// Insert string subscript i into the global hash table.
// Sequence and information about the string are in
// global variables Data, String_Start, String_Info, ....
static
void
Put_String_In_Hash(int i) {
String_Ref_t ref = 0;
char * p, * window;
int kmers_inserted = 0;
int skip_ct;
uint64 key, key_is_bad;
int j;
if (String_Info [i] . length < Kmer_Len)
return;
p = window = Data + String_Start [i];
key = key_is_bad = 0;
for (j = 0; j < Kmer_Len; j ++) {
key_is_bad |= (uint64) (Char_Is_Bad [(int) * p]) << j;
key |= (uint64) (Bit_Equivalent [(int) * (p ++)]) << (2 * j);
}
setStringRefStringNum(ref, i);
if (i > MAX_STRING_NUM) {
fprintf (stderr, "Too many strings for hash table--exiting\n");
exit (1);
}
setStringRefOffset(ref, TRUELY_ZERO);
skip_ct = 0;
setStringRefEmpty(ref, TRUELY_ZERO);
if (key_is_bad == false) {
Hash_Insert (ref, key, window);
kmers_inserted ++;
}
while ((* p) != '\0') {
window ++;
{
String_Ref_t newoff = getStringRefOffset(ref) + 1;
assert(newoff < OFFSET_MASK);
setStringRefOffset(ref, newoff);
}
if (++ skip_ct > HASH_KMER_SKIP)
skip_ct = 0;
key_is_bad >>= 1;
key_is_bad |= (uint64) (Char_Is_Bad [(int) * p]) << (Kmer_Len - 1);
key >>= 2;
key |= (uint64) (Bit_Equivalent [(int) * (p ++)]) << (2 * (Kmer_Len - 1));
if (skip_ct == 0 && ! key_is_bad) {
Hash_Insert (ref, key, window);
kmers_inserted ++;
}
}
}
int Hash_Expand(HashTable hashT) {
int oldCount = hashT->array_size;
int newCount = hashT->array_size * 2;
int x;
HashElem *oldTable = hashT->table;
HashElem aux, aux2;
hashT->table = (HashElem *) malloc(sizeof (HashElem) * newCount);
hashT->array_size = newCount;
hashT->size = 0;
for (x = 0; x < newCount; x++) {
hashT->table[x] = NULL;
}
for (x = 0; x < oldCount; x++) {
aux = oldTable[x];
while (aux != NULL) {
Hash_Insert(hashT, aux->data);
aux2 = aux;
aux = aux->next;
free(aux2);
}
}
free(oldTable);
hashT->array_size = newCount;
return 0;
}
void* thread_code(void *arg)
{
struct hash_job_desc *jd = (struct hash_job_desc *) arg;
int numOfOps = NUM_OPS_PER_THREAD;
int i = 0;
int *addlist = malloc(sizeof(int) * numOfOps);
if (addlist == NULL) {
printf(" cannot allocate more ..., reduce space \n");
exit(-1);
}
while (i < numOfOps) {
// addlist[i] = rand() % (numOfOps * num_threads);
// since key is unique...
addlist[i] = i + (numOfOps * jd->tid);
Hash_Insert(&h, addlist + i, addlist[i]);
(jd->ic)++;
i++;
}
i = 0;
while (i < numOfOps) {
if (i % 3 == 0) {
Hash_Delete(&h, addlist[i]);
(jd->dc)++;
}
i++;
}
i = 0;
while (i < numOfOps) {
if (Hash_Lookup(&h, addlist[i]) != NULL)
(jd->lc)++;
i++;
}
// printf(" END Thread-%04d with %6d ic, %6d dc, %6d lc\n",
// jd->tid, jd->ic, jd->dc, jd->lc);
free(addlist);
return NULL;
}
int main()
{
pthread_t thread[3];
counter_t counter;
printf("Testing Counter...\n");
printf("Begin single thread test\n");
printf("Counter Init\n");
Counter_Init(&counter, 0);
printf("Counter_GetValue\n");
int counter_val = Counter_GetValue(&counter);
printf("expected 0 got %d\n", counter_val);
printf("Counter_Increment\n");
Counter_Increment(&counter);
counter_val = counter_val = Counter_GetValue(&counter);
printf("expected 1 got %d\n", counter_val);
printf("Counter_Decrement\n");
Counter_Decrement(&counter);
counter_val = Counter_GetValue(&counter);
printf("expected 0 got %d\n", counter_val);
printf("Begin multithreaded test\n");
printf("Counter Init\n");
Counter_Init(&counter, 0);
pthread_create(&thread[0], NULL, Counter_Increment, (void*)&counter);
printf("Counter is at %d after 1 increment call\n", Counter_GetValue(&counter));
pthread_create(&thread[1], NULL, Counter_Increment, (void*)&counter);
printf("Counter is at %d after 2 increment calls\n", Counter_GetValue(&counter));
pthread_create(&thread[2], NULL, Counter_Increment, (void*)&counter);
printf("Counter is at %d after 3 increment calls\n", Counter_GetValue(&counter));
pthread_join(thread[0], NULL);
pthread_join(thread[1], NULL);
pthread_join(thread[2], NULL);
printf("Count after 3 threads = %d\n", Counter_GetValue(&counter));
printf("Done Testing Counter\n\n");
list_insert_arg insert_arg[3];
list_lookup_arg lookup_arg[3];
list_t list;
printf("Testing list...\n");
printf("Begin single-thread test\n");
printf("List_Init()\n");
List_Init(&list);
printf("List_Insert()\n");
List_Insert(&list, (void *)0x1, 1);
List_Insert(&list, (void *)0x2, 2);
List_Insert(&list, (void *)0x3, 3);
printf("Expected %p got %p\n", (void *)0x1, List_Lookup(&list, 1));
printf("Expected %p got %p\n", (void *)0x3, List_Lookup(&list, 3));
printf("Expected %p got %p\n", (void *)0x2, List_Lookup(&list, 2));
printf("List_Delete()\n");
List_Delete(&list, 1);
printf("Expected %p got %p\n", (void *)0x2, List_Lookup(&list, 2));
printf("Expected %p got %p\n", (void *)0x3, List_Lookup(&list, 3));
printf("Expected %p got %p\n", NULL, List_Lookup(&list, 1));
printf("Single-thread test completed\n");
printf("Begin multi-thread test\n");
printf("List_Init()\n");
List_Init(&list);
printf("Parallel List_Insert()\n");
insert_arg[0].list = &list;
insert_arg[0].element = (void *)0x1;
insert_arg[0].key = 1;
pthread_create(&thread[0], NULL, pthread_list_insert, &insert_arg[0]);
insert_arg[1].list = &list;
insert_arg[1].element = (void *)0x2;
insert_arg[1].key = 2;
pthread_create(&thread[1], NULL, pthread_list_insert, &insert_arg[1]);
insert_arg[2].list = &list;
insert_arg[2].element = (void *)0x3;
insert_arg[2].key = 3;
pthread_create(&thread[2], NULL, pthread_list_insert, &insert_arg[2]);
pthread_join(thread[0], NULL);
pthread_join(thread[1], NULL);
pthread_join(thread[2], NULL);
printf("Parallel List_Insert() completed\n");
printf("Parallel List_Lookup()\n");
lookup_arg[0].list = &list;
lookup_arg[0].key = 1;
pthread_create(&thread[0], NULL, pthread_list_lookup, &lookup_arg[0]);
lookup_arg[1].list = &list;
lookup_arg[1].key = 2;
pthread_create(&thread[1], NULL, pthread_list_lookup, &lookup_arg[1]);
lookup_arg[2].list = &list;
lookup_arg[2].key = 3;
pthread_create(&thread[2], NULL, pthread_list_lookup, &lookup_arg[2]);
pthread_join(thread[0], NULL);
pthread_join(thread[1], NULL);
pthread_join(thread[2], NULL);
printf("Parallel List_Lookup() completed\n");
printf("List_Delete()\n");
List_Delete(&list, 1);
printf("Expected %p got %p\n", (void *)0x2, List_Lookup(&list, 2));
printf("Expected %p got %p\n", (void *)0x3, List_Lookup(&list, 3));
printf("Expected %p got %p\n", NULL, List_Lookup(&list, 1));
printf("Multi-thread test completed\n");
printf("Done testing list\n\n");
hash_t hash;
printf("Testing hash...\n");
printf("Begin single-thread test\n");
printf("Hash_Init()\n");
Hash_Init(&hash, 2);
printf("Hash_Insert()\n");
Hash_Insert(&hash, (void *)0x1, 1);
Hash_Insert(&hash, (void *)0x2, 2);
Hash_Insert(&hash, (void *)0x3, 3);
printf("Hash_Lookup()\n");
printf("Expected %p got %p\n", (void *)0x2, Hash_Lookup(&hash, 2));
printf("Expected %p got %p\n", (void *)0x3, Hash_Lookup(&hash, 3));
printf("Expected %p got %p\n", (void *)0x1, Hash_Lookup(&hash, 1));
printf("Hash_Delete()\n");
Hash_Delete(&hash, 1);
printf("Hash_Lookup()\n");
printf("Expected %p got %p\n", (void *)0x2, Hash_Lookup(&hash, 2));
printf("Expected %p got %p\n", (void *)0x3, Hash_Lookup(&hash, 3));
printf("Expected %p got %p\n", NULL, Hash_Lookup(&hash, 1));
printf("Single-thread test completed\n");
printf("Done testing hash...\n");
return 0;
}
LRESULT CALLBACK WndProc(
HWND hWnd,
UINT nMessage,
WPARAM wParam,
LPARAM lParam
)
{
RECT ClientRect;
switch (nMessage)
{
case WM_CREATE_IRC_WINDOW:
if (Hash_Get(pHash, (char*)wParam))
{
ContextIRC.hCurrentWindow = Hash_Get(pHash, (char*)wParam);
}
else
{
static HWND __hWnd__;
__hWnd__ = Create_Window(__hWnd__, hWnd);
if (((char*)wParam)[0] == '#')
{
ShowWindow(ContextIRC.hCurrentWindow, SW_HIDE);
ContextIRC.hCurrentWindow = __hWnd__;
strArray_Add(ChannelNames, szChannel);
Hash_Insert(pHash, ContextIRC.hCurrentWindow, (char*)wParam);
ShowWindow(Hash_Get(pHash, (char*)wParam), SW_SHOW);
ResizeWindows(ContextIRC.dwOldWidth, ContextIRC.dwOldHeight);
SendMessage(ContextIRC.hCurrentWindow, WM_SETFONT, (WPARAM)ContextIRC.hFont, (LPARAM)TRUE);
}
else
{
ContextIRC.hCurrentWindow = Array_Index(pArray, Array_Num(pArray));
ContextIRC.hCurrentWindow = __hWnd__;
Hash_Insert(pHash, ContextIRC.hCurrentWindow, (char*)wParam);
ResizeWindows(ContextIRC.dwOldWidth, ContextIRC.dwOldHeight);
SendMessage(ContextIRC.hCurrentWindow, WM_SETFONT, (WPARAM)ContextIRC.hFont, (LPARAM)TRUE);
}
ContextIRC.hCurrentWindow = Array_Index(pArray, Array_Num(pArray));
Hash_Insert(pHash, ContextIRC.hCurrentWindow, (char*)wParam);
SendMessage(ContextIRC.hCurrentWindow, WM_SETFONT, (WPARAM)ContextIRC.hFont, (LPARAM)TRUE);
break;
}
case WM_CREATE:
pArray = Array_Init(pArray);
ContextIRC.hCurrentWindow = Create_Window(ContextIRC.hCurrentWindow, hWnd);
ContextIRC.hFont = InitFont(ContextIRC.hCurrentWindow);
ContextIRC.hTypeBuffer = InitTypeBuffer(ContextIRC.hFont, hWnd);
ContextIRC.hParentProc = SetWindowLongPtr(ContextIRC.hTypeBuffer, GWL_WNDPROC, (LONG_PTR)TypeBufferProc);
ContextIRC.hNetworkThread = CreateThread(NULL, 0, Connect, NULL, 0, &ContextIRC.hNetworkThreadID);
break;
case WM_DESTROY:
DestroyContext();
PostQuitMessage(0);
break;
case WM_HOTKEY:
{
register uint32_t nIndex = 0;
if (wParam == IRCContext->LeftKey)
{
if (Array_Num(pArray) <= 0)
break;
for (nIndex = Array_Num(pArray); nIndex > 0; nIndex--)
{
if (ContextIRC.hCurrentWindow == Array_Index(pArray, 0))
{
ShowWindow(ContextIRC.hCurrentWindow, SW_HIDE);
ContextIRC.hCurrentWindow = Array_Index(pArray, Array_Num(pArray));
strcpy_s(szChannel, 96, strArray_Index(ChannelNames, strArray_Num(ChannelNames)));
ShowWindow(ContextIRC.hCurrentWindow, SW_SHOW);
MoveWindow(ContextIRC.hCurrentWindow, 0, 0, ContextIRC.dwOldWidth, ContextIRC.dwOldHeight, TRUE);
break;
}
nIndex--;
ShowWindow(ContextIRC.hCurrentWindow, SW_HIDE);
ContextIRC.hCurrentWindow = Array_Index(pArray, nIndex);
strcpy_s(szChannel, 96, strArray_Index(ChannelNames, nIndex - 1));
ShowWindow(ContextIRC.hCurrentWindow, SW_SHOW);
MoveWindow(ContextIRC.hCurrentWindow, 0, 0, ContextIRC.dwOldWidth, ContextIRC.dwOldHeight, TRUE);
break;
}
}
if (wParam == IRCContext->RightKey)
{
for (nIndex = 0; nIndex <= Array_Num(pArray); nIndex++)
{
if (Array_Num(pArray) <= 0)
break;
if (ContextIRC.hCurrentWindow == Array_Index(pArray, nIndex))
{
if (ContextIRC.hCurrentWindow == Array_Index(pArray, Array_Num(pArray)))
{
ShowWindow(ContextIRC.hCurrentWindow, SW_HIDE);
ContextIRC.hCurrentWindow = Array_Index(pArray, 0);
strcpy_s(szChannel, 96, strArray_Index(ChannelNames, 0));
ShowWindow(ContextIRC.hCurrentWindow, SW_SHOW);
MoveWindow(ContextIRC.hCurrentWindow, 0, 0, ContextIRC.dwOldWidth, ContextIRC.dwOldHeight, TRUE);
break;
}
nIndex++;
ShowWindow(ContextIRC.hCurrentWindow, SW_HIDE);
ContextIRC.hCurrentWindow = Array_Index(pArray, nIndex);
strcpy_s(szChannel, 96, strArray_Index(ChannelNames, nIndex - 1));
ShowWindow(ContextIRC.hCurrentWindow, SW_SHOW);
MoveWindow(ContextIRC.hCurrentWindow, 0, 0, ContextIRC.dwOldWidth, ContextIRC.dwOldHeight, TRUE);
break;
}
}
}
break;
}
case WM_SIZE:
ResizeWindows(LOWORD(lParam), HIWORD(lParam) - IRCContext->nTypeHeight);
GetClientRect(hWnd, &ClientRect);
ContextIRC.dwOldWidth = LOWORD(lParam);
ContextIRC.dwOldHeight = HIWORD(lParam);
MoveWindow(ContextIRC.hTypeBuffer, 0, ClientRect.bottom - IRCContext->nTypeHeight, LOWORD(lParam), IRCContext->nTypeHeight, TRUE);
break;
default:
return DefWindowProc(hWnd, nMessage, wParam, lParam);
}
return 0;
}
// Insert string subscript i into the global hash table.
// Sequence and information about the string are in
// global variables basesData, String_Start, String_Info, ....
static
void
Put_String_In_Hash(uint32 curID, uint32 i) {
String_Ref_t ref = 0;
int skip_ct;
uint64 key;
uint64 key_is_bad;
int j;
uint32 kmers_skipped = 0;
uint32 kmers_bad = 0;
uint32 kmers_inserted = 0;
char *p = basesData + String_Start[i];
char *window = basesData + String_Start[i];
key = key_is_bad = 0;
for (uint32 j=0; j<G.Kmer_Len; j ++) {
key_is_bad |= (uint64) (Char_Is_Bad[(int) * p]) << j;
key |= (uint64) (Bit_Equivalent[(int) * (p ++)]) << (2 * j);
}
setStringRefStringNum(ref, i);
if (i > MAX_STRING_NUM)
fprintf (stderr, "Too many strings for hash table--exiting\n"), exit(1);
setStringRefOffset(ref, TRUELY_ZERO);
skip_ct = 0;
setStringRefEmpty(ref, TRUELY_ZERO);
if (key_is_bad == false) {
Hash_Insert(ref, key, window);
kmers_inserted++;
} else {
kmers_bad++;
}
while (*p != 0) {
window++;
String_Ref_t newoff = getStringRefOffset(ref) + 1;
assert(newoff < OFFSET_MASK);
setStringRefOffset(ref, newoff);
if (++skip_ct > HASH_KMER_SKIP)
skip_ct = 0;
key_is_bad >>= 1;
key_is_bad |= (uint64) (Char_Is_Bad[(int) * p]) << (G.Kmer_Len - 1);
key >>= 2;
key |= (uint64) (Bit_Equivalent[(int) * (p ++)]) << (2 * (G.Kmer_Len - 1));
if (skip_ct > 0) {
kmers_skipped++;
continue;
}
if (key_is_bad) {
kmers_bad++;
continue;
}
Hash_Insert(ref, key, window);
kmers_inserted++;
}
//fprintf(stderr, "STRING %u skipped %u bad %u inserted %u\n",
// curID, kmers_skipped, kmers_bad, kmers_inserted);
}
