extern Chain* chainCreateComplement(Chain* chain, SWPrefs* swPrefs) {
Chain* complement = (Chain*) malloc(sizeof(struct Chain));
complement->subchain = 0;
complement->length = chain->length;
int nameLen = strlen(chain->name) + strlen(COMPLEMENT_LABEL) + 1;
complement->name = (char*) malloc(nameLen * sizeof(char));
sprintf(complement->name, "%s%s", COMPLEMENT_LABEL, chain->name);
complement->codes = (ChainCode*) malloc(complement->length * sizeof(ChainCode));
complement->items = (ChainItem*) malloc(complement->length * sizeof(ChainItem));
int normal;
int reverse;
ChainItem item;
ChainItem newItem;
Matcher* matcher = swPrefsGetMatcher(swPrefs);
for (
normal = 0, reverse = chain->length - 1;
normal < chain->length;
++normal, --reverse
) {
item = chain->items[reverse];
switch (item) {
case 'A':
newItem = 'T';
break;
case 'C':
newItem = 'G';
break;
case 'T':
newItem = 'A';
break;
case 'G':
newItem = 'C';
break;
default:
newItem = item;
}
complement->items[normal] = newItem;
complement->codes[normal] = matcherGetCode(matcher, newItem,
swPrefsShotgun(swPrefs));
}
if (swPrefsSolveOnly(swPrefs)) {
complement->reverseCodes = NULL;
complement->reverseItems = NULL;
} else {
addReversedChain(complement);
}
return complement;
}
static void readFromBuffer(Chain* chain, char* fileBuffer, SWPrefs* swPrefs) {
Matcher* matcher = swPrefsGetMatcher(swPrefs);
int shotgun = swPrefsShotgun(swPrefs);
int fileLength = strlen(fileBuffer);
// Maximum chain length is equal to input file length.
chain->items = (ChainItem*) malloc(sizeof(ChainItem) * fileLength);
chain->codes = (ChainCode*) malloc(sizeof(ChainCode) * fileLength);
chain->length = 0;
int fileCharIdx;
int isSpace; // boolean
ChainItem chainItem;
ChainItem chainCode;
int fillItems = (matcherGetType(matcher) == MATCHER_MATCH_MISMATCH);
int start = 0;
while (fileBuffer[start] != '\n') start++;
chain->name = malloc((start + 1) * sizeof(char));
chain->name = strncpy(chain->name, fileBuffer, start);
chain->name[start] = '\0';
// Read all items into the item array. Use matcher object to get the item
// codes and write them to code array.
for (fileCharIdx = start; fileCharIdx < fileLength; ++fileCharIdx) {
isSpace = isspace(fileBuffer[fileCharIdx]);
if (isSpace) {
continue;
}
chainItem = (ChainItem) toupper(fileBuffer[fileCharIdx]);
chain->items[chain->length] = chainItem;
if (fillItems) matcherAddItem(matcher, chainItem);
chainCode = (ChainCode) matcherGetCode(matcher, chainItem, shotgun);
chain->codes[chain->length] = chainCode;
if (chain->codes[chain->length] == MATCHER_CODE_NOT_FOUND) {
printf("Item not in matching table %c.\n", chainItem);
exit(-1);
}
chain->length++;
}
if (!TEST_MODE) {
printf("%.55s... length:%14d\n", chain->name, chain->length);
}
}
extern SWData* swSolveGPU(Chain* rowChain, Chain* columnChain,
SWPrefs* swPrefs) {
int matcherType = matcherGetType(swPrefsGetMatcher(swPrefs));
if (matcherType == MATCHER_MATRIX) {
return swSolveGPUSM(rowChain, columnChain, swPrefs);
} else {
return swSolveGPUMM(rowChain, columnChain, swPrefs);
}
}
extern Chain* chainCreateFromBuffer(char* fileBuffer, SWPrefs* swPrefs) {
Chain* chain = (Chain*) malloc(sizeof(struct Chain));
chain->subchain = 0;
readFromBuffer(chain, fileBuffer, swPrefsGetMatcher(swPrefs));
if (swPrefsSolveOnly(swPrefs)) {
chain->reverseCodes = NULL;
chain->reverseItems = NULL;
} else {
addReversedChain(chain);
}
return chain;
}
