/*
** Locate a user function given a name, a number of arguments and a flag
** indicating whether the function prefers UTF-16 over UTF-8. Return a
** pointer to the FuncDef structure that defines that function, or return
** NULL if the function does not exist.
**
** If the createFlag argument is true, then a new (blank) FuncDef
** structure is created and liked into the "db" structure if a
** no matching function previously existed. When createFlag is true
** and the nArg parameter is -1, then only a function that accepts
** any number of arguments will be returned.
**
** If createFlag is false and nArg is -1, then the first valid
** function found is returned. A function is valid if either xFunc
** or xStep is non-zero.
**
** If createFlag is false, then a function with the required name and
** number of arguments may be returned even if the eTextRep flag does not
** match that requested.
*/
FuncDef *sqlite3FindFunction(
sqlite3 *db, /* An open database */
const char *zName, /* Name of the function. Not null-terminated */
int nName, /* Number of characters in the name */
int nArg, /* Number of arguments. -1 means any number */
u8 enc, /* Preferred text encoding */
int createFlag /* Create new entry if true and does not otherwise exist */
){
FuncDef *p; /* Iterator variable */
FuncDef *pBest = 0; /* Best match found so far */
int bestScore = 0; /* Score of best match */
int h; /* Hash value */
assert( enc==SQLITE_UTF8 || enc==SQLITE_UTF16LE || enc==SQLITE_UTF16BE );
if( nArg<-1 ) nArg = -1;
h = (sqlite3UpperToLower[(u8)zName[0]] + nName) % ArraySize(db->aFunc.a);
/* First search for a match amongst the application-defined functions.
*/
p = functionSearch(&db->aFunc, h, zName, nName);
while( p ){
int score = matchQuality(p, nArg, enc);
if( score>bestScore ){
pBest = p;
bestScore = score;
}
p = p->pNext;
}
/* If no match is found, search the built-in functions.
**
** Except, if createFlag is true, that means that we are trying to
** install a new function. Whatever FuncDef structure is returned will
** have fields overwritten with new information appropriate for the
** new function. But the FuncDefs for built-in functions are read-only.
** So we must not search for built-ins when creating a new function.
*/
if( !createFlag && !pBest ){
FuncDefHash *pHash = &GLOBAL(FuncDefHash, sqlite3GlobalFunctions);
p = functionSearch(pHash, h, zName, nName);
while( p ){
int score = matchQuality(p, nArg, enc);
if( score>bestScore ){
pBest = p;
bestScore = score;
}
p = p->pNext;
}
}
/* If the createFlag parameter is true and the search did not reveal an
** exact match for the name, number of arguments and encoding, then add a
** new entry to the hash table and return it.
*/
if( createFlag && (bestScore<6 || pBest->nArg!=nArg) &&
(pBest = sqlite3DbMallocZero(db, sizeof(*pBest)+nName+1))!=0 ){
pBest->zName = (char *)&pBest[1];
pBest->nArg = (u16)nArg;
pBest->iPrefEnc = enc;
memcpy(pBest->zName, zName, nName);
pBest->zName[nName] = 0;
sqlite3FuncDefInsert(&db->aFunc, pBest);
}
if( pBest && (pBest->xStep || pBest->xFunc || createFlag) ){
return pBest;
}
return 0;
}
/*
** Locate a user function given a name, a number of arguments and a flag
** indicating whether the function prefers UTF-16 over UTF-8. Return a
** pointer to the FuncDef structure that defines that function, or return
** NULL if the function does not exist.
**
** If the createFlag argument is true, then a new (blank) FuncDef
** structure is created and liked into the "db" structure if a
** no matching function previously existed.
**
** If nArg is -2, then the first valid function found is returned. A
** function is valid if xSFunc is non-zero. The nArg==(-2)
** case is used to see if zName is a valid function name for some number
** of arguments. If nArg is -2, then createFlag must be 0.
**
** If createFlag is false, then a function with the required name and
** number of arguments may be returned even if the eTextRep flag does not
** match that requested.
*/
FuncDef *sqlite3FindFunction(
sqlite3 *db, /* An open database */
const char *zName, /* Name of the function. zero-terminated */
int nArg, /* Number of arguments. -1 means any number */
u8 enc, /* Preferred text encoding */
u8 createFlag /* Create new entry if true and does not otherwise exist */
){
FuncDef *p; /* Iterator variable */
FuncDef *pBest = 0; /* Best match found so far */
int bestScore = 0; /* Score of best match */
int h; /* Hash value */
int nName; /* Length of the name */
assert( nArg>=(-2) );
assert( nArg>=(-1) || createFlag==0 );
nName = sqlite3Strlen30(zName);
/* First search for a match amongst the application-defined functions.
*/
p = (FuncDef*)sqlite3HashFind(&db->aFunc, zName);
while( p ){
int score = matchQuality(p, nArg, enc);
if( score>bestScore ){
pBest = p;
bestScore = score;
}
p = p->pNext;
}
/* If no match is found, search the built-in functions.
**
** If the DBFLAG_PreferBuiltin flag is set, then search the built-in
** functions even if a prior app-defined function was found. And give
** priority to built-in functions.
**
** Except, if createFlag is true, that means that we are trying to
** install a new function. Whatever FuncDef structure is returned it will
** have fields overwritten with new information appropriate for the
** new function. But the FuncDefs for built-in functions are read-only.
** So we must not search for built-ins when creating a new function.
*/
if( !createFlag && (pBest==0 || (db->mDbFlags & DBFLAG_PreferBuiltin)!=0) ){
bestScore = 0;
h = (sqlite3UpperToLower[(u8)zName[0]] + nName) % SQLITE_FUNC_HASH_SZ;
p = functionSearch(h, zName);
while( p ){
int score = matchQuality(p, nArg, enc);
if( score>bestScore ){
pBest = p;
bestScore = score;
}
p = p->pNext;
}
}
/* If the createFlag parameter is true and the search did not reveal an
** exact match for the name, number of arguments and encoding, then add a
** new entry to the hash table and return it.
*/
if( createFlag && bestScore<FUNC_PERFECT_MATCH &&
(pBest = sqlite3DbMallocZero(db, sizeof(*pBest)+nName+1))!=0 ){
FuncDef *pOther;
pBest->zName = (const char*)&pBest[1];
pBest->nArg = (u16)nArg;
pBest->funcFlags = enc;
memcpy((char*)&pBest[1], zName, nName+1);
pOther = (FuncDef*)sqlite3HashInsert(&db->aFunc, pBest->zName, pBest);
if( pOther==pBest ){
sqlite3DbFree(db, pBest);
sqlite3OomFault(db);
return 0;
}else{
pBest->pNext = pOther;
}
}
if( pBest && (pBest->xSFunc || createFlag) ){
return pBest;
}
return 0;
}
void Query::performQuery()
{
vector<int> impNodes;
topKImpNodes(G, (*pOrthinfolist), params.n_imp, impNodes);
debug(46, "got important nodes\n");
debug(47, "got important nodes2\n");
DBMatchMap dbmap;
Filter filter;
filter.setDatabase(db);
filter.setQueryParams(params);
filter.setGraph(G, pOrthinfolist);
filter.setTablePrefix(tablePrefix);
vector<Neighborhood> nbs;
getAllNeighborhoods(G, (*pOrthinfolist), nbs);
debug(46, "got all neighbors2\n");
debug(47, "got all neighbors\n");
for(int i=0; i<params.n_imp; i++)
{
filter.probeIndex(nbs[impNodes[i]], dbmap);
}
vector<Gid_Num_Score> gnsvec;
DBMatchMap::iterator iter;
int allhits=0;
debug(46, "after filtering\n");
debug(47, "after filtering2\n");
for(iter=dbmap.begin(); iter!=dbmap.end(); iter++)
{
Gid_Num_Score gns;
gns.dbgid=iter->first;
gns.numMatches=iter->second->size();
gns.score=0;
if(gns.numMatches==params.n_imp)
allhits++;
for(int i=0; i<gns.numMatches; i++)
gns.score+=(*(iter->second))[i]->minscore;
gnsvec.push_back(gns);
//debug(41, "dbgid: "<<gns.dbgid<<endl);
//debug(41, "num Node matches: "<<gns.numMatches<<endl);
//debug(41, "Total min score: "<<gns.score<<endl);
}
int dbnum=max(params.top_k, allhits);
std::sort(gnsvec.begin(), gnsvec.end(), orderGidNumScore);
//clean the hash_map
for(unsigned int i=dbnum; i<gnsvec.size(); i++)
{
//debug(41, "remove dbgid= "<< gnsvec[i].dbgid<<endl);
removeFromMatchMap(gnsvec[i].dbgid, dbmap);
}
debug(46, "before the actual match \n");
debug(47, "before the actual match \n");
//now is the match algorithm
for(iter=dbmap.begin(); iter!=dbmap.end(); iter++)
{
//call mcb_matching to find the best match for the important nodes
debug(41, "match dbgid = "<<iter->first<<"\n");
OrthologInfoList orthinfolist_db;
HashGraph* DBG=readGraphFromDB(db, tablePrefix, iter->first, orthinfolist_db);
GraphMatch* gm=new GraphMatch;
gm->dbgid=iter->first;
mcb_matching(DBG, *(iter->second), gm);
debug(46, "gm->dbgid"<<gm->dbgid<<endl);
debug(47, "gm->dbgid2 = 2 = "<<gm->dbgid<<endl);
debug(46, "before growMatch\n");
debug(47, "before growMatch2\n");
debug(46, "DBG->n()"<<DBG->n()<<endl);
debug(47, "DBG->n()"<<DBG->n()<<endl);
debug(46, "orthinfolist_db[0].size()"<<orthinfolist_db[0].size()<<endl);
debug(46, "gm->mappings.size()"<<gm->mappings.size()<<endl);
debug(47, "orthinfolist_db[0].size()"<<orthinfolist_db[0].size()<<endl);
debug(47, "gm->mappings.size()"<<gm->mappings.size()<<endl);
growMatch(nbs, DBG, &orthinfolist_db, gm);
gm->score=matchQuality(DBG, gm);
mlist.push_back(gm);
delete DBG;
debug(46, "grow match succeeds\n");
debug(47, "grow match succeeds\n");
}
}
