c;

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

char *trimSpaces(char *s)
/* Remove leading and trailing white space. */
{
if (s != NULL)
    {
    s = skipLeadingSpaces(s);
    eraseTrailingSpaces(s);
    }
return s;
}

void spaceOut(FILE *f, int count)
/* Put out some spaces to file. */
{
while (--count >= 0)
    fputc(' ', f);
}

void starOut(FILE *f, int count)
/* Put out some asterisks to file. */
{
while (--count >= 0)
    fputc('*', f);
}

boolean hasWhiteSpace(char *s)
/* Return TRUE if there is white space in string. */
{
char c;
while ((c = *s++) != 0)
    if (isspace(c))
        return TRUE;
return FALSE;
}

char *firstWordInLine(char *line)
/* Returns first word in line if any (white space separated).
 * Puts 0 in place of white space after word. */
{
char *e;
line = skipLeadingSpaces(line);
if ((e = skipToSpaces(line)) != NULL)
    *e = 0;
return line;
}

char *lastWordInLine(char *line)
/* Returns last word in line if any (white space separated).
 * Returns NULL if string is empty.  Removes any terminating white space
 * from line. */
{
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;
}

char *nextWord(char **pLine)
/* Return next word in *pLine and advance *pLine to next
 * word. */
{
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;
}

char *nextTabWord(char **pLine)
/* Return next tab-separated word. */
{
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;
}

int stringArrayIx(char *string, char *array[], int arraySize)
/* Return index of string in array or -1 if not there. */
{
int i;
for (i=0; i<arraySize; ++i)
    if (!differentWord(array[i], string))
        return i;
return -1;
}

int ptArrayIx(void *pt, void *array, int arraySize)
/* Return index of pt in array or -1 if not there. */
{
int i;
void **a = array;
for (i=0; i<arraySize; ++i)
    {
    if (pt == a[i])
        return i;
    }
return -1;
}



FILE *mustOpen(char *fileName, char *mode)
/* Open a file - or squawk and die. */
{
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;
}

void mustWrite(FILE *file, void *buf, size_t size)
/* Write to a file or squawk and die. */
{
if (size != 0 && fwrite(buf, size, 1, file) != 1)
    {
    errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
    }
}


void mustRead(FILE *file, void *buf, size_t size)
/* Read from a file or squawk and die. */
{
if (size != 0 && fread(buf, size, 1, file) != 1)
    errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
}

void writeString(FILE *f, char *s)
/* Write a 255 or less character string to a file.
 * This will write the length of the string in the first
 * byte then the string itself. */
{
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);
}

char *readString(FILE *f)
/* Read a string (written with writeString) into
 * memory.  freeMem the result when done. */
{
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;
}

char *mustReadString(FILE *f)
/* Read a string.  Squawk and die at EOF or if any problem. */
{
char *s = readString(f);
if (s == NULL)
    errAbort("Couldn't read string");
return s;
}

 
boolean fastReadString(FILE *f, char buf[256])
/* Read a string into buffer, which must be long enough
 * to hold it.  String is in 'writeString' format. */
{
UBYTE bLen;
int len;
if (!readOne(f, bLen))
    return FALSE;
if ((len = bLen)> 0)
    mustRead(f, buf, len);
buf[len] = 0;
return TRUE;
} 

void writeBits64(FILE *f, bits64 x)
/* Write out 64 bit number in manner that is portable across architectures */
{
int i;
UBYTE buf[8];
for (i=7; i>=0; --i)
    {
    buf[i] = (UBYTE)(x&0xff);
    x >>= 8;
    }
mustWrite(f, buf, 8);
}

bits64 readBits64(FILE *f)
/* Write out 64 bit number in manner that is portable across architectures */
{
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;
}


char *addSuffix(char *head, char *suffix)
/* Return a needMem'd string containing "headsuffix". Should be free'd
 when finished. */
{
char *ret = NULL;
int size = strlen(head) + strlen(suffix) +1;
ret = needMem(sizeof(char)*size);
snprintf(ret, size, "%s%s", head, suffix);
return ret;
}

void chopSuffix(char *s)
/* Remove suffix (last . in string and beyond) if any. */
{
char *e = strrchr(s, '.');
if (e != NULL)
    *e = 0;
}
    
void chopSuffixAt(char *s, char c)
/* Remove end of string from first occurrence of char c. 
 * chopSuffixAt(s, '.') is equivalent to regular chopSuffix. */
{
char *e = strrchr(s, c);
if (e != NULL)
    *e = 0;
}

char *chopPrefixAt(char *s, char c)
/* Like chopPrefix, but can chop on any character, not just '.' */
{
char *e = strchr(s, c);
if (e == NULL) return s;
*e++ = 0;
return e;
}

char *chopPrefix(char *s)
/* This will replace the first '.' in a string with
 * 0, and return the character after this.  If there
 * is no '.' in the string this will just return the
 * unchanged s passed in. */
{
return chopPrefixAt(s, '.');
}


    
boolean carefulCloseWarn(FILE **pFile)
/* Close file if open and null out handle to it. 
 * Return FALSE and print a warning message if there
 * is a problem.*/
{
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;
}

void carefulClose(FILE **pFile)
/* Close file if open and null out handle to it. 
 * Warn and abort if there's a problem. */
{
if (!carefulCloseWarn(pFile))
    noWarnAbort();
}
        
char *firstWordInFile(char *fileName, char *wordBuf, int wordBufSize)
/* Read the first word in file into wordBuf. */
{
FILE *f = mustOpen(fileName, "r");
fgets(wordBuf, wordBufSize, f);
fclose(f);
return trimSpaces(wordBuf);
}

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

int intAbs(int a)
/* Return integer absolute value */
{
return (a >= 0 ? a : -a);
}

int  rangeIntersection(int start1, int end1, int start2, int end2)
/* Return amount of bases two ranges intersect over, 0 or negative if no
 * intersection. */
{
int s = max(start1,start2);
int e = min(end1,end2);
return e-s;
}

int positiveRangeIntersection(int start1, int end1, int start2, int end2)
/* Return number of bases in intersection of two ranges, or
 * zero if they don't intersect. */
{
int ret = rangeIntersection(start1,end1,start2,end2);
if (ret < 0)
    ret = 0;
return ret;
}

bits32 byteSwap32(bits32 a)
/* Return byte-swapped version of a */
{
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;
}

void removeReturns(char *dest, char *src) 
/* Removes the '\r' character from a string.
 * The source and destination strings can be the same, if there are 
 * no other threads */
{
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* readLine(FILE* fh)
/* Read a line of any size into dynamic memory, return null on EOF */
{
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;
}

boolean fileExists(char *fileName)
/* Return TRUE if file exists (may replace this with non-
 * portable faster way some day). */
{
/* 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;
}

/*
 Friendly name for strstrNoCase
*/
char *containsStringNoCase(char *haystack, char *needle)
{
return strstrNoCase(haystack, needle);
}

char *strstrNoCase(char *haystack, char *needle)
/*
  A case-insensitive strstr function
Will also robustly handle null strings
param haystack - The string to be searched
param needle - The string to look for in the haystack string

return - The position of the first occurence of the desired substring
or -1 if it is not found
 */
{
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;
}

int vasafef(char* buffer, int bufSize, char *format, va_list args)
/* Format string to buffer, vsprintf style, only with buffer overflow
 * checking.  The resulting string is always terminated with zero byte. */
{
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;
}

int safef(char* buffer, int bufSize, char *format, ...)
/* Format string to buffer, vsprintf style, only with buffer overflow
 * checking.  The resulting string is always terminated with zero byte. */
{
int sz;
va_list args;
va_start(args, format);
sz = vasafef(buffer, bufSize, format, args);
va_end(args);
return sz;
}

void safecpy(char *buf, size_t bufSize, const char *src)
/* copy a string to a buffer, with bounds checking.*/
{
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);
}

void safencpy(char *buf, size_t bufSize, const char *src, size_t n)
/* copy n characters from a string to a buffer, with bounds checking.
 * Unlike strncpy, always null terminates the result */
{
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';
}

void safecat(char *buf, size_t bufSize, const char *src)
/* Append  a string to a buffer, with bounds checking.*/
{
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);
}

void safencat(char *buf, size_t bufSize, const char *src, size_t n)
/* append n characters from a string to a buffer, with bounds checking. */
{
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';
}


static char *naStr = "n/a";
static char *emptyStr = "";

char *naForNull(char *s)
/* Return 'n/a' if s is NULL, otherwise s. */
{
if (s == NULL) 
   s = naStr;
return s;
}

char *naForEmpty(char *s)
/* Return n/a if s is "" or NULL, otherwise s. */
{
if (s == NULL || s[0] == 0)
    s = naStr;
return s;
}

char *emptyForNull(char *s)
/* Return "" if s is NULL, otherwise s. */
{
if (s == NULL)
   s = emptyStr;
return s;
}

char *nullIfAllSpace(char *s)
/* Return NULL if s is all spaces, otherwise s. */
{
s = skipLeadingSpaces(s);
if (s != NULL)
    if (s[0] == 0)
        s = NULL;
return s;
}

char *trueFalseString(boolean b)
/* Return "true" or "false" */
{
return (b ? "true" : "false");
}

void uglyTime(char *label, ...)
/* Print label and how long it's been since last call.  Call with 
 * a NULL label to initialize. */
{
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);
}

void makeDirs(char* path)
/* make a directory, including parent directories */
{
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);
}

char *skipNumeric(char *s)
/* Return first char of s that's not a digit */
{
while (isdigit(*s))
   ++s;
return s;
}

char *skipToNumeric(char *s)
/* skip up to where numeric digits appear */
{
while (*s != 0 && !isdigit(*s))
    ++s;
return s;
}

char *splitOffNonNumeric(char *s)
/* Split off non-numeric part, e.g. mm of mm8. Result should be freed when done */
{
return cloneStringZ(s,skipToNumeric(s)-s);
}

char *splitOffNumber(char *db)
/* Split off number part, e.g. 8 of mm8. Result should be freed when done */
{
return cloneString(skipToNumeric(db));
}

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