void cStream::runBenchmarkTuned()
{
initializeVariables();
runChecks();
runTunedTests();
checkSTREAMresults();
calculateBandwidthResults();
outputSummary();
}; // void cStream::runBenchmarkTuned()
void flushSummaryBlocks(struct hash *componentHash, FILE *f)
/* flush any pending summary blocks */
{
struct mafSummary *ms;
struct hashCookie hc = hashFirst(componentHash);
while ((ms = (struct mafSummary *)hashNextVal(&hc)) != NULL)
{
outputSummary(f, ms);
}
}
//Provided main function from the Stegman Textbook for this course from page 232
int main (void) {
char code;
double amount, service, balance;
double amtCheck, amtDeposit, openBalance, closeBalance;
int numCheck, numDeposit;
if (!(fpIn = fopen("account.txt", "r"))) {
printf("account.txt could not be opened for input.");
exit(1);
}
if (!(fpOut = fopen("csis.txt", "w"))) {
printf("csis.text could not be opened for output");
exit(1);
}
amount = 0.0;
service = 0.0;
balance = 0.0;
amtCheck = 0.0;
amtDeposit = 0.0;
openBalance = 0.0;
closeBalance = 0.0;
numCheck = 0;
numDeposit = 0;
outputHeaders();
while (!feof(fpIn)) {
fscanf(fpIn, "%c %lf\n", &code, &amount);
if (code == 'I') {
initialBalance(amount, &balance, &service, &openBalance);
} else if (code == 'D') {
deposit(amount, &balance, &service, &numDeposit, &amtDeposit);
} else {
check(amount, &balance, &service, &numCheck, &amtCheck);
}
}
closeBalance = balance - service;
outputSummary(numDeposit, amtDeposit, numCheck, amtCheck, openBalance, service, closeBalance);
fclose(fpIn);
fclose(fpOut);
return 0;
}
long processMaf(struct mafAli *maf, struct hash *componentHash,
FILE *f, struct mafFile *mf, char *fileName)
/* Compute scores for each pairwise component in the maf and output to .tab file */
{
struct mafComp *mc = NULL, *nextMc = NULL;
struct mafSummary *ms, *msPending;
struct mafAli pairMaf;
long componentCount = 0;
struct mafComp *mcMaster = mafMaster(maf, mf, fileName);
struct mafComp *oldMasterNext = mcMaster->next;
char *e, *chrom;
char src[256];
strcpy(src, mcMaster->src);
chrom = chopPrefix(src);
for (mc = maf->components; mc != NULL; mc = nextMc)
{
nextMc = mc->next;
if (sameString(mcMaster->src, mc->src) || mc->size == 0)
continue;
/* create maf summary for this alignment component */
AllocVar(ms);
ms->chrom = cloneString(chrom);
/* both MAF and BED format define chromStart as 0-based */
ms->chromStart = mcMaster->start;
/* BED chromEnd is start+size */
ms->chromEnd = mcMaster->start + mcMaster->size;
ms->src = cloneString(mc->src);
/* remove trailing components (following initial .) to src name */
if ((e = strchr(ms->src, '.')) != NULL)
*e = 0;
/* construct pairwise maf for scoring */
ZeroVar(&pairMaf);
pairMaf.textSize = maf->textSize;
pairMaf.components = mcMaster;
mcMaster->next = mc;
mc->next = NULL;
ms->score = scorePairwise(&pairMaf);
ms->leftStatus[0] = mc->leftStatus;
ms->rightStatus[0] = mc->rightStatus;
/* restore component links to allow memory recovery */
mcMaster->next = oldMasterNext;
mc->next = nextMc;
/* output to .tab file, or save for merging with another block
* if this one is too small */
/* handle pending alignment block for this species, if any */
if ((msPending = (struct mafSummary *) hashFindVal(componentHash, ms->src)) != NULL)
{
/* there is a pending alignment block */
/* either merge it with the current block, or output it */
if (sameString(ms->chrom, msPending->chrom) &&
(ms->chromStart+1 - msPending->chromEnd < mergeGap))
{
/* merge pending block with current */
ms->score = mergeScores(msPending, ms);
ms->chromStart = msPending->chromStart;
ms->leftStatus[0] = msPending->leftStatus[0];
ms->rightStatus[0] = ms->rightStatus[0];
}
else
outputSummary(f, msPending);
hashRemove(componentHash, msPending->src);
mafSummaryFree(&msPending);
}
/* handle current alignment block (possibly merged) */
if (ms->chromEnd - ms->chromStart > minSize)
{
/* current block is big enough to output */
outputSummary(f, ms);
mafSummaryFree(&ms);
}
else
hashAdd(componentHash, ms->src, ms);
componentCount++;
}
return componentCount;
}
