static struct slName *setup_labels(char *long_form, struct slName *bw_list, struct slName **labels_from_bw_list)
{
struct slName *lf_labels = NULL;
if (long_form && !sameString(long_form, "on"))
/* first check labels from CL */
{
lf_labels = slNameListFromComma(long_form);
int num_labels = slCount(lf_labels);
if (num_labels != slCount(bw_list))
errAbort("number of labels provided should equal the number of bigWigs given");
}
/* from file */
else
{
if (*labels_from_bw_list)
{
if (slCount(*labels_from_bw_list) == slCount(bw_list))
lf_labels = *labels_from_bw_list;
else
slNameFreeList(labels_from_bw_list);
}
if (!lf_labels)
lf_labels = slNameCloneList(bw_list);
}
return lf_labels;
}
static struct joinerTable *tableFromField(struct joinerField *jf)
/* Extract database/table info out of field. */
{
struct joinerTable *table;
AllocVar(table);
table->table = cloneString(jf->table);
table->dbList = slNameCloneList(jf->dbList);
return table;
}
struct annoOption *annoOptionCloneList(struct annoOption *list)
/* Return a newly allocated copy of list. */
{
struct annoOption *newList = NULL, *afo;
for (afo = list; afo != NULL; afo = afo->next)
{
struct annoOption *newAfo = CloneVar(afo);
newAfo->spec.name = cloneString(afo->spec.name);
newAfo->value = NULL;
unsigned opFlags = opFlags;
if (opFlags & OPTION_MULTI)
{
switch (opFlags & OPTION_TYPE_MASK)
{
case OPTION_STRING:
newAfo->value = slNameCloneList((struct slName *)(afo->value));
break;
default:
errAbort("annoOptionCloneList: OPTION_MULTI implemented only for "
"OPTION_STRING (not 0x%x)", opFlags);
}
}
else
{
switch (opFlags & OPTION_TYPE_MASK)
{
// For numeric singleton values, we are overloading value.
case OPTION_DOUBLE:
case OPTION_FLOAT:
case OPTION_LONG_LONG:
case OPTION_INT:
case OPTION_BOOLEAN:
newAfo->value = afo->value;
break;
case OPTION_STRING:
newAfo->value = cloneString((char *)afo->value);
break;
default:
errAbort("annoOptionCloneList: unrecognized op type 0x%x", opFlags);
}
}
slAddHead(&newList, newAfo);
}
slReverse(&newList);
return newList;
}
static void joinerExpand(struct joiner *joiner)
/* Expand joiners that have [] in them. */
{
struct joinerSet *js, *nextJs, *newJs, *newList = NULL;
for (js=joiner->jsList; js != NULL; js = nextJs)
{
char *startBracket, *endBracket;
nextJs = js->next;
if ((startBracket = strchr(js->name, '[')) != NULL)
{
char *dbStart,*dbEnd;
char *dbCommaList;
struct joinerField *jf, *newJf;
struct dyString *dy = dyStringNew(0);
endBracket = strchr(startBracket, ']');
if (endBracket == NULL)
errAbort("[ without ] line %d of %s", js->lineIx, joiner->fileName);
dbCommaList = cloneStringZ(startBracket+1, endBracket - startBracket - 1);
dbStart = dbCommaList;
while (dbStart != NULL)
{
/* Parse out comma-separated list. */
dbEnd = strchr(dbStart, ',');
if (dbEnd != NULL)
{
*dbEnd++ = 0;
if (dbEnd[0] == 0)
dbEnd = NULL;
}
if (dbStart[0] == 0)
errAbort("Empty element in comma separated list line %d of %s",
js->lineIx, joiner->fileName);
/* Make up name for new joiner. */
dyStringClear(dy);
dyStringAppendN(dy, js->name, startBracket-js->name);
dyStringAppend(dy, dbStart);
dyStringAppend(dy, endBracket+1);
/* Allocate new joiner and fill in most data elements. */
AllocVar(newJs);
newJs->name = cloneString(dy->string);
newJs->typeOf = cloneString(js->typeOf);
newJs->external = cloneString(js->external);
newJs->description = cloneString(js->description);
newJs->isFuzzy = js->isFuzzy;
newJs->lineIx = js->lineIx;
newJs->isDependency = js->isDependency;
/* Fill in new joiner fieldList */
for (jf = js->fieldList; jf != NULL; jf = jf->next)
{
char *bs = NULL, *be = NULL;
/* Allocate vars and do basic fields. */
AllocVar(newJf);
newJf->dbList = slNameCloneList(jf->dbList);
newJf->field = cloneString(jf->field);
newJf->chopBefore = slNameCloneList(jf->chopBefore);
newJf->chopAfter = slNameCloneList(jf->chopBefore);
newJf->separator = cloneString(jf->separator);
newJf->indexOf = jf->indexOf;
newJf->isPrimary = jf->isPrimary;
newJf->unique = jf->unique;
newJf->full = jf->full;
newJf->minCheck = jf->minCheck;
newJf->splitPrefix = cloneString(jf->splitPrefix);
newJf->exclude = slNameCloneList(jf->exclude);
/* Do substituted table field. */
if ((bs = strchr(jf->table, '[')) != NULL)
be = strchr(bs, ']');
if (bs == NULL || be == NULL)
errAbort("Missing [] in field '%s' line %d of %s",
jf->table, jf->lineIx, joiner->fileName);
dyStringClear(dy);
dyStringAppendN(dy, jf->table, bs - jf->table);
dyStringAppend(dy, dbStart);
dyStringAppend(dy, be+1);
newJf->table = cloneString(dy->string);
slAddHead(&newJs->fieldList, newJf);
}
newJs->expanded = TRUE;
slReverse(&newJs->fieldList);
slAddHead(&newList, newJs);
dbStart = dbEnd;
}
dyStringFree(&dy);
freez(&dbCommaList);
joinerSetFree(&js);
}
else
{
slAddHead(&newList, js);
}
}
slReverse(&newList);
joiner->jsList = newList;
}
