// parse pattern string in one of two formats:
// "repeats,color1,color1time,led1,color2,color2time,led2,..."
// "repeats,color1,color1time,color2,color2time,..."
// returns true if parsing was succesful, false if not
bool Blink1Pattern::fromPatternStr(QString tmp) {
//qDebug() << "fromPatternStr: "<<tmp;
tmp.replace(" ",""); // remove any whitepsace from mucking up parsing
QStringList list=tmp.split(",");
int lcount = list.count()-1;
// determine format type:
// if 3-tuple, then every 3rd entry has a '#'
// if 2-type, then every 2nd entry has a '#'
int count2=0, count3=0;
for( int i=1; i<list.count(); i+=2 ) {
if( list.at(i).contains('#') ) count2++;
}
for( int i=1; i<list.count(); i+=3 ) {
if( list.at(i).contains('#') ) count3++;
}
int format = (count3>count2) ? 3 : (count3==count2) ? 0 : 2;
// for pattern string "reps,color,time", min is 3 elemnets & pair count must be even
if( lcount % 2 == 0 && ((format==2 && lcount >= 2) || format==0) ) {
for(int i=1;i<list.count();i+=2){
QString colorstr = list.at(i);
double time = list.at(i+1).toDouble();
if( !colorstr.contains('#') ) // color must be in hexcode #cccccc format
return false; // (might not need this with format check above
addColorAndTime( colorstr, time );
}
setRepeats(list.at(0).toInt());
return true;
}
// for pattern string "reps,color,time,led", min is 4 elemnets & pair count must be 3-tuple
else if( lcount % 3 == 0 && ((format==3 && lcount >= 3) || format==0) ) {
for(int i=1;i<list.count();i+=3) {
QString colorstr = list.at(i);
double time = list.at(i+1).toDouble();
int ledn = list.at(i+2).toInt();
if( !colorstr.contains('#') ) // color must be in hexcode #cccccc format
return false;
addColorAndTime( colorstr, time );
editLed(colors.count()-1, ledn);
}
setRepeats(list.at(0).toInt());
return true;
}
return false;
}
void Blink1Pattern::fromJson( QJsonObject obj)
{
setName( obj.value("name").toString() );
setRepeats(obj.value("repeats").toInt());
QString tmp=obj.value("pattern").toString();
fromPatternStr(tmp);
setDate(obj.value("date").toDouble());
setReadOnly(obj.value("readonly").toBool());
setSystem(obj.value("system").toBool());
}
static void getRepeatsUnsplitTable(struct sqlConnection *conn,
struct hash *chromHash, char *table)
/* Return a tree of ranges for sequence gaps all chromosomes,
* from specified table
*/
{
struct sqlResult *sr;
char **row;
struct rbTreeNode **stack = lmAlloc(qLm, 256 * sizeof(stack[0]));
struct rbTree *allTree = rbTreeNewDetailed(simpleRangeCmp, qLm, stack);
struct rbTreeNode **newstack = lmAlloc(qLm, 256 * sizeof(newstack[0]));
struct rbTree *newTree = rbTreeNewDetailed(simpleRangeCmp, qLm, newstack);
char *prevChrom = NULL;
struct simpleRange *prevRange = NULL, *prevNewRange = NULL;
char query[256];
sqlSafef(query, ArraySize(query), "select chrom,chromStart,chromEnd from %s "
"order by chrom,chromStart", table);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
struct simpleRange *range;
if (prevChrom == NULL)
prevChrom = cloneString(row[0]);
else if (! sameString(prevChrom, row[0]))
{
rbTreeAdd(allTree, prevRange);
if (prevNewRange != NULL)
rbTreeAdd(newTree, prevNewRange);
setRepeats(prevChrom, chromHash, allTree, newTree);
freeMem(prevChrom);
prevRange = prevNewRange = NULL;
stack = lmAlloc(qLm, 256 * sizeof(stack[0]));
allTree = rbTreeNewDetailed(simpleRangeCmp, qLm, stack);
prevChrom = cloneString(row[0]);
}
lmAllocVar(allTree->lm, range);
range->start = sqlUnsigned(row[1]);
range->end = sqlUnsigned(row[2]);
if (prevRange == NULL)
prevRange = range;
else if (overlap(range, prevRange))
{
/* merge r into prevR & discard; prevR gets passed forward. */
if (range->end > prevRange->end)
prevRange->end = range->end;
if (range->start < prevRange->start)
prevRange->start = range->start;
}
else
{
rbTreeAdd(allTree, prevRange);
prevRange = range;
}
}
if (prevChrom != NULL)
{
rbTreeAdd(allTree, prevRange);
if (prevNewRange != NULL)
rbTreeAdd(newTree, prevNewRange);
setRepeats(prevChrom, chromHash, allTree, newTree);
freeMem(prevChrom);
}
sqlFreeResult(&sr);
} /* void getRepeatsUnsplitTable() */
static void getRepeatsUnsplit(struct sqlConnection *conn,
struct hash *chromHash, struct hash *arHash)
/* Return a tree of ranges for sequence gaps all chromosomes,
* assuming an unsplit table -- when the table is unsplit, it's
* probably for a scaffold assembly where we *really* don't want
* to do one query per scaffold! */
{
struct sqlResult *sr;
char **row;
struct rbTreeNode **stack = lmAlloc(qLm, 256 * sizeof(stack[0]));
struct rbTree *allTree = rbTreeNewDetailed(simpleRangeCmp, qLm, stack);
struct rbTreeNode **newstack = lmAlloc(qLm, 256 * sizeof(newstack[0]));
struct rbTree *newTree = rbTreeNewDetailed(simpleRangeCmp, qLm, newstack);
char *prevChrom = NULL;
struct simpleRange *prevRange = NULL, *prevNewRange = NULL;
sr = sqlGetResult(conn,
"NOSQLINJ select genoName,genoStart,genoEnd,repName,repClass,repFamily from rmsk "
"order by genoName,genoStart");
while ((row = sqlNextRow(sr)) != NULL)
{
struct simpleRange *range;
char arKey[512];
if (prevChrom == NULL)
prevChrom = cloneString(row[0]);
else if (! sameString(prevChrom, row[0]))
{
rbTreeAdd(allTree, prevRange);
if (prevNewRange != NULL)
rbTreeAdd(newTree, prevNewRange);
setRepeats(prevChrom, chromHash, allTree, newTree);
freeMem(prevChrom);
prevRange = prevNewRange = NULL;
stack = lmAlloc(qLm, 256 * sizeof(stack[0]));
allTree = rbTreeNewDetailed(simpleRangeCmp, qLm, stack);
if (arHash != NULL)
{
stack = lmAlloc(qLm, 256 * sizeof(stack[0]));
newTree = rbTreeNewDetailed(simpleRangeCmp, qLm, stack);
}
prevChrom = cloneString(row[0]);
}
lmAllocVar(allTree->lm, range);
range->start = sqlUnsigned(row[1]);
range->end = sqlUnsigned(row[2]);
if (prevRange == NULL)
prevRange = range;
else if (overlap(range, prevRange))
{
/* merge r into prevR & discard; prevR gets passed forward. */
if (range->end > prevRange->end)
prevRange->end = range->end;
if (range->start < prevRange->start)
prevRange->start = range->start;
}
else
{
rbTreeAdd(allTree, prevRange);
prevRange = range;
}
sprintf(arKey, "%s.%s.%s", row[3], row[4], row[5]);
if (arHash != NULL && hashLookup(arHash, arKey))
{
lmAllocVar(newTree->lm, range);
range->start = sqlUnsigned(row[1]);
range->end = sqlUnsigned(row[2]);
if (prevNewRange == NULL)
prevNewRange = range;
else if (overlap(range, prevNewRange))
{
/* merge r into prevR & discard; prevR gets passed forward. */
if (range->end > prevNewRange->end)
prevNewRange->end = range->end;
if (range->start < prevNewRange->start)
prevNewRange->start = range->start;
}
else
{
rbTreeAdd(newTree, prevNewRange);
prevNewRange = range;
}
}
}
if (prevChrom != NULL)
{
rbTreeAdd(allTree, prevRange);
if (prevNewRange != NULL)
rbTreeAdd(newTree, prevNewRange);
setRepeats(prevChrom, chromHash, allTree, newTree);
freeMem(prevChrom);
}
sqlFreeResult(&sr);
}
