static void parseAnn(struct gff3File *g3f, char *line)
/* parse an annotation line */
{
// extra column to check for too many
char *words[gffNumCols+1];
int numWords = chopString(line, "\t", words, gffNumCols+1);
if (numWords != gffNumCols)
gff3FileErr(g3f, "expected %d tab-separated columns: %s", gffNumCols, line);
struct gff3Ann *g3a = gff3FileAlloc(g3f, sizeof(struct gff3Ann));
g3a->file = g3f;
g3a->lineNum = g3f->lf->lineIx;
parseFields(g3a, words);
parseAttrs(g3a, words[8]);
parseStdAttrs(g3a);
slAddHead(&g3f->anns, g3a);
}
word_t Regex_constructor(CrocThread* t)
{
croc_hfield(t, 0, _Ptrs);
if(!croc_isNull(t, -1))
croc_eh_throwStd(t, "StateError", "Attempting to call constructor on an already-initialized Regex");
auto pat = checkCrocstrParam(t, 1);
auto attrs = parseAttrs(optCrocstrParam(t, 2, ""));
auto re = compilePattern(t, pat, attrs);
const char* error;
auto extra = pcre_study(re, 0, &error);
if(error != nullptr)
{
(*pcre_free)(re);
croc_eh_throwStd(t, "ValueError", "Error compiling regex: %s", error);
}
croc_memblock_new(t, sizeof(PtrStruct));
auto ptrs = cast(PtrStruct*)croc_memblock_getData(t, -1);
ptrs->re = re;
ptrs->extra = extra;
croc_hfielda(t, 0, _Ptrs);
int numGroups;
pcre_fullinfo(re, extra, PCRE_INFO_CAPTURECOUNT, &numGroups);
croc_memblock_new(t, sizeof(int) * ((numGroups + 1) * 3));
croc_hfielda(t, 0, _GroupIdx);
getNameTable(t, re, extra);
croc_hfielda(t, 0, _Names);
return 0;
}
