int main() {
uint64_t data = 0xdead;
uint16_t addr = 1;
printf("[INFO] Write R[%d] = %lx\n", addr, data);
doWrite(addr, data);
printf("[INFO] Read R[%d]\n", addr);
uint64_t y = doRead(addr);
printf("[INFO] Received %lx\n", y);
assert(y == data);
uint64_t data_accum = -0x1fbe;
printf("[INFO] Accum R[%d] with %lx\n", addr, data_accum);
y = doAccum(addr, data_accum);
printf("[INFO] Received %lx\n", y);
assert(y == data);
printf("[INFO] Read R[%d]\n", addr);
y = doRead(addr);
printf("[INFO] Received %lx\n", y);
assert(y == data + data_accum);
data = 0xbeef;
uint64_t data_addr = doTranslate((void *) &data);
printf("[INFO] Load %lx (0x%lx) via L1 data cache\n",
data, data_addr);
y = doLoad(addr, data_addr);
printf("[INFO] Received %lx\n", y);
return 0;
}
/* translate nuc sequence into an sequence of amino acids */
void translateProtein(struct speciesInfo *si)
{
struct dnaSeq thisSeq;
aaSeq *outSeq;
thisSeq.dna = si->nucSequence;
thisSeq.size = si->size;
outSeq = doTranslate(&thisSeq, 0, 0, FALSE);
si->aaSequence = outSeq->dna;
si->aaSize = outSeq->size;
}
void outSpeciesExons(FILE *f, char *dbName, struct speciesInfo *si,
struct exonInfo *giList)
{
int exonNum = 1;
struct dnaSeq thisSeq;
aaSeq *outSeq;
int exonCount = 0;
struct exonInfo *gi = giList;
for(; gi; gi = gi->next)
exonCount++;
for(gi = giList; gi; gi = gi->next, exonNum++)
{
struct speciesInfo *siTemp = si;
if (gi->frame->strand[0] == '-')
slReverse(&gi->frame);
struct mafFrames *startFrame = gi->frame;
assert(startFrame->isExonStart == TRUE);
struct mafFrames *lastFrame = startFrame;
assert(gi->exonSize < MAX_EXON_SIZE);
while(lastFrame->next)
lastFrame = lastFrame->next;
assert(lastFrame->isExonEnd == TRUE);
for(; siTemp ; siTemp = siTemp->next)
{
char *ptr = exonBuffer;
switch(startFrame->frame)
{
case 0: /* just copy the sequence over */
memcpy(ptr,
&siTemp->nucSequence[gi->exonStart], gi->exonSize);
ptr += gi->exonSize;
break;
case 1: /* we need to grab one nuc from the end
* of the previous exon */
*ptr++ = siTemp->nucSequence[gi->exonStart - 1];
memcpy(ptr,
&siTemp->nucSequence[gi->exonStart], gi->exonSize);
ptr += gi->exonSize;
break;
case 2: /* we need to delete the first nuc from this exon
* because we included it on the last exon */
memcpy(ptr,
&siTemp->nucSequence[gi->exonStart+1], gi->exonSize - 1);
ptr += gi->exonSize - 1;
break;
}
int lastFrame = (startFrame->frame + gi->exonSize) % 3;
if (lastFrame == 1) /* delete the last nucleotide */
--ptr;
else if (lastFrame == 2) /* add one more nucleotide from
* the next exon */
*ptr++ = siTemp->nucSequence[gi->exonStart + gi->exonSize];
*ptr++ = 0; /* null terminate */
thisSeq.dna = exonBuffer;
thisSeq.size = ptr - exonBuffer;
outSeq = doTranslate(&thisSeq, 0, 0, FALSE);
if (!allDashes(outSeq->dna))
{
fprintf(f, ">%s_%s_%d_%d %d %d %d %s",
gi->name,
siTemp->name, exonNum, exonCount,
outSeq->size,
startFrame->frame, lastFrame,
siTemp->curPosString->name);
//dbName, gi->frame->chrom,
//gi->chromStart+1, gi->chromEnd, startFrame->strand[0]);
maybePrintGeneName(gi->name, f);
fprintf(f, "\n%s\n", outSeq->dna);
}
siTemp->curPosString = siTemp->curPosString->next;
}
fprintf(f, "\n");
}
fprintf(f, "\n");
}
static void outSpeciesExons(FILE *f, char *dbName, struct speciesInfo *si,
struct exonInfo *giList, boolean doBlank, boolean doTable, int numCols)
{
int exonNum = 1;
struct dnaSeq thisSeq;
aaSeq *outSeq;
int exonCount = 0;
struct exonInfo *gi = giList;
for(; gi; gi = gi->next)
{
if (gi->exonSize > 1)
exonCount++;
}
for(gi = giList; gi; gi = gi->next, exonNum++)
{
struct speciesInfo *siTemp = si;
if (gi->exonSize == 1)
continue;
for(; siTemp ; siTemp = siTemp->next)
{
char *ptr = exonBuffer;
switch(gi->frame)
{
case 0: /* just copy the sequence over */
memcpy(ptr,
&siTemp->nucSequence[gi->exonStart], gi->exonSize);
ptr += gi->exonSize;
break;
case 1: /* we need to grab one nuc from the end
* of the previous exon */
*ptr++ = siTemp->nucSequence[gi->exonStart - 1];
memcpy(ptr,
&siTemp->nucSequence[gi->exonStart], gi->exonSize);
ptr += gi->exonSize;
break;
case 2: /* we need to delete the first nuc from this exon
* because we included it on the last exon */
memcpy(ptr,
&siTemp->nucSequence[gi->exonStart+1], gi->exonSize - 1);
ptr += gi->exonSize - 1;
break;
}
int lastFrame = (gi->frame + gi->exonSize) % 3;
if (lastFrame == 1) /* delete the last nucleotide */
--ptr;
else if (lastFrame == 2) /* add one more nucleotide from
* the next exon */
*ptr++ = siTemp->nucSequence[gi->exonStart + gi->exonSize];
*ptr++ = 0; /* null terminate */
thisSeq.dna = exonBuffer;
thisSeq.size = ptr - exonBuffer;
outSeq = doTranslate(&thisSeq, 0, 0, FALSE);
char buffer[10 * 1024];
safef(buffer, sizeof buffer, "%s_%s_%d_%d %d %d %d %s",
gi->name,
siTemp->name, exonNum, exonCount,
outSeq->size,
gi->frame, lastFrame,
siTemp->curPosString->name);
if (doBlank || !allDashes(outSeq->dna))
{
if (doTable)
{
if (numCols == -1)
fprintf(f, "%s ", buffer);
else
{
if (strlen(buffer) > numCols)
buffer[numCols] = 0;
fprintf(f, "%-*s ", numCols, buffer);
}
}
else
fprintf(f, ">%s\n", buffer);
fprintf(f, "%s\n", outSeq->dna);
}
siTemp->curPosString = siTemp->curPosString->next;
}
fprintf(f, "\n");
}
fprintf(f, "\n");
}
