dfd893ed6eb311a9b7c8844db7fec58642083c39 angie Fri Jan 9 15:46:14 2015 -0800 New toy CGI hgChooseDb based on PPT mockup and ideas from Ann and Matt: popular species icons and autocomplete search for species, as an alternative to hgGateway's menus. Uses the new ReactJS/ImmutableJS framework. hgChooseDb.c has three modes of operation: - HTML output for simple main page with a
container to be filled in by javascript - cart-based JSON responses to ajax requests from javascript (using hg/lib/cartJson.c) - no cart; fast JSON responses to species-search autocomplete requests hgChooseDb.jsx is the React/JSX UI view code, compiled to bundle/reactHgChooseDb.js. hgChooseDbModel.js is a subclass of js/model/lib/ImModel.js that gets initial state from the server and then responds to user actions. diff --git src/inc/common.h src/inc/common.h index e7e23cf..45ce154 100644 --- src/inc/common.h +++ src/inc/common.h @@ -1,1486 +1,1489 @@ /* Common.h - functions that are commonly used. Includes * routines for managing singly linked lists, some basic * string manipulation stuff, and other stuff of the * short but useful nature. * * This file is copyright 2002-2005 Jim Kent, but license is hereby * granted for all use - public, private or commercial. */ #ifndef COMMON_H /* Wrapper to avoid including this twice. */ #define COMMON_H /* Some stuff to support large files in Linux. */ #ifndef _LARGEFILE_SOURCE #define _LARGEFILE_SOURCE 1 #endif #ifndef _GNU_SOURCE #define _GNU_SOURCE #endif #ifndef _FILE_OFFSET_BITS #define _FILE_OFFSET_BITS 64 #endif /* Some stuff for safer pthreads. */ #ifndef _REENTRANT #define _REENTRANT #endif #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #if defined(MACHTYPE_ppc) #include #endif #if defined(__APPLE__) #if defined(__i686__) /* The i686 apple math library defines warn. */ #define warn jkWarn #endif #endif #ifdef __CYGWIN32__ #include #endif #ifndef NAN #define NAN (0.0 / 0.0) #endif #ifndef WIFEXITED #define WIFEXITED(stat) (((*((int *) &(stat))) & 0xff) == 0) #endif #ifndef WEXITSTATUS #define WEXITSTATUS(stat) (short)(((*((int *) &(stat))) >> 8) & 0xffff) #endif #ifndef WIFSIGNALED #define WIFSIGNALED(stat) (((*((int *) &(stat)))) && ((*((int *) &(stat))) == ((*((int *) &(stat))) &0x00ff))) #endif #ifndef WTERMSIG #define WTERMSIG(stat) ((*((int *) &(stat))) & 0x7f) #endif #ifndef WIFSTOPPED #define WIFSTOPPED(stat) (((*((int *) &(stat))) & 0xff) == 0177) #endif #ifndef WSTOPSIG #define WSTOPSIG(stat) (((*((int *) &(stat))) >> 8) & 0xff) #endif #ifndef HUGE #define HUGE MAXFLOAT #endif /* Let's pretend C has a boolean type. */ #define TRUE 1 #define FALSE 0 #define boolean int #ifndef __cplusplus #ifndef bool #define bool char #endif #endif /* Some other type synonyms */ #define UBYTE unsigned char /* Wants to be unsigned 8 bits. */ #define BYTE signed char /* Wants to be signed 8 bits. */ #define UWORD unsigned short /* Wants to be unsigned 16 bits. */ #define WORD short /* Wants to be signed 16 bits. */ #define bits64 unsigned long long /* Wants to be unsigned 64 bits. */ #define bits32 unsigned /* Wants to be unsigned 32 bits. */ #define bits16 unsigned short /* Wants to be unsigned 16 bits. */ #define bits8 unsigned char /* Wants to be unsigned 8 bits. */ #define signed32 int /* Wants to be signed 32 bits. */ #define bits8 unsigned char /* Wants to be unsigned 8 bits. */ #define BIGNUM 0x3fffffff /* A really big number */ #define BIGDOUBLE 1.7E+308 /* Close to biggest double-precision number */ #define LIMIT_2or8GB (2147483647 * ((sizeof(size_t)/4)*(sizeof(size_t)/4))) /* == 2 Gb for 32 bit machines, 8 Gb for 64 bit machines */ #define LIMIT_2or6GB (2147483647 + (2147483647 * ((sizeof(size_t)/4)-1)) + \ (2147483647 * ((sizeof(size_t)/4)-1))) /* == 2 Gb for 32 bit machines, 6 Gb for 64 bit machines */ /* Default size of directory path, file name and extension string buffers */ #define PATH_LEN 512 #define FILENAME_LEN 128 #define FILEEXT_LEN 64 /* inline functions: To declare a function inline, place the entire function * in a header file and prefix it with the INLINE macro. If used with a * compiler that doesn't support inline, change the INLINE marco to be simply * `static'. */ #ifndef INLINE #define INLINE static inline #endif /* stdargs compatibility: in a unix universe a long time ago, types of va_list * were passed by value. It was assume one could do things like: * * va_start(args); * vfprintf(fh1, fmt, args); * vfprintf(fh2, fmt, args); * va_end(args); * * and life would good. However this is not true on some modern systems (for * instance gcc/glibc on x86_64), where va_args can be a pointer to some type * of object). The second call to vfprintf() would then crash, since the * first call modified the object that va_args was pointing to. C99 adds a * va_copy macro that to address this issue. Many non-C99 system include this * macro, sometimes called __va_copy. Here we ensure that va_copy is defined. * If if doesn't exist, we try to define it in terms of __va_copy. If that is * not available, we make the assumption that va_list can be copied by value * and create our own. Our implementation is the same as used on Solaris. */ #if defined(__va_copy) && !defined(va_copy) # define va_copy __va_copy #endif #if !defined(va_copy) # define va_copy(to, from) ((to) = (from)) #endif /* Cast a pointer to a long long. Use to printf format points as long-longs * in a 32/64bit portable manner. Format should use %llx for the result. * Needed because casting a pointer to a different sized number cause a * warning with gcc */ #define ptrToLL(p) ((long long)((size_t)p)) /* How big is this array? */ #define ArraySize(a) (sizeof(a)/sizeof((a)[0])) #define uglyf printf /* debugging printf */ #define uglyAbort errAbort /* debugging error abort. */ #define uglyOut stdout /* debugging fprintf target. */ void *needMem(size_t size); /* Need mem calls abort if the memory allocation fails. The memory * is initialized to zero. */ void *needLargeMem(size_t size); /* This calls abort if the memory allocation fails. The memory is * not initialized to zero. */ void *needLargeZeroedMem(size_t size); /* Request a large block of memory and zero it. */ void *needLargeMemResize(void* vp, size_t size); /* Adjust memory size on a block, possibly relocating it. If vp is NULL, * a new memory block is allocated. Memory not initted. */ void *needLargeZeroedMemResize(void* vp, size_t oldSize, size_t newSize); /* Adjust memory size on a block, possibly relocating it. If vp is NULL, a * new memory block is allocated. If block is grown, new memory is zeroed. */ void *needHugeMem(size_t size); /* No checking on size. Memory not initted to 0. */ void *needHugeZeroedMem(size_t size); /* Request a large block of memory and zero it. */ void *needHugeMemResize(void* vp, size_t size); /* Adjust memory size on a block, possibly relocating it. If vp is NULL, * a new memory block is allocated. No checking on size. Memory not * initted. */ void *needHugeZeroedMemResize(void* vp, size_t oldSize, size_t newSize); /* Adjust memory size on a block, possibly relocating it. If vp is NULL, a * new memory block is allocated. No checking on size. If block is grown, * new memory is zeroed. */ void *needMoreMem(void *old, size_t copySize, size_t newSize); /* Allocate a new buffer, copy old buffer to it, free old buffer. */ void *cloneMem(void *pt, size_t size); /* Allocate a new buffer of given size, and copy pt to it. */ #define CloneVar(pt) cloneMem(pt, sizeof((pt)[0])) /* Allocate copy of a structure. */ void *wantMem(size_t size); /* Want mem just calls malloc - no zeroing of memory, no * aborting if request fails. */ void freeMem(void *pt); /* Free memory will check for null before freeing. */ void freez(void *ppt); /* Pass address of pointer. Will free pointer and set it * to NULL. Typical use: * s = needMem(1024); * ... * freez(&s); */ #define AllocVar(pt) (pt = needMem(sizeof(*pt))) /* Shortcut to allocating a single variable on the heap and * assigning pointer to it. */ #define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size))) #define AllocA(type) needMem(sizeof(type)) /* Shortcut to allocating a variable on heap of a specific type. */ #define AllocN(type,count) ((type*)needLargeZeroedMem(sizeof(type) * (count))) /* Shortcut to allocating an array on the heap of a specific type. */ #define ExpandArray(array, oldCount, newCount) \ (array = needMoreMem((array), (oldCount)*sizeof((array)[0]), (newCount)*sizeof((array)[0]))) /* Expand size of dynamically allocated array. */ #define CopyArray(source, dest,count) memcpy(dest,source,(count)*sizeof(dest[0])) /* Copy count elements of array from source to dest. */ #define CloneArray(a, count) cloneMem(a, (count)*sizeof(a[0])) /* Make new dynamic array initialized with count elements of a */ void errAbort(char *format, ...) /* Abort function, with optional (printf formatted) error message. */ #if defined(__GNUC__) __attribute__((format(printf, 1, 2))) #endif ; void errnoAbort(char *format, ...) /* Prints error message from UNIX errno first, then does errAbort. */ #if defined(__GNUC__) __attribute__((format(printf, 1, 2))) #endif ; #define internalErr() errAbort("Internal error %s %d", __FILE__, __LINE__) /* Generic internal error message */ void warn(char *format, ...) /* Issue a warning message. */ #if defined(__GNUC__) __attribute__((format(printf, 1, 2))) #endif ; void warnWithBackTrace(char *format, ...) /* Issue a warning message and append backtrace. */ #if defined(__GNUC__) __attribute__((format(printf, 1, 2))) #endif ; void verbose(int verbosity, char *format, ...) /* Write printf formatted message to log (which by * default is stdout) if global verbose variable * is set to verbosity or higher. Default level is 1. */ #if defined(__GNUC__) __attribute__((format(printf, 2, 3))) #endif ; void verboseTimeInit(void); /* Initialize or reinitialize the previous time for use by verboseTime. */ void verboseTime(int verbosity, char *label, ...) /* Print label and how long it's been since last call. Start time can be * initialized with verboseTimeInit, otherwise the elapsed time will be * zero. */ #if defined(__GNUC__) __attribute__((format(printf, 2, 3))) #endif ; void verboseDot(); /* Write I'm alive dot (at verbosity level 1) */ int verboseLevel(); /* Get verbosity level. */ void verboseSetLevel(int verbosity); /* Set verbosity level in log. 0 for no logging, * higher number for increasing verbosity. */ INLINE void zeroBytes(void *vpt, int count) /* fill a specified area of memory with zeroes */ { memset(vpt, '\0', count); } #define ZeroVar(v) zeroBytes(v, sizeof(*v)) void reverseBytes(char *bytes, long length); /* Reverse the order of the bytes. */ void reverseInts(int *a, int length); /* Reverse the order of the integer array. */ void reverseUnsigned(unsigned *a, int length); /* Reverse the order of the unsigned array. */ void reverseDoubles(double *a, int length); /* Reverse the order of the double array. */ void reverseStrings(char **a, int length); /* Reverse the order of the char* array. */ void swapBytes(char *a, char *b, int length); /* Swap buffers a and b. */ /******* Some things to manage simple lists - structures that begin ****** ******* with a pointer to the next element in the list. ******/ struct slList { struct slList *next; }; int slCount(const void *list); /* Return # of elements in list. */ void *slElementFromIx(void *list, int ix); /* Return the ix'th element in list. Returns NULL * if no such element. */ int slIxFromElement(void *list, void *el); /* Return index of el in list. Returns -1 if not on list. */ INLINE void slAddHead(void *listPt, void *node) /* 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. */ { struct slList **ppt = (struct slList **)listPt; struct slList *n = (struct slList *)node; n->next = *ppt; *ppt = n; } INLINE void slSafeAddHead(void *listPt, void *node) /* Add new node to start of list. Now that slAddHead is an inline instead of * a macro, this function is obsolete. */ { slAddHead(listPt, node); } void slAddTail(void *listPt, void *node); /* 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. This is sometimes * convenient but relatively slow. For longer lists * it's better to slAddHead, and slReverse when done. */ void *slPopHead(void *listPt); /* Return head of list and remove it from list. (Fast) */ void *slPopTail(void *listPt); /* Return tail of list and remove it from list. (Not so fast) */ void *slCat(void *a, void *b); /* 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) * After this it is no longer safe to use a or b. */ void *slLastEl(void *list); /* Returns last element in list or NULL if none. */ void slReverse(void *listPt); /* Reverse order of a list. * Usage: * slReverse(&list); */ typedef int CmpFunction(const void *elem1, const void *elem2); void slSort(void *pList, CmpFunction *compare); /* Sort a singly linked list with Qsort and a temporary array. * The arguments to the compare function in real, non-void, life * are pointers to pointers. */ void slUniqify(void *pList, CmpFunction *compare, 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. */ void slSortMerge(void *pA, void *b, CmpFunction *compare); // Merges and sorts a pair of singly linked lists using slSort. void slSortMergeUniq(void *pA, void *b, CmpFunction *compare, void (*free)()); // Merges and sorts a pair of singly linked lists leaving only unique // items via slUniqufy. duplicate itens are defined by the compare routine // returning 0. If free is provided, items dropped from list can disposed of. boolean slRemoveEl(void *vpList, void *vToRemove); /* Remove element from singly linked list. Usage: * slRemove(&list, el); * Returns TRUE if element in list. */ void slFreeList(void *listPt); /* Free all elements in list and set list pointer to null. * Usage: * slFreeList(&list); */ /******* slInt - an int on a list - the first of many singly linked list structures *******/ struct slInt /* List of integers. */ { struct slInt *next; /* Next in list. */ int val; /* Integer value. */ }; struct slInt *slIntNew(int x); #define newSlInt slIntNew /* Return a new double. */ int slIntCmp(const void *va, const void *vb); /* Compare two slInts. */ int slIntCmpRev(const void *va, const void *vb); /* Compare two slInts in reverse direction. */ struct slInt * slIntFind(struct slInt *list, int target); /* Find target in slInt list or return NULL */ struct slUnsigned /* List of unsigned */ { struct slUnsigned *next; /* Next in list */ unsigned val; /* Unsigned value */ }; struct slUnsigned *slUnsignedNew(unsigned x); /* Return a new slUnsigned. */ /******* slDouble - a double on a list *******/ struct slDouble /* List of double-precision numbers. */ { struct slDouble *next; /* Next in list. */ double val; /* Double-precision value. */ }; struct slDouble *slDoubleNew(double x); #define newSlDouble slDoubleNew /* Return a new int. */ int slDoubleCmp(const void *va, const void *vb); /* Compare two slDoubles. */ double slDoubleMedian(struct slDouble *list); /* Return median value on list. */ /******* slName - a zero terminated string on a list *******/ struct slName /* List of names. The name array is allocated to accommodate full name */ { struct slName *next; /* Next in list. */ char name[1]; /* Allocated at run time to length of string. */ }; struct slName *newSlName(char *name); #define slNameNew newSlName /* Return a new slName. */ #define slNameFree freez /* Free a single slName */ #define slNameFreeList slFreeList /* Free a list of slNames */ struct slName *slNameNewN(char *name, int size); /* Return new slName of given size. */ int slNameCmpCase(const void *va, const void *vb); /* Compare two slNames, ignore case. */ int slNameCmp(const void *va, const void *vb); /* Compare two slNames. */ int slNameCmpStringsWithEmbeddedNumbers(const void *va, const void *vb); /* Compare strings such as gene names that may have embedded numbers, * so that bmp4a comes before bmp14a */ void slNameSortCase(struct slName **pList); /* Sort slName list, ignore case. */ void slNameSort(struct slName **pList); /* Sort slName list. */ boolean slNameInList(struct slName *list, char *string); /* Return true if string is in name list -- case insensitive. */ boolean slNameInListUseCase(struct slName *list, char *string); /* Return true if string is in name list -- case sensitive. */ void *slNameFind(void *list, char *string); /* Return first element of slName list (or any other list starting * with next/name fields) that matches string. */ 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. */ 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 *slNameAddHead(struct slName **pList, char *name); /* Add name to start of list and return it. */ struct slName *slNameAddTail(struct slName **pList, char *name); /* Add name to end of list (not efficient for long lists), * and return it. */ struct slName *slNameCloneList(struct slName *list); /* Return clone of list. */ 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. */ #define slNameListFromComma(s) slNameListFromString(s, ',') /* Parse out comma-separated list. */ struct slName *slNameListOfUniqueWords(char *text,boolean respectQuotes); // Return list of unique words found by parsing string delimited by whitespace. // If respectQuotes then ["Lucy and Ricky" 'Fred and Ethyl'] will yield 2 slNames no quotes struct slName *slNameListFromStringArray(char *stringArray[], int arraySize); /* Return list of slNames from an array of strings of length arraySize. * If a string in the array is NULL, the array will be treated as * NULL-terminated. */ char *slNameListToString(struct slName *list, char delimiter); /* Return string created by joining all names with the delimiter. */ struct slName *slNameLoadReal(char *fileName); /* load file lines that are not blank or start with a '#' into a slName * list */ struct slName *slNameIntersection(struct slName *a, struct slName *b); /* return intersection of two slName lists. */ /******* slRef - a void pointer on a list *******/ struct slRef /* Singly linked list of generic references. */ { struct slRef *next; /* Next in list. */ void *val; /* A reference to something. */ }; struct slRef *slRefNew(void *val); /* Create new slRef element. */ struct slRef *refOnList(struct slRef *refList, void *val); /* Return ref if val is already on list, otherwise NULL. */ void refAdd(struct slRef **pRefList, void *val); /* Add reference to list. */ void refAddUnique(struct slRef **pRefList, void *val); /* Add reference to list if not already on list. */ void slRefFreeListAndVals(struct slRef **pList); /* Free up (with simple freeMem()) each val on list, and the list itself as well. */ struct slRef *refListFromSlList(void *list); /* Make a reference list that mirrors a singly-linked list. */ /******* slPair - a name/value pair on list where value not always a string *******/ struct slPair /* A name/value pair. */ { struct slPair *next; /* Next in list. */ char *name; /* Name of item. */ void *val; /* Pointer to item data. */ }; struct slPair *slPairNew(char *name, void *val); /* Allocate new name/value pair. */ void slPairAdd(struct slPair **pList, char *name, void *val); /* Add new slPair to head of list. */ void slPairFree(struct slPair **pEl); /* Free up struct and name. (Don't free up values.) */ void slPairFreeList(struct slPair **pList); /* Free up list. (Don't free up values.) */ void slPairFreeVals(struct slPair *list); /* Free up all values on list. */ void slPairFreeValsAndList(struct slPair **pList); /* Free up all values on list and list itself */ struct slPair *slPairFind(struct slPair *list, char *name); /* Return list element of given name, or NULL if not found. */ void *slPairFindVal(struct slPair *list, char *name); /* Return value associated with name in list, or NULL if not found. */ struct slPair *slPairListFromString(char *str,boolean respectQuotes); // Return slPair list parsed from list in string like: [name1=val1 name2=val2 ...] // if respectQuotes then string can have double quotes: [name1="val 1" "name 2"=val2 ...] // resulting pair strips quotes: {name1}={val 1},{name 2}={val2} // Returns NULL if parse error. Free this up with slPairFreeValsAndList. #define slPairFromString(s) slPairListFromString(s,FALSE) char *slPairListToString(struct slPair *list,boolean quoteIfSpaces); // Returns an allocated string of pairs in form of [name1=val1 name2=val2 ...] // If requested, will wrap name or val in quotes if contain spaces: [name1="val 1" "name 2"=val2] char *slPairNameToString(struct slPair *list, char delimiter,boolean quoteIfSpaces); // Return string created by joining all names (ignoring vals) with the delimiter. // If requested, will wrap name in quotes if contain spaces: [name1,"name 2" ...] int slPairCmpCase(const void *va, const void *vb); /* Compare two slPairs, ignore case. */ void slPairSortCase(struct slPair **pList); /* Sort slPair list, ignore case. */ int slPairCmp(const void *va, const void *vb); /* Compare two slPairs. */ int slPairValCmpCase(const void *va, const void *vb); /* Case insensitive compare two slPairs on their values (must be string). */ int slPairValCmp(const void *va, const void *vb); /* Compare two slPairs on their values (must be string). */ void slPairValSortCase(struct slPair **pList); /* Sort slPair list on values (must be string), ignore case. */ void slPairValSort(struct slPair **pList); /* Sort slPair list on values (must be string). */ int slPairIntCmp(const void *va, const void *vb); // Compare two slPairs on their integer values. void slPairIntSort(struct slPair **pList); // Sort slPair list on integer values. int slPairAtoiCmp(const void *va, const void *vb); // Compare two slPairs on their strings interpreted as integer values. void slPairValAtoiSort(struct slPair **pList); // Sort slPair list on string values interpreted as integers. /******* Some old stuff maybe we could trim. *******/ void gentleFree(void *pt); /* check pointer for NULL before freeing. * (Actually plain old freeMem does that these days.) */ /******* Some math stuff *******/ void doubleSort(int count, double *array); /* Sort an array of doubles. */ double doubleMedian(int count, double *array); /* Return median value in array. This will sort * the array as a side effect. */ void doubleBoxWhiskerCalc(int count, double *array, double *retMin, double *retQ1, double *retMedian, double *retQ3, double *retMax); /* Calculate what you need to draw a box and whiskers plot from an array of doubles. */ void slDoubleBoxWhiskerCalc(struct slDouble *list, double *retMin, double *retQ1, double *retMedian, double *retQ3, double *retMax); /* Calculate what you need to draw a box and whiskers plot from a list of slDoubles. */ int intMedian(int count, int *array); /* Return median value in array. This will sort * the array as a side effect. */ void intSort(int count, int *array); /* Sort an array of ints. */ /******* Some stuff for processing strings. *******/ char *cloneStringZ(const char *s, int size); /* Make a zero terminated copy of string in memory */ char *cloneString(const char *s); /* Make copy of string in dynamic memory */ char *cloneLongString(char *s); /* Make clone of long string. */ char *catTwoStrings(char *a, char *b); /* Allocate new string that is a concatenation of two strings. */ 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. */ #define sameWord(a,b) (!differentWord(a,b)) /* Return TRUE if two strings are same ignoring case */ #define differentString(a,b) (strcmp(a,b)) /* Returns FALSE if two strings same. */ 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. */ #define sameOk(a,b) (differentStringNullOk(a,b) == 0) /* returns TRUE if two strings same, NULLs OK */ #define sameString(a,b) (strcmp(a,b)==0) /* Returns TRUE if two strings same. */ #define sameStringN(a,b,c) (strncmp(a,b,c)==0) /* Returns TRUE if two strings start with the same c characters. */ #define isEmpty(string) ((string) == NULL || (string)[0] == 0) #define isNotEmpty(string) (! isEmpty(string)) int cmpStringsWithEmbeddedNumbers(const char *a, const char *b); /* Compare strings such as gene names that may have embedded numbers, * so that bmp4a comes before bmp14a */ int cmpWordsWithEmbeddedNumbers(const char *a, const char *b); /* Case insensitive version of cmpStringsWithEmbeddedNumbers. */ boolean startsWith(const char *start, const char *string); /* Returns TRUE if string begins with start. */ +boolean startsWithNoCase(const char *start, const char *string); +/* Returns TRUE if string begins with start, case-insensitive. */ + boolean startsWithWord(char *firstWord, char *line); /* Return TRUE if first white-space-delimited word in line * is same as firstWord. Comparison is case sensitive. */ boolean startsWithWordByDelimiter(char *firstWord,char delimit, char *line); /* Return TRUE if first word in line is same as firstWord as delimited by delimit. Comparison is case sensitive. Delimit of ' ' uses isspace() */ #define stringIn(needle, haystack) strstr(haystack, needle) /* Returns position of needle in haystack or NULL if it's not there. */ /* char *stringIn(char *needle, char *haystack); */ char *rStringIn(char *needle, char *haystack); /* Return last position of needle in haystack, or NULL if it's not there. */ 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 * findWordByDelimiter(char *word,char delimit, char *line); /* Return pointer to first word in line matching 'word' and delimited by 'delimit'. Comparison is case sensitive. Delimit of ' ' uses isspace() */ boolean endsWith(char *string, char *end); /* Returns TRUE if string ends with end. */ char lastChar(char *s); /* Return last character in string. */ void trimLastChar(char *s); /* Erase last character in string. */ char *lastNonwhitespaceChar(char *s); // Return pointer to last character in string that is not whitespace. char *matchingCharBeforeInLimits(char *limit, char *s, char c); /* Look for character c sometime before s, but going no further than limit. * Return NULL if not found. */ boolean wildMatch(const char *wildCard, const char *string); /* does a case insensitive wild card match with a string. * * matches any string or no character. * ? matches any single character. * anything else etc must match the character exactly. */ boolean sqlMatchLike(char *wildCard, char *string); /* Match using % and _ wildcards. */ boolean anyWild(const char *string); /* Return TRUE if any wild card characters in string. */ char *memMatch(char *needle, int nLen, char *haystack, int hLen); /* Returns first place where needle (of nLen chars) matches * haystack (of hLen chars) */ void toUpperN(char *s, int n); /* Convert a section of memory to upper case. */ void toLowerN(char *s, int n); /* Convert a section of memory to lower case. */ void toggleCase(char *s, int size); /* toggle upper and lower case chars in string. */ char *strUpper(char *s); #define touppers(s) (void)strUpper(s) /* Convert entire string to upper case. */ char *strLower(char *s); #define tolowers(s) (void)strLower(s) /* Convert entire string to lower case */ char *replaceChars(char *string, char *oldStr, char *newStr); /* 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 strSwapStrs(char *string, int sz,char *oldStr, char *newStr); /* Swaps all occurrences of the oldStr with the newStr in string. Need not be same size Swaps in place but restricted by sz. Returns count of swaps or -1 for sz failure.*/ char * memSwapChar(char *s, int len, char oldChar, char newChar); /* Substitute newChar for oldChar throughout memory of given length. old or new may be null */ #define strSwapChar(s,old,new) memSwapChar((s),strlen(s),(old),(new)) #define subChar(s,old,new) (void)memSwapChar((s),strlen(s),(old),(new)) /* Substitute newChar for oldChar throughout string s. */ void stripChar(char *s, char c); /* Remove all occurences of c from s. */ char *stripEnclosingChar(char *inout,char encloser); // Removes enclosing char if found at both beg and end, preserving pointer // Note: handles brackets '(','{' and '[' by complement at end #define stripEnclosingDoubleQuotes(inout) stripEnclosingChar((inout),'"') #define stripEnclosingSingleQuotes(inout) stripEnclosingChar((inout),'\'') void stripString(char *s, char *strip); /* Remove all occurences of strip from s. */ int countCase(char *s,boolean upper); // Count letters with case (upper or lower) int countChars(char *s, char c); /* Return number of characters c in string s. */ int countCharsN(char *s, char c, int size); /* Return number of characters c in string s of given size. */ int countLeadingChars(char *s, char c); /* Count number of characters c at start of string. */ int countLeadingDigits(const char *s); /* Return number of leading digits in s */ int countLeadingNondigits(const char *s); /* Count number of leading non-digit characters in s. */ int countSame(char *a, char *b); /* Count number of characters that from start in a,b that are same. */ int countSeparatedItems(char *string, char separator); /* Count number of items in string you would parse out with given * separator, assuming final separator is optional. */ int chopString(char *in, char *sep, char *outArray[], int outSize); /* 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. */ extern char crLfChopper[]; extern char whiteSpaceChopper[]; /* Some handy predefined separators. */ int chopByWhite(char *in, char *outArray[], int outSize); /* Like chopString, but specialized for white space separators. */ #define chopLine(line, words) chopByWhite(line, words, ArraySize(words)) /* Chop line by white space. */ int chopByWhiteRespectDoubleQuotes(char *in, char *outArray[], int outSize); /* Like chopString, but specialized for white space separators. * Further, any doubleQuotes (") are respected. * If doubleQuote encloses whole string, then they are removed: * "Fred and Ethyl" results in word [Fred and Ethyl] * If doubleQuotes exist inside string they are retained: * Fred "and Ethyl" results in word [Fred "and Ethyl"] * Special note "" is a valid, though empty word. */ int chopByChar(char *in, char chopper, char *outArray[], int outSize); /* Chop based on a single character. */ #define chopTabs(string, words) chopByChar(string, '\t', words, ArraySize(words)) /* Chop string by tabs. */ #define chopCommas(string, words) chopByChar(string, ',', words, ArraySize(words)) /* Chop string by commas. */ char *skipBeyondDelimit(char *s,char delimit); /* Returns NULL or pointer to first char beyond one (or more contiguous) delimit char. If delimit is ' ' then skips beyond first patch of whitespace. */ char *skipLeadingSpaces(char *s); /* Return first white space or NULL if none.. */ char *skipToSpaces(char *s); /* Return first white space. */ void eraseTrailingSpaces(char *s); /* Replace trailing white space with zeroes. */ void eraseWhiteSpace(char *s); /* Remove white space from a string */ void eraseNonAlphaNum(char *s); /* Remove non-alphanumeric chars from string */ char *trimSpaces(char *s); /* Remove leading and trailing white space. */ void repeatCharOut(FILE *f, char c, int count); /* Write character to file repeatedly. */ void spaceOut(FILE *f, int count); /* Put out some spaces to file. */ void starOut(FILE *f, int count); /* Put out some asterisks to file. */ boolean hasWhiteSpace(char *s); /* Return TRUE if there is white space in string. */ char *firstWordInLine(char *line); /* Returns first word in line if any (white space separated). * Puts 0 in place of white space after word. */ 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 *nextWord(char **pLine); /* Return next word in *pLine and advance *pLine to next * word. Returns NULL when no more words. */ char *nextWordRespectingQuotes(char **pLine); // return next word but respects single or double quotes surrounding sets of words. char *cloneFirstWord(char *line); /* Clone first word in line */ char *cloneNotFirstWord(char *s); /* Clone part of string after first word. */ char *nextTabWord(char **pLine); /* Return next tab-separated word. */ char *cloneFirstWordByDelimiter(char *line,char delimit); /* Returns a cloned first word, not harming the memory passed in Delimiter of ' ' will delimit by isspace() */ #define cloneFirstWordInLine(line) cloneFirstWordByDelimiter((line),' ') #define cloneFirstWordByTab(line) cloneFirstWordByDelimiter((line),'\t') /* Returns a cloned first word, not harming the memory passed in */ char *cloneNextWordByDelimiter(char **line,char delimit); /* Returns a cloned first word, advancing the line pointer but not harming memory passed in. Delimit ' ' uses isspace() */ #define cloneNextWord(line) cloneNextWordByDelimiter((line),' ') #define cloneNextWordByTab(line) cloneNextWordByDelimiter((line),'\t') char *nextStringInList(char **pStrings); /* returns pointer to the first string and advances pointer to next in list of strings dilimited by 1 null and terminated by 2 nulls. */ int cntStringsInList(char *pStrings); /* returns count of strings in a list of strings dilimited by 1 null and terminated by 2 nulls. */ int stringArrayIx(char *string, char *array[], int arraySize); /* Return index of string in array or -1 if not there. */ int ptArrayIx(void *pt, void *array, int arraySize); /* Return index of pt in array or -1 if not there. */ #define stringIx(string, array) stringArrayIx( (string), (array), ArraySize(array)) /* Some stuff that is left out of GNU .h files!? */ #ifndef SEEK_SET #define SEEK_SET 0 #endif #ifndef SEEK_CUR #define SEEK_CUR 1 #endif #ifndef SEEK_END #define SEEK_END 2 #endif #ifndef FILEPATH_H void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN], char extension[FILEEXT_LEN]); /* Split a full path into components. The dir component will include the * trailing / if any. The extension component will include the starting * . if any. Pass in NULL for dir, name, or extension if you don't care about * that part. */ #endif /* FILEPATH_H */ char *addSuffix(char *head, char *suffix); /* Return a needMem'd string containing "headsuffix". Should be free'd when finished. */ void chopSuffix(char *s); /* Remove suffix (last . in string and beyond) if any. */ void chopSuffixAt(char *s, char c); /* Remove end of string from last occurrence of char c. * chopSuffixAt(s, '.') is equivalent to regular chopSuffix. */ 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. */ char *chopPrefixAt(char *s, char c); /* Like chopPrefix, but can chop on any character, not just '.' */ FILE *mustOpen(char *fileName, char *mode); /* Open a file - or squawk and die. */ void mustWrite(FILE *file, void *buf, size_t size); /* Write to file or squawk and die. */ #define writeOne(file, var) mustWrite((file), &(var), sizeof(var)) /* Write out one variable to file. */ void mustRead(FILE *file, void *buf, size_t size); /* Read size bytes from a file or squawk and die. */ #define mustReadOne(file, var) mustRead((file), &(var), sizeof(var)) /* Read one variable from file or die. */ void mustGetLine(FILE *file, char *buf, int charCount); /* Read at most charCount-1 bytes from file, but stop after newline if one is * encountered. The string in buf is '\0'-terminated. (See man 3 fgets.) * Die if there is an error. */ int mustOpenFd(char *fileName, int flags); /* Open a file descriptor (see man 2 open) or squawk and die. */ void mustReadFd(int fd, void *buf, size_t size); /* Read size bytes from a file descriptor or squawk and die. */ void mustWriteFd(int fd, void *buf, size_t size); /* Write size bytes to file descriptor fd or die. (See man 2 write.) */ off_t mustLseek(int fd, off_t offset, int whence); /* Seek to given offset, relative to whence (see man lseek) in file descriptor fd or errAbort. * Return final offset (e.g. if this is just an (fd, 0, SEEK_CUR) query for current position). */ void mustCloseFd(int *pFd); /* Close file descriptor *pFd if >= 0, abort if there's an error, set *pFd = -1. */ #define writeOneFd(fd, var) mustWriteFd((fd), &(var), sizeof(var)) /* Write out one variable to file descriptor fd. */ #define readOne(file, var) (fread(&(var), sizeof(var), 1, (file)) == 1) /* Read one variable from file. Returns FALSE if can't do it. */ #define readOneFd(fd, var) (read((fd), &(var), sizeof(var)) == sizeof(var)) /* Read one variable from file. Returns FALSE if can't do it. */ #define mustReadOneFd(fd, var) mustReadFd((fd), &(var), sizeof(var)) /* Read one variable from file or die. */ #define memReadOne(pPt, var) memRead((pPt), &(var), sizeof(var)) /* Read one variable from memory. */ 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. */ char *readString(FILE *f); /* Read a string (written with writeString) into * memory. freeMem the result when done. Returns * NULL at EOF. */ char *mustReadString(FILE *f); /* Read a string. Squawk and die at EOF or if any problem. */ 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. * Returns FALSE at EOF. */ void msbFirstWriteBits64(FILE *f, bits64 x); /* Write out 64 bit number in manner that is portable across architectures */ bits64 msbFirstReadBits64(FILE *f); /* Write out 64 bit number in manner that is portable across architectures */ void carefulClose(FILE **pFile); /* Close file if open and null out handle to it. */ 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.*/ char *firstWordInFile(char *fileName, char *wordBuf, int wordBufSize); /* Read the first word in file into wordBuf. */ struct fileOffsetSize /* A piece of a file. */ { struct fileOffsetSize *next; /* Next in list. */ bits64 offset; /* Start offset of block. */ bits64 size; /* Size of block. */ }; int fileOffsetSizeCmp(const void *va, const void *vb); /* Help sort fileOffsetSize by offset. */ struct fileOffsetSize *fileOffsetSizeMerge(struct fileOffsetSize *inList); /* Returns a new list which is inList transformed to have adjacent blocks * merged. Best to use this with a sorted list. */ void fileOffsetSizeFindGap(struct fileOffsetSize *list, struct fileOffsetSize **pBeforeGap, struct fileOffsetSize **pAfterGap); /* Starting at list, find all items that don't have a gap between them and the previous item. * Return at gap, or at end of list, returning pointers to the items before and after the gap. */ void mustSystem(char *cmd); /* Execute cmd using "sh -c" or die. (See man 3 system.) fail on errors */ int roundingScale(int a, int p, int q); /* returns rounded a*p/q */ int intAbs(int a); /* Return integer absolute value */ #define logBase2(x)(log(x)/log(2)) /* return log base two of number */ #define round(a) ((int)((a)+0.5)) /* Round floating point val to nearest integer. */ #define roundll(a) ((long long)((a)+0.5)) /* Round floating point val to nearest long long. */ #ifndef min #define min(a,b) ( (a) < (b) ? (a) : (b) ) /* Return min of a and b. */ #endif #ifndef max #define max(a,b) ( (a) > (b) ? (a) : (b) ) /* Return max of a and b. */ #endif 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 positiveRangeIntersection(int start1, int end1, int start2, int end2); /* Return amount of bases two ranges intersect over, 0 if no * intersection. */ INLINE void memRead(char **pPt, void *buf, int size) /* Copy memory from *pPt to buf, and advance *pPt by size. */ { memcpy(buf, *pPt, size); *pPt += size; } INLINE void memWrite(char **pPt, void *buf, int size) /* Copy memory from buf to *pPt and advance *pPt by size. */ { memcpy(*pPt, buf, size); *pPt += size; } #define memWriteOne(pPt, var) memWrite((pPt), &(var), sizeof(var)) /* Write out one variable to memory stream. */ INLINE void memWriteFloat(char **pPt, float val) /* Write out floating point val to file. Mostly to convert from double... */ { memWriteOne(pPt, val); } bits64 byteSwap64(bits64 a); /* Swap from intel to sparc order of a 64 bit quantity. */ bits64 readBits64(FILE *f, boolean isSwapped); /* Read and optionally byte-swap 64 bit entity. */ bits64 fdReadBits64(int fd, boolean isSwapped); /* Read and optionally byte-swap 64 bit entity. */ bits64 memReadBits64(char **pPt, boolean isSwapped); /* Read and optionally byte-swap 64 bit entity from memory buffer pointed to by * *pPt, and advance *pPt past read area. */ bits32 byteSwap32(bits32 a); /* Swap from intel to sparc order of a 32 bit quantity. */ bits32 readBits32(FILE *f, boolean isSwapped); /* Read and optionally byte-swap 32 bit entity. */ bits32 fdReadBits32(int fd, boolean isSwapped); /* Read and optionally byte-swap 32 bit entity. */ bits32 memReadBits32(char **pPt, boolean isSwapped); /* Read and optionally byte-swap 32 bit entity from memory buffer pointed to by * *pPt, and advance *pPt past read area. */ bits16 byteSwap16(bits16 a); /* Swap from intel to sparc order of a 16 bit quantity. */ bits16 readBits16(FILE *f, boolean isSwapped); /* Read and optionally byte-swap 16 bit entity. */ bits16 fdReadBits16(int fd, boolean isSwapped); /* Read and optionally byte-swap 16 bit entity. */ bits16 memReadBits16(char **pPt, boolean isSwapped); /* Read and optionally byte-swap 32 bit entity from memory buffer pointed to by * *pPt, and advance *pPt past read area. */ double byteSwapDouble(double a); /* Return byte-swapped version of a */ double readDouble(FILE *f, boolean isSwapped); /* Read and optionally byte-swap double-precision floating point entity. */ double memReadDouble(char **pPt, boolean isSwapped); /* Read and optionally byte-swap double-precision floating point entity * from memory buffer pointed to by *pPt, and advance *pPt past read area. */ float byteSwapFloat(float a); /* Return byte-swapped version of a */ float readFloat(FILE *f, boolean isSwapped); /* Read and optionally byte-swap single-precision floating point entity. */ float memReadFloat(char **pPt, boolean isSwapped); /* Read and optionally byte-swap single-precision floating point entity * from memory buffer pointed to by *pPt, and advance *pPt past read area. */ 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 threads */ int intExp(char *text); /* Convert text to integer expression and evaluate. * Throws if it finds a non-number. */ double doubleExp(char *text); /* Convert text to floating point expression and * evaluate. */ char* readLine(FILE* fh); /* Read a line of any size into dynamic memory, return null on EOF */ off_t fileSize(char *fileName); /* The size of a file. */ boolean fileExists(char *fileName); /* Does a file exist? */ /* Friendly name for strstrNoCase */ char *containsStringNoCase(char *haystack, char *needle); char *strstrNoCase(char *haystack, char *needle); /* A case-insensitive strstr */ 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 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. */ #ifdef __GNUC__ __attribute__((format(printf, 3, 4))) #endif ; void safecpy(char *buf, size_t bufSize, const char *src); /* copy a string to a buffer, with bounds checking.*/ 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 */ void safecat(char *buf, size_t bufSize, const char *src); /* Append a string to a buffer, with bounds checking.*/ 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. */ char *naForNull(char *s); /* Return 'n/a' if s is NULL, otherwise s. */ char *naForEmpty(char *s); /* Return n/a if s is "" or NULL, otherwise s. */ char *emptyForNull(char *s); /* Return "" if s is NULL, otherwise s. */ char *nullIfAllSpace(char *s); /* Return NULL if s is all spaces, otherwise s. */ char *trueFalseString(boolean b); /* Return "true" or "false" */ void uglyTime(char *label, ...); /* Print label and how long it's been since last call. Call with * a NULL label to initialize. */ /* In case the development environment does not supply INFINITY */ #if !defined(INFINITY) #define INFINITY (1.0/0.0) #endif void makeDirs(char* path); /* make a directory, including parent directories */ char *skipNumeric(char *s); /* Return first char of s that's not a digit */ char *skipToNumeric(char *s); /* skip up to where numeric digits appear */ char *splitOffNonNumeric(char *s); /* Split off non-numeric part, e.g. mm of mm8. Result should be freed when done */ char *splitOffNumber(char *db); /* Split off number part, e.g. 8 of mm8. Result should be freed when done */ void childExecFailedExit(char *msg); /* Child exec failed, so quit without atexit cleanup */ void vaDumpStack(char *format, va_list args); /* debugging function to run the pstack program on the current process. In * prints a message, following by a new line, and then the stack track. Just * prints errors to stderr rather than aborts. For debugging purposes * only. */ void dumpStack(char *format, ...) /* debugging function to run the pstack program on the current process. In * prints a message, following by a new line, and then the stack track. Just * prints errors to stderr rather than aborts. For debugging purposes * only. */ #if defined(__GNUC__) __attribute__((format(printf, 1, 2))) #endif ; // SETTING_ON set of macros are frequently used comparisons of string values for boolean questions. // Notice the subtle difference between NOT_ON and IS_OFF. // NOT_ON could be NULL but IS_OFF must be explicitly set #define SETTING_IS_ON(setting) ( setting && (sameWord(setting,"on") || sameWord(setting,"true") \ || sameWord(setting,"yes") || sameWord(setting,"enabled") \ || atoi(setting) != 0) ) #define SETTING_NOT_ON(setting) (!SETTING_IS_ON(setting)) #define SETTING_IS_OFF(setting) ( setting && (sameWord(setting,"off") \ || sameWord(setting,"false") || sameWord(setting,"no") \ || sameWord(setting,"disabled") || sameWord(setting,"0")) ) // Standard bit mask macros #define BITS_ADD( flags,bits) ((flags) = ((flags) | (bits))) #define BITS_REMOVE( flags,bits) ((flags) = ((flags) & ~(bits))) #define BITS_ARE_ON( flags,bits) (((flags) & (bits)) == (bits)) #define BITS_ARE_OFF(flags,bits) (((flags) & (bits)) == 0) // It is sometimes useful to distinguish between 3 "boolean" states: TRUE, FALSE and UNKNOWN enum enumBool { beUnknown=0, // Not yet set ebYes=1, // already set to TRUE ebNo=-1 // already set to FALSE }; #define SET_TO_YES(ebool) { (ebool) = ebYes; } #define SET_TO_NO(ebool) { (ebool) = ebNo; } #define IS_YES(ebool) ((ebool) == ebYes) #define IS_NO(ebool) ((ebool) == ebNo) #define IS_KNOWN(ebool) (IS_YES(ebool) || IS_NO(ebool)) #define IS_TRUE IS_YES #define IS_FALSE IS_NO time_t mktimeFromUtc (struct tm *t); /* Return time_t for tm in UTC (GMT) * Useful for stuff like converting to time_t the * last-modified HTTP response header * which is always GMT. Returns -1 on failure of mktime */ time_t dateToSeconds(const char *date,const char*format); // Convert a string date to time_t boolean dateIsOld(const char *date,const char*format); // Is this string date older than now? boolean dateIsOlderBy(const char *date,const char*format, time_t seconds); // Is this string date older than now by this many seconds? char *dateAddTo(char *date,char *format,int addYears,int addMonths,int addDays); /* Add years,months,days to a formatted date and returns the new date as a cloned string * format is a strptime/strftime format: %F = yyyy-mm-dd */ boolean haplotype(const char *name); /* Is this name a haplotype name ? _hap or _alt in the name */ #endif /* COMMON_H */