static
void getLenOfPspSeqs(FILE *fptr, Psprior *psp) {
char c;
char prevC = 0;
int seqInd = -1;
boolean inHeader = FALSE;
boolean inSeq = FALSE;
while ((c = fgetc(fptr)) != EOF) {
if( c == '>' ) {
inHeader = TRUE;
inSeq = FALSE;
if(prevC != '>') {
seqInd++; //do not increment if >> in header
}
if(seqInd >= psp->numseqs) {
print_error("ERROR in getLenOfSeqs: number of seqs exceed max.");
}
psp->seqlen[seqInd] = 0;
}
else if ( inHeader && c == '\n') {
inHeader = FALSE;
inSeq = TRUE;
}
else if (inSeq) {
if(isFloatingPoint(prevC) && isSpaceChar(c)) {
psp->seqlen[seqInd]++;
//fprintf(stderr, "case1\n");
}
else if(isSpaceChar(prevC) && isSpaceChar(c)) {
//do nothing
//fprintf(stderr, "case2\n");
}
else if(isSpaceChar(prevC) && isFloatingPoint(c)) {
//do nothing
//fprintf(stderr, "case3\n");
}
else if(isFloatingPoint(prevC) && isFloatingPoint(c)) {
//do nothing
//fprintf(stderr, "case4\n");
}
else {
fprintf(stderr, "character: %d %d\n", (int)prevC, (int)c);
fprintf(stderr, "seqind: %d\n", seqInd);
fprintf(stderr, "Invalid format found: %c%c\n", prevC, c);
exit(1);
}
}
prevC = c;
}
}
static integer cmdCount(char *cmdLine, integer deflt) {
while (isSpaceChar((codePoint) *cmdLine))
cmdLine++;
if (uniStrLen(cmdLine) == 0)
return deflt;
else
return parseInteger(cmdLine, uniStrLen(cmdLine));
}
static DebugWaitFor dbgShowGlobal(char *line, processPo p, termPo loc, insWord ins, void *cl) {
char buff[MAX_SYMB_LEN];
integer pos = 0;
integer ix = 0;
integer llen = uniStrLen(line);
enum {
initSte, inVar
} st = initSte;
while (ix < llen) {
codePoint cp = nextCodePoint(line, &ix, llen);
switch (st) {
case initSte:
if (!isSpaceChar(cp)) {
st = inVar;
appendCodePoint(buff, &pos, NumberOf(buff), cp);
}
continue;
case inVar:
if (!isSpaceChar(cp)) {
appendCodePoint(buff, &pos, NumberOf(buff), cp);
continue;
} else
break;
}
}
if (uniStrLen(buff) > 0) {
appendCodePoint(buff, &pos, NumberOf(buff), 0);
globalPo glb = globalVar(buff);
if (glb != Null) {
termPo val = getGlobal(glb);
if (val != Null)
outMsg(debugOutChnnl, "%s = %,*T\n", buff, displayDepth, val);
else
outMsg(debugOutChnnl, "%s not set\n", buff);
}
}
resetDeflt("n");
return moreDebug;
}
//returns the length of the sequence
//This function can easily leads to buffer overflow, but I don't care about security now.
static
int readSinglePspSeq(FILE *fptr, Psprior *psp, int seqInd) {
//int siteInd = 0;
double flt = NAN;
int c;
for(int i = 0; i < psp->seqlen[seqInd]; i++) {
fscanf (fptr, "%lf", &flt);
psp->prior[seqInd][i] = flt;
}
while((c = fgetc(fptr)) != '>' && c!= EOF) {
if( isSpaceChar(c)) {
continue;
}
else {
fprintf(stderr, "ERROR: invalid character found at end of sequence %c", c);
}
}
ungetc(c, fptr);
return psp->seqlen[seqInd];
}