State *post2nfa(char *postfix)
{
FragStack stk;
int index = 0;
for (char *p = postfix; *p; p++, index++) {
switch (*p) {
case '&':
{
FragPtr f2 = stk.back();
stk.pop_back();
FragPtr f1 = stk.back();
stk.pop_back();
f1->patchTo(f2->start);
stk.push_back(newFrag(f1->start, f2->out));
} break;
case '|':
{
FragPtr f2 = stk.back();
stk.pop_back();
FragPtr f1 = stk.back();
stk.pop_back();
State *s = new State(SPLIT, f1->start, f2->start);
stk.push_back(newFrag(s, append(f1->out, f2->out)));
} break;
case '?':
{
FragPtr f = stk.back();
stk.pop_back();
State *s = new State(SPLIT, f->start, NULL);
stk.push_back(newFrag(s, append(f->out, list1(&s->out1))));
} break;
case '*':
{
FragPtr f = stk.back();
stk.pop_back();
State *s = new State(SPLIT, f->start, NULL);
f->patchTo(s);
stk.push_back(newFrag(s, list1(&s->out1)));
} break;
case '+':
{
FragPtr f = stk.back();
stk.pop_back();
State *s = new State(SPLIT, f->start, NULL);
f->patchTo(s);
stk.push_back(newFrag(f->start, list1(&s->out1)));
} break;
default:
{
State *s = new State(*p, NULL, NULL);
stk.push_back(newFrag(s, list1(&s->out)));
} break;
}
begin(index);
drawNfa(stk, index);
end();
}
assert(stk.size() == 1);
FragPtr f = stk.back();
stk.pop_back();
f->patchTo(&match);
stk.push_back(f);
begin(index);
drawNfa(stk, index);
end();
return f->start;
}
void readFinfFiles(char *gsDir)
/* Read in .finf files and save info in cloneHash/cloneList. */
{
struct lineFile *lf;
struct clone *clone = NULL;
struct endInfo *end;
char fileName[512];
int i;
char *words[7];
char lastClone[64];
char cloneName[64];
int gsInfoCount = 0;
struct frag *frag;
boolean isFin;
char *s, *e;
strcpy(lastClone, "");
for (i=0; i<ArraySize(gsFiles); ++i)
{
isFin = (i <= 0);
sprintf(fileName, "%s/%s", gsDir, gsFiles[i]);
printf("Reading info from %s\n", fileName);
lf = lineFileOpen(fileName, TRUE);
while (lineFileRow(lf, words))
{
if (!sameString(words[1], lastClone))
{
struct clone *oldClone;
strcpy(lastClone, words[1]);
strcpy(cloneName, words[1]);
AllocVar(clone);
s = strchr(cloneName, '.');
if (s == NULL)
errAbort("Bad clone name format line %d of %s\n", lf->lineIx, lf->fileName);
if (strlen(s) >= sizeof(clone->version))
errAbort("Bad clone name format line %d of %s\n", lf->lineIx, lf->fileName);
strcpy(clone->version, s);
chopSuffix(cloneName);
clone->size = atoi(words[3]);
if ((oldClone = hashFindVal(cloneHash, cloneName)) != NULL)
{
if (isFin && clone->size == oldClone->size && sameString(clone->version, oldClone->version))
warn("Apparently benign duplication of %s line %d of %s", cloneName, lf->lineIx, lf->fileName);
else
warn("%s duplicated line %d of %s (size %d oldSize %d)", cloneName, lf->lineIx, lf->fileName,
clone->size, oldClone->size);
}
hashAddSaveName(cloneHash, cloneName, clone, &clone->name);
clone->isFin = isFin;
slAddHead(&cloneList, clone);
}
frag = newFrag(words[0], lf);
slAddTail(&clone->fragList, frag);
++clone->fragCount;
if (!clone->isFin && !sameString(words[6], "?") && !sameString(words[6], "i")
&& !sameString(words[6], "w"))
{
char *s = strchr(words[0], '~');
char c;
if (s == NULL)
errAbort("Expecting ~ in fragment name line %d of %s\n", lf->lineIx, lf->fileName);
++s;
AllocVar(end);
end->contig = cloneString(s);
subChar(s, '.', '_');
end->text = cloneString(words[6]);
c = lastChar(end->text);
if (!(c == 'L' || c == 'R'))
c = '?';
end->lr = c;
slAddHead(&clone->gsList, end);
++gsInfoCount;
}
}
lineFileClose(&lf);
}
printf("Found %d ends in %d clones\n", gsInfoCount, slCount(cloneList));
}
