// Returns false on EOI or error
bool pop ()
{
m_cur_char = readOne ();
if (!eoi() && !error())
m_cur_loc.feed (m_cur_char);
return !error() && !eoi();
}
std::vector<DatasetElem> DatasetReader::readAll() {
std::vector<DatasetElem> dataset;
DatasetElem elem;
while (readOne(elem)) {
dataset.push_back(elem);
}
return dataset;
}
void oocMaskCounts(char *oocFile, bits32 *tileCounts, int tileSize, bits32 maxPat)
/* Set items of tileCounts to maxPat if they are in oocFile.
* Effectively masks this out of index.*/
{
if (oocFile != NULL)
{
bits32 sig, psz;
FILE *f = mustOpen(oocFile, "rb");
boolean mustSwap = FALSE;
mustReadOne(f, sig);
mustReadOne(f, psz);
if (sig == oocSig)
mustSwap = FALSE;
else if (sig == oocSigSwapped)
{
mustSwap = TRUE;
psz = byteSwap32(psz);
}
else
errAbort("Bad signature on %s\n", oocFile);
if (psz != tileSize)
errAbort("Oligo size mismatch in %s. Expecting %d got %d\n",
oocFile, tileSize, psz);
if (mustSwap)
{
union {bits32 whole; UBYTE bytes[4];} u,v;
while (readOne(f, u))
{
v.bytes[0] = u.bytes[3];
v.bytes[1] = u.bytes[2];
v.bytes[2] = u.bytes[1];
v.bytes[3] = u.bytes[0];
tileCounts[v.whole] = maxPat;
}
}
else
{
bits32 oli;
while (readOne(f, oli))
tileCounts[oli] = maxPat;
}
fclose(f);
}
}
void DataReader::read(pn_data_t* data)
{
/*
while (pn_data_next(data)) {
readOne(data);
}
*/
do {
readOne(data);
} while (pn_data_next(data));
}
int HexBinaryDecoderBuf::readFromDevice()
{
int c;
int n;
if ((n = readOne()) == -1) return -1;
if (n >= '0' && n <= '9')
c = n - '0';
else if (n >= 'A' && n <= 'F')
c = n - 'A' + 10;
else if (n >= 'a' && n <= 'f')
c = n - 'a' + 10;
else throw DataFormatException();
c <<= 4;
if ((n = readOne()) == -1) throw DataFormatException();
if (n >= '0' && n <= '9')
c |= n - '0';
else if (n >= 'A' && n <= 'F')
c |= n - 'A' + 10;
else if (n >= 'a' && n <= 'f')
c |= n - 'a' + 10;
else throw DataFormatException();
return c;
}
I pString_Connection::syncDoRead(A *pdataobj)
{
I result;
MSBuffer *hb=headBuffer();
MSBuffer *db=readBuffer();
ipcWarn(wrnlvl(),"%t pString_Connection::syncDoRead\n");
*pdataobj=readOne();
if(*pdataobj==(A)0)
{
if(isInReset())
result=syncFillError("reset","Reset occurred. No message read.");
else result=0;
}
else result=1;
return result;
}
struct cdaAli *wormCdaAlisInRange(char *chromId, int start, int end)
/* Return list of cdna alignments that overlap range. */
{
struct cdaAli *list = NULL, *el;
char fileName[512];
FILE *ixFile, *aliFile;
bits32 sig;
int s, e;
long fpos;
aliFile = wormOpenGoodAli();
sprintf(fileName, "%s%s.alx", cdnaDir, chromId);
ixFile = mustOpen(fileName, "rb");
mustReadOne(ixFile, sig);
if (sig != alxSig)
errAbort("Bad signature on %s", fileName);
for (;;)
{
if (!readOne(ixFile, s))
break;
mustReadOne(ixFile, e);
mustReadOne(ixFile, fpos);
if (e <= start)
continue;
if (s >= end)
break;
AllocVar(el);
fseek(aliFile, fpos, SEEK_SET);
el = cdaLoadOne(aliFile);
if (el == NULL)
errAbort("Truncated cdnaAli file");
slAddHead(&list, el);
}
slReverse(&list);
fclose(aliFile);
fclose(ixFile);
return list;
}
struct xaAli *xaRdRange(FILE *ix, FILE *data,
int start, int end, boolean condensed)
/* Return list of all xaAlis that range from start to end.
* Assumes that ix and data files are open. If condensed
* don't fill int query, target, qSym, tSym, or hSym. */
{
int s, e;
int maxS, minE;
long offset;
struct xaAli *list = NULL, *xa;
/* Scan through index file looking for things in range.
* When find one read it from data file and add it to list. */
fseek(ix, sizeof(bits32), SEEK_SET);
for (;;)
{
if (!readOne(ix, s))
break;
mustReadOne(ix, e);
mustReadOne(ix, offset);
if (s >= end)
break;
maxS = max(s, start);
minE = min(e, end);
if (minE - maxS > 0)
{
fseek(data, offset, SEEK_SET);
xa = xaReadNext(data, condensed);
slAddHead(&list, xa);
}
}
slReverse(&list);
return list;
}
struct patSpace *makePatSpace(struct dnaSeq **seqArray, int arraySize, char *oocFileName)
/* Allocate a pattern space and fill from sequences. (Each element of
seqArray is a list of sequences. */
{
struct patSpace *ps = newPatSpace();
int i;
int startIx = 0;
int total = 0;
long startTime, endTime;
struct dnaSeq *seq;
int globalOver = 0, localOver = 0;
bits16 maxPat;
bits16 *listSizes;
startTime = clock1000();
maxPat = ps->maxPat = maxPatCount;
for (i=0; i<arraySize; ++i)
{
for (seq = seqArray[i]; seq != NULL; seq = seq->next)
{
total += seq->size;
countPatSpace(seq, ps);
}
}
endTime = clock1000();
printf("%4.2f seconds to countPatSpace %d bases\n", 0.001*(endTime-startTime), total );
listSizes = ps->listSizes;
/* Scan through over-popular patterns and set their count to value
* where they won't be added to pat space. */
{
bits32 sig, psz;
FILE *f = mustOpen(oocFileName, "rb");
bits32 oli;
mustReadOne(f, sig);
mustReadOne(f, psz);
if (sig != oocSig)
errAbort("Bad signature on %s\n", oocFileName);
if (psz != patSize)
errAbort("Oligo size mismatch in %s. Expecting %d got %d\n",
oocFileName, patSize, psz);
while (readOne(f, oli))
listSizes[oli] = maxPat;
fclose(f);
}
startTime = clock1000();
allocPatSpaceLists(ps);
endTime = clock1000();
printf("%4.2f seconds to allocPatSpaceLists\n", 0.001*(endTime-startTime) );
startTime = clock1000();
/* Zero out pattern counts that aren't oversubscribed. */
for (i=0; i<patSpaceSize; ++i)
{
if (listSizes[i] < maxPat)
listSizes[i] = 0;
}
if (dumpMe)
fprintf(dumpOut, "BlockIx vs. Seq position table:\n");
for (i=0; i<arraySize; ++i)
{
int j;
for (seq = seqArray[i], j=0; seq != NULL; seq = seq->next, ++j)
{
startIx = addToPatSpace(i, j, seq, startIx, ps);
if (startIx >= maxBlockCount)
errAbort("Too many blocks, can only handle %d\n", maxBlockCount);
}
}
ps->blocksUsed = startIx;
if (dumpMe)
fprintf(dumpOut, "\n");
printf("%d blocks of %d used\n", ps->blocksUsed, maxBlockCount);
/* Zero local over-popular patterns. */
for (i=0; i<patSpaceSize; ++i)
{
if (listSizes[i] >= maxPat)
listSizes[i] = 0;
}
endTime = clock1000();
printf("%4.2f seconds to addToPatSpace\n", 0.001*(endTime-startTime) );
return ps;
}
static GraphType init(int argc, char *argv[], opts_t* opts)
{
int c;
GraphType graphType = unknown;
cmd = argv[0];
opterr = 0;
while ((c = getopt(argc, argv, optList)) != -1) {
switch (c) {
case 'c':
graphType = circle;
if (setOne(optarg, opts))
errexit(c);
break;
case 'C':
graphType = cylinder;
if (setTwo(optarg, opts))
errexit(c);
break;
case 'M':
graphType = mobius;
if (setTwo(optarg, opts))
errexit(c);
break;
case 'd':
opts->directed = 1;
break;
case 'G':
opts->isPartial = 1;
case 'g':
graphType = grid;
optarg = setFold (optarg, opts);
if (setTwo(optarg, opts))
errexit(c);
break;
case 'h':
graphType = hypercube;
if (setOne(optarg, opts))
errexit(c);
break;
case 'k':
graphType = complete;
if (setOne(optarg, opts))
errexit(c);
break;
case 'b':
graphType = completeb;
if (setTwo(optarg, opts))
errexit(c);
break;
case 'B':
graphType = ball;
if (setTwo(optarg, opts))
errexit(c);
break;
case 'm':
graphType = trimesh;
if (setOne(optarg, opts))
errexit(c);
break;
case 'r':
graphType = randomg;
if (setTwo(optarg, opts))
errexit(c);
break;
case 'R':
graphType = randomt;
if (setOne(optarg, opts))
errexit(c);
break;
case 'n':
opts->pfx = optarg;
break;
case 'N':
opts->name = optarg;
break;
case 'o':
opts->outfile = openFile(optarg, "w");
break;
case 'p':
graphType = path;
if (setOne(optarg, opts))
errexit(c);
break;
case 'S':
graphType = sierpinski;
if (setOne(optarg, opts))
errexit(c);
break;
case 's':
graphType = star;
if (setOne(optarg, opts))
errexit(c);
break;
case 't':
graphType = tree;
if (setTwoOpt(optarg, opts, 2))
errexit(c);
break;
case 'T':
graphType = torus;
if (setTwoTwoOpt(optarg, opts, 0))
errexit(c);
break;
case 'i':
if (readOne(optarg,&(opts->cnt)))
errexit(c);
break;
case 'v':
opts->Verbose = 1;
break;
case 'w':
graphType = wheel;
if (setOne(optarg, opts))
errexit(c);
break;
case '?':
if (optopt == '?')
usage(0);
else
fprintf(stderr, "Unrecognized flag \"-%c\" - ignored\n",
optopt);
break;
}
}
argc -= optind;
argv += optind;
if (!opts->outfile)
opts->outfile = stdout;
if (graphType == unknown) {
fprintf(stderr, "Graph type not set\n");
usage(1);
}
return graphType;
}
