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;
}
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;
}
extern Chain* chainCreateReverse(Chain* chain) {
Chain* reverse = (Chain*) malloc(sizeof(struct Chain));
reverse->subchain = 1;
reverse->length = chain->length;
int nameLen = strlen(chain->name) + strlen(REVERSE_LABEL) + 1;
reverse->name = (char*) malloc(nameLen * sizeof(char));
sprintf(reverse->name, "%s%s", REVERSE_LABEL, chain->name);
if (chain->reverseCodes == NULL) {
addReversedChain(chain);
}
reverse->codes = chain->reverseCodes;
reverse->items = chain->reverseItems;
reverse->reverseCodes = chain->codes;
reverse->reverseItems = chain->items;
return reverse;
}