void printHashset(struct HashSet *hashset, FILE *file)
{
int bucketNumber;
for (bucketNumber = 0; bucketNumber < hashset->numberBuckets;
bucketNumber++)
printBucket(hashset, bucketNumber, file);
}
/***********************************************************************
* Suffix Array Induced Sorting (SAIS) is a linear time/space suffix
* array construction algorithm which competes with BPR2 for top
* time/space requirements. TODO: reference paper here.
*
* Currently this code is being changes to enable testing of run-removal
* on the code. Run removal enforces stricter conditions on the input
* sequence which allows for some of the logic to be simplified. This
* experimental approach is particularly useful for inputs with small
* alphabets in the general case, but definitionally saves on sequences
* which are known to have many runs of identical values in the sequence.
*
* @source :The sequence to construct the suffix array on.
* @runsRem :
*
* @alphabetSize : not actually alphabet size, but highest value seen in
* alphabet. Might change in future.
*
*
* Notes
* 0 = undefined, 1 = L, 2 = S, 3 = {LMS, M}
***********************************************************************/
sequence SAIS(const u8 *source, const size_t sourceLength,
const sequence runsRem, const u8 alphabetSize){
//DECLARATIONS//////////////////////////////////////////////////////////
sequence toReturn, sanityCheck;
size_t **bucket;
size_t **oldBucket;
size_t i;
size_t *bucketSize;
size_t *bucketFrontCounter;
size_t *bucketEndCounter;
unsigned char *LMSandLS;
////INITIALIZATION//////////////////////////////////////////////////////
LMSandLS = malloc(sizeof(unsigned char) * runsRem.size);
bucket = malloc(sizeof(*bucket) * alphabetSize);
oldBucket = malloc(sizeof(*oldBucket) * alphabetSize);
bucketSize = calloc(sizeof(size_t)* alphabetSize, 1);
bucketFrontCounter = calloc(sizeof(size_t)* alphabetSize, 1);
bucketEndCounter = calloc(sizeof(size_t)* alphabetSize, 1);
sanityCheck = initSequence(runsRem.size);
memset(sanityCheck.S, 0, sizeof(*sanityCheck.S) * sanityCheck.size);
sanityCheck.size = 0;
/*prescan for buckets************************************************/
//calculate bucket sizes
for(i = 0; i < runsRem.size; i++) bucketSize[source[runsRem.S[i]]]++;
//calculate bucket start and stops
for(short i = 0; i < alphabetSize; i++){
bucket[i] = calloc(sizeof(size_t), bucketSize[i]);
oldBucket[i] = calloc(sizeof(size_t), bucketSize[i]);
}
#ifdef DEBUG
//first place where bucket data can be printed
fprintf(stderr, "%lu\n", runsRem.size);
printBucket(bucket, alphabetSize, bucketSize);
#endif
//OPERATION/////////////////////////////////////////////////////////////
/*set up L, S, and LMS metadata**************************************/
/*The paper stipulates an additional universally minimal character
* which is definitionally LMS, but here it is simulated.*/
//Assign characters' values right to left (end to beginning) for L, S,
//and LMS
size_t loopUntil = runsRem.size - 2;
LMSandLS[runsRem.size-1] = _L_;
for(i = loopUntil; i != ((size_t)0)-1; i--)
LMSandLS[i] = source[runsRem.S[i]] > source[runsRem.S[i+1]] ? _L_ : _S_;
i=0;
while(1){
while(i < loopUntil && LMSandLS[i] == _L_) i++;
if(i >= loopUntil) break;
LMSandLS[i++] = _LMS_;
while(i < loopUntil && LMSandLS[i] == _S_) i++;
if(i >= loopUntil) break;
}
#ifdef DEBUG
printLMSandLS(LMSandLS, runsRem.size);
fprintf(stderr, "\n\nAdding to buckets\n\n");
#endif
/*PRIMEER***************************************Add entries to buckets*/
//This is supposed to prepare the data to be induce sorted.
memcpy(bucketEndCounter, bucketSize, sizeof(*bucketEndCounter) * alphabetSize);
bucket[source[runsRem.S[runsRem.size-1]]][0] = runsRem.size-1;
//bucketFrontCounter[bucketLocation]++;
//LMS type right-to-left scan -- Add LMS entries to the ends of
//various buckets going from right to left. The result is partially
//full buckets with LMS entries in acending order.
for(size_t i = runsRem.size-1; i != ((size_t)0)-1; i--){
if(LMSandLS[i] == _LMS_){
const unsigned char target = source[runsRem.S[i]];
bucket[target][--bucketEndCounter[target]] = i;
}
}
/*LOOP OVER UNTIL COMPLETE*********************************************/
//TODO: there's some really ugly ways to make this run faster.
//L type left-to-right scan, not exactly a direct reasoning for this,
//please refer to the paper. Bounds checking was used in place of
//checking for negative values so that -1 didn't have to be used,
//allowing architentually maximal string length.
char goOn;
do{
goOn = 0;
memset(sanityCheck.S, 0, sizeof(*sanityCheck.S) * runsRem.size);
sanityCheck.size = 0;
//step 3 of setting up SA
//L type right to left scan.
memcpy(bucketEndCounter, bucketSize, sizeof(*bucketEndCounter) * alphabetSize);
for(i = alphabetSize-1; i != ((size_t)0)-1 ; i--){
for(size_t j = bucketSize[i]-1; j != ((size_t)0)-1; j--){
if(!bucket[i][j]) continue;
const size_t target = bucket[i][j]-1;
if(LMSandLS[target] == _L_ || LMSandLS[target] == _LMS_){
char KILLYOSELF = 0;
if(source[runsRem.S[target]] == source[runsRem.S[runsRem.size-1]] && bucketEndCounter[source[runsRem.S[target]]]-1 == 0){
KILLYOSELF = 1;
printf("Trying to write over something you're blatently not supposed to write over.\n");
}
for(size_t k = 0; k < sanityCheck.size; k++)
if(sanityCheck.S[k] == target){
KILLYOSELF=1;
printf("trying to write a %lu a second time.\n", target);
}
if(KILLYOSELF){
printf("KILL YO SELF in r to l\n");
exit(1);
}
const unsigned char target2 = source[runsRem.S[target]];
bucket[target2][--bucketEndCounter[target2]] = target;
sanityCheck.S[sanityCheck.size++] = target;
}
}
}
#ifdef DEBUG
printBucket(bucket, alphabetSize, bucketSize);
#endif
//S type left to right scan.
memset(bucketFrontCounter, 0, sizeof(*bucketFrontCounter) * alphabetSize);
//bucket[source[runsRem.S[runsRem.size-1]]][0] = runsRem.size-1;
bucketFrontCounter[source[runsRem.S[runsRem.size-1]]] = 1;//protect last index
for(int i = 0; i < alphabetSize; i++){
for(size_t j = 0; j < bucketSize[i]; j++){
if(!bucket[i][j]) continue;
const size_t target = bucket[i][j]-1;
if(LMSandLS[target] == _S_){
char KILLYOSELF = 0;
if(source[runsRem.S[target]] == source[runsRem.S[runsRem.size-1]] && bucketEndCounter[source[runsRem.S[target]]]-1 == 0){
KILLYOSELF = 1;
printf("Trying to write over something you're blatently not supposed to write over.\n");
}
for(size_t k = 0; k < sanityCheck.size; k++)
if(sanityCheck.S[k] == target){
KILLYOSELF=1;
printf("trying to write a %lu a second time.\n", target);
}
if(KILLYOSELF){
printf("KILL YO SELF in l to r\n");
exit(1);
}
const unsigned char target2 = source[runsRem.S[target]];
bucket[target2][bucketFrontCounter[target2]++] = target;
sanityCheck.S[sanityCheck.size++] = target;
}
}
}
for(i = 0; i < alphabetSize; i ++)
if(memcmp(bucket[i], oldBucket[i], bucketSize[i] * sizeof(size_t))){
for(size_t j = i; j < alphabetSize; j++)
if(bucketSize[j])
memcpy(oldBucket[j], bucket[j], sizeof(*bucket) * bucketSize[j]);
goOn = 1;
break;
}
}while(goOn);
#ifdef DEBUG
printBucket(bucket, alphabetSize, bucketSize);
#endif
//CLEAN UP//////////////////////////////////////////////////////////////
free(LMSandLS);
toReturn = initSequence(runsRem.size);
toReturn.size = 0;
for(i = 0; i < alphabetSize; i++)
for(size_t j = 0; j < bucketSize[i]; j++)
toReturn.S[toReturn.size++] = bucket[i][j];
return toReturn;
}
