void DexRegion::processSimply()
{
LOG("DexRegion::processSimply %s", getRegionName());
if (getIRList() == NULL) { return ; }
OptCtx oc;
OC_show_comp_time(oc) = g_show_comp_time;
CHAR const* ru_name = getRegionName();
constructIRBBlist();
ASSERT0(verifyIRandBB(getBBList(), this));
//All IRs have been moved to each IRBB.
setIRList(NULL);
PassMgr * passmgr = initPassMgr();
ASSERT0(passmgr);
ASSERT0(g_cst_bb_list);
IR_CFG * cfg = (IR_CFG*)passmgr->registerPass(PASS_CFG);
ASSERT0(cfg);
cfg->initCfg(oc);
ASSERT0(g_do_cfg_dom);
cfg->LoopAnalysis(oc);
destroyPassMgr();
//Do not allocate register.
getPrno2Vreg()->clean();
getPrno2Vreg()->copy(*getDex2IR()->getPR2Vreg());
return;
}
bool DexRegion::HighProcess(OptCtx & oc)
{
CHAR const* ru_name = getRegionName();
g_indent = 0;
SimpCtx simp;
SIMP_if(&simp) = true;
SIMP_doloop(&simp) = true;
SIMP_dowhile(&simp) = true;
SIMP_whiledo(&simp) = true;
SIMP_switch(&simp) = false;
SIMP_break(&simp) = true;
SIMP_continue(&simp) = true;
setIRList(simplifyStmtList(getIRList(), &simp));
ASSERT0(verify_simp(getIRList(), simp));
ASSERT0(verify_irs(getIRList(), NULL, this));
constructIRBBlist();
ASSERT0(verifyIRandBB(getBBList(), this));
//All IRs have been moved to each IRBB.
setIRList(NULL);
HighProcessImpl(oc);
return true;
}
void CityRegionImplementation::notifyExit(SceneObject* object) {
//pre: no 2 different city regions should ever overlap, only 2 Regions of the same city region
if (object->isTangibleObject()) {
TangibleObject* tano = cast<TangibleObject*>(object);
ManagedReference<Region*> activeRegion = tano->getActiveRegion().castTo<Region*>();
if (activeRegion != NULL) {
ManagedReference<CityRegion*> city = activeRegion->getCityRegion();
object->setCityRegion(city);
if (city == _this.getReferenceUnsafeStaticCast()) // if its the same city we wait till the object exits the last region
return;
} else {
object->setCityRegion(NULL);
}
} else {
object->setCityRegion(NULL);
}
if (object->isBazaarTerminal() || object->isVendor()) {
if (object->isBazaarTerminal())
bazaars.drop(object->getObjectID());
AuctionTerminalDataComponent* terminalData = NULL;
DataObjectComponentReference* data = object->getDataObjectComponent();
if(data != NULL && data->get() != NULL && data->get()->isAuctionTerminalData())
terminalData = cast<AuctionTerminalDataComponent*>(data->get());
if(terminalData != NULL)
terminalData->updateUID();
}
if (object->isPlayerCreature())
currentPlayers.decrement();
if (isClientRegion())
return;
if (object->isCreatureObject()) {
CreatureObject* creature = cast<CreatureObject*>(object);
StringIdChatParameter params("city/city", "city_leave_city"); //You have left %TO.
params.setTO(getRegionName());
creature->sendSystemMessage(params);
removeSpecializationModifiers(creature);
}
if (object->isStructureObject()) {
float x = object->getWorldPositionX();
float y = object->getWorldPositionY();
StructureObject* structure = cast<StructureObject*>(object);
Locker slocker(&structureListMutex);
if (structure->isBuildingObject()) {
BuildingObject* building = cast<BuildingObject*>(object);
uint64 ownerID = structure->getOwnerObjectID();
ZoneServer* zoneServer = building->getZoneServer();
if (zoneServer != NULL) {
ManagedReference<CreatureObject*> owner = zoneServer->getObject(ownerID).castTo<CreatureObject*>();
if(owner != NULL && owner->isPlayerCreature() && building->isResidence() && isCitizen(ownerID)) {
CityManager* cityManager = zoneServer->getCityManager();
cityManager->unregisterCitizen(_this.getReferenceUnsafeStaticCast(), owner);
}
}
}
completeStructureList.drop(structure->getObjectID());
if (structure->isCivicStructure()) {
removeStructure(structure);
} else if (structure->isCommercialStructure()) {
removeCommercialStructure(structure);
}
}
if (object->isDecoration() && object->getParent().get() == NULL) {
removeDecoration(object);
}
}
void CityRegionImplementation::notifyEnter(SceneObject* object) {
if (object->getCityRegion().get() != _this.getReferenceUnsafeStaticCast() && object->isPlayerCreature())
currentPlayers.increment();
object->setCityRegion(_this.getReferenceUnsafeStaticCast());
if (object->isBazaarTerminal() || object->isVendor()) {
if (object->isBazaarTerminal())
bazaars.put(object->getObjectID(), cast<TangibleObject*>(object));
AuctionTerminalDataComponent* terminalData = NULL;
DataObjectComponentReference* data = object->getDataObjectComponent();
if(data != NULL && data->get() != NULL && data->get()->isAuctionTerminalData())
terminalData = cast<AuctionTerminalDataComponent*>(data->get());
if(terminalData != NULL)
terminalData->updateUID();
}
if (isClientRegion())
return;
if (object->isCreatureObject()) {
CreatureObject* creature = cast<CreatureObject*>(object);
StringIdChatParameter params("city/city", "city_enter_city"); //You have entered %TT (%TO).
params.setTT(getRegionName());
UnicodeString strRank = StringIdManager::instance()->getStringId(String("@city/city:rank" + String::valueOf(cityRank)).hashCode());
if (citySpecialization.isEmpty()) {
params.setTO(strRank);
}
else {
UnicodeString citySpec = StringIdManager::instance()->getStringId(citySpecialization.hashCode());
params.setTO(strRank + ", " + citySpec);
}
creature->sendSystemMessage(params);
applySpecializationModifiers(creature);
}
if (object->isStructureObject()) {
StructureObject* structure = cast<StructureObject*>(object);
CityManager* cityManager = getZone()->getZoneServer()->getCityManager();
Locker slocker(&structureListMutex);
if (isLoaded() && !completeStructureList.contains(structure->getObjectID()) && structure->getBaseMaintenanceRate() > 0) {
cityManager->sendAddStructureMails(_this.getReferenceUnsafeStaticCast(), structure);
}
if (structure->isBuildingObject()) {
BuildingObject* building = cast<BuildingObject*>(object);
uint64 ownerID = structure->getOwnerObjectID();
ManagedReference<CreatureObject*> owner = zone->getZoneServer()->getObject(ownerID).castTo<CreatureObject*>();
if(owner != NULL && owner->isPlayerCreature() && building->isResidence() && !isCitizen(ownerID)) {
cityManager->registerCitizen(_this.getReferenceUnsafeStaticCast(), owner);
}
}
completeStructureList.put(structure->getObjectID());
if (structure->isCivicStructure() && !structure->isDecoration()) {
addStructure(structure);
} else if (structure->isCommercialStructure()) {
addCommercialStructure(structure);
}
if (registered) {
zone->registerObjectWithPlanetaryMap(structure);
}
}
if (object->isDecoration() && object->getParent().get() == NULL) {
addDecoration(object);
}
if (registered && cityMissionTerminals.contains(object)) {
zone->registerObjectWithPlanetaryMap(object);
}
if (!registered && citySkillTrainers.contains(object)) {
zone->unregisterObjectWithPlanetaryMap(object);
}
}
void doSummaryStatsWiggle(struct sqlConnection *conn)
/* Put up page showing summary stats for wiggle track. */
{
// grab the right trackDb for the current table. The curTrack variable
// has the composite trackDb in it
struct trackDb *track = hTrackDbForTrack(database, curTable);
char *table = curTable;
struct region *region, *regionList = getRegions();
char *regionName = getRegionName();
long long regionSize = 0;
long long gapTotal = 0;
long startTime = 0, wigFetchTime = 0;
char splitTableOrFileName[HDB_MAX_TABLE_STRING];
struct customTrack *ct = NULL;
boolean isCustom = FALSE;
struct wiggleDataStream *wds = NULL;
unsigned long long valuesMatched = 0;
int regionCount = 0;
int regionsDone = 0;
unsigned span = 0;
char *dataConstraint;
double ll = 0.0;
double ul = 0.0;
boolean hasConstraint = FALSE;
char *table2 = NULL;
boolean fullGenome = FALSE;
boolean statsHeaderDone = FALSE;
boolean gotSome = FALSE;
char *shortLabel = table;
long long statsItemCount = 0; /* global accumulators for overall */
int statsSpan = 0; /* stats summary on a multiple region */
double statsSumData = 0.0; /* output */
double statsSumSquares = 0.0; /* " " */
double lowerLimit = INFINITY; /* " " */
double upperLimit = -1.0 * INFINITY; /* " " */
startTime = clock1000();
if (track != NULL)
shortLabel = track->shortLabel;
/* Count the regions, when only one, we can do more stats */
for (region = regionList; region != NULL; region = region->next)
++regionCount;
htmlOpen("%s (%s) Wiggle Summary Statistics", shortLabel, table);
if (anySubtrackMerge(database, curTable))
hPrintf("<P><EM><B>Note:</B> subtrack merge is currently ignored on this "
"page (not implemented yet). Statistics shown here are only for "
"the primary table %s (%s).</EM>", shortLabel, table);
fullGenome = fullGenomeRegion();
WIG_INIT; /* ct, isCustom, hasConstraint, wds and table2 are set here */
for (region = regionList; region != NULL; region = region->next)
{
struct bed *intersectBedList = NULL;
int operations;
++regionsDone;
if (table2)
intersectBedList = bedTable2(conn, region, table2);
operations = wigFetchStats;
#if defined(NOT)
/* can't do the histogram now, that operation times out */
if (1 == regionCount)
operations |= wigFetchAscii;
#endif
wds->setChromConstraint(wds, region->chrom);
if (fullGenome)
wds->setPositionConstraint(wds, 0, 0);
else
wds->setPositionConstraint(wds, region->start, region->end);
if (hasConstraint)
wds->setDataConstraint(wds, dataConstraint, ll, ul);
/* depending on what is coming in on regionList, we may need to be
* smart about how often we call getData for these custom tracks
* since that is potentially a large file read each time.
*/
if (isCustom)
{
if (ct->dbTrack)
{
struct sqlConnection *trashConn = hAllocConn(CUSTOM_TRASH);
struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName);
span = minSpan(trashConn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, tdb);
wds->setSpanConstraint(wds, span);
valuesMatched = getWigglePossibleIntersection(wds, region,
CUSTOM_TRASH, table2, &intersectBedList,
splitTableOrFileName, operations);
hFreeConn(&trashConn);
}
else
{
valuesMatched = getWigglePossibleIntersection(wds, region, NULL,
table2, &intersectBedList, splitTableOrFileName, operations);
/* XXX We need to properly get the smallest span for custom tracks */
/* This is not necessarily the correct answer here */
if (wds->stats)
span = wds->stats->span;
else
span = 1;
}
}
else
{
if (hFindSplitTable(database, region->chrom, table, splitTableOrFileName, sizeof splitTableOrFileName, NULL))
{
span = minSpan(conn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, track);
wds->setSpanConstraint(wds, span);
valuesMatched = getWigglePossibleIntersection(wds, region,
database, table2, &intersectBedList, splitTableOrFileName,
operations);
if (intersectBedList)
span = 1;
}
}
/* when doing multiple regions, we need to print out each result as
* it happens to keep the connection open to the browser and
* prevent any timeout since this could take a while.
* (worst case test is quality track on panTro1)
*/
if (wds->stats)
statsItemCount += wds->stats->count;
if (wds->stats && (regionCount > 1) && (valuesMatched > 0))
{
double sumData = wds->stats->mean * wds->stats->count;
double sumSquares;
if (wds->stats->count > 1)
sumSquares = (wds->stats->variance * (wds->stats->count - 1)) +
((sumData * sumData)/wds->stats->count);
else
sumSquares = sumData * sumData;
/* global accumulators for overall summary */
statsSpan = wds->stats->span;
statsSumData += sumData;
statsSumSquares += sumSquares;
if (wds->stats->lowerLimit < lowerLimit)
lowerLimit = wds->stats->lowerLimit;
if ((wds->stats->lowerLimit + wds->stats->dataRange) > upperLimit)
upperLimit = wds->stats->lowerLimit + wds->stats->dataRange;
if (statsHeaderDone)
wds->statsOut(wds, database, "stdout", TRUE, TRUE, FALSE, TRUE);
else
{
wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, TRUE);
statsHeaderDone = TRUE;
}
wds->freeStats(wds);
gotSome = TRUE;
}
if ((regionCount > MAX_REGION_DISPLAY) &&
(regionsDone >= MAX_REGION_DISPLAY))
{
hPrintf("<TR><TH ALIGN=CENTER COLSPAN=12> Can not display more "
"than %d regions, <BR> would take too much time </TH></TR>\n",
MAX_REGION_DISPLAY);
break; /* exit this for loop */
}
} /*for (region = regionList; region != NULL; region = region->next) */
if (hasConstraint)
freeMem(dataConstraint); /* been cloned into wds */
if (1 == regionCount)
{
statsPreamble(wds, regionList->chrom, regionList->start, regionList->end,
span, valuesMatched, table2);
/* 3 X TRUE = sort results, html table output, with header,
* the FALSE means close the table after printing, no more rows to
* come. The case in the if() statement was already taken care of
* in the statsPreamble() printout. No need to do that again.
*/
if ( ! ((valuesMatched == 0) && table2) )
wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, FALSE);
regionSize = basesInRegion(regionList,0);
gapTotal = gapsInRegion(conn, regionList,0);
}
else
{ /* this is a bit of a kludge here since these printouts are done in the
* library source wigDataStream.c statsOut() function and
* this is a clean up of that. That function should be
* pulled out of there and made independent and more
* versatile.
*/
long long realSize;
double variance;
double stddev;
/* Too expensive to lookup the numbers for thousands of regions */
regionSize = basesInRegion(regionList,MAX_REGION_DISPLAY);
gapTotal = gapsInRegion(conn, regionList,MAX_REGION_DISPLAY);
realSize = regionSize - gapTotal;
/* close the table which was left open in the loop above */
if (!gotSome)
hPrintf("<TR><TH ALIGN=CENTER COLSPAN=12> No data found matching this request </TH></TR>\n");
hPrintf("<TR><TH ALIGN=LEFT> SUMMARY: </TH>\n");
hPrintf("\t<TD> </TD>\n"); /* chromStart */
hPrintf("\t<TD> </TD>\n"); /* chromEnd */
hPrintf("\t<TD ALIGN=RIGHT> ");
printLongWithCommas(stdout, statsItemCount);
hPrintf(" </TD>\n" );
hPrintf("\t<TD ALIGN=RIGHT> %d </TD>\n", statsSpan);
hPrintf("\t<TD ALIGN=RIGHT> ");
printLongWithCommas(stdout, statsItemCount*statsSpan);
hPrintf(" (%.2f%%) </TD>\n",
100.0*(double)(statsItemCount*statsSpan)/(double)realSize);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", lowerLimit);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", upperLimit);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", upperLimit - lowerLimit);
if (statsItemCount > 0)
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", statsSumData/statsItemCount);
else
hPrintf("\t<TD ALIGN=RIGHT> 0.0 </TD>\n");
stddev = 0.0;
variance = 0.0;
if (statsItemCount > 1)
{
variance = (statsSumSquares -
((statsSumData * statsSumData)/(double) statsItemCount)) /
(double) (statsItemCount - 1);
if (variance > 0.0)
stddev = sqrt(variance);
}
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", variance);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", stddev);
hPrintf("</TR>\n");
wigStatsTableHeading(stdout, TRUE);
hPrintf("</TABLE></TD></TR></TABLE></P>\n");
}
#if defined(NOT)
/* can't do the histogram now, that operation times out */
/* Single region, we can do the histogram */
if ((valuesMatched > 1) && (1 == regionCount))
{
float *valuesArray = NULL;
size_t valueCount = 0;
struct histoResult *histoGramResult;
/* convert the ascii data listings to one giant float array */
valuesArray = wds->asciiToDataArray(wds, valuesMatched, &valueCount);
/* histoGram() may return NULL if it doesn't work */
histoGramResult = histoGram(valuesArray, valueCount,
NAN, (unsigned) 0, NAN, (float) wds->stats->lowerLimit,
(float) (wds->stats->lowerLimit + wds->stats->dataRange),
(struct histoResult *)NULL);
printHistoGram(histoGramResult, TRUE); /* TRUE == html output */
freeHistoGram(&histoGramResult);
wds->freeAscii(wds);
wds->freeArray(wds);
}
#endif
wds->freeStats(wds);
wiggleDataStreamFree(&wds);
wigFetchTime = clock1000() - startTime;
webNewSection("Region and Timing Statistics");
hTableStart();
stringStatRow("region", regionName);
numberStatRow("bases in region", regionSize);
numberStatRow("bases in gaps", gapTotal);
floatStatRow("load and calc time", 0.001*wigFetchTime);
wigFilterStatRow(conn);
stringStatRow("intersection", cartUsualString(cart, hgtaIntersectTable, "off"));
hTableEnd();
htmlClose();
} /* void doSummaryStatsWiggle(struct sqlConnection *conn) */
void doSummaryStatsBed(struct sqlConnection *conn)
/* Put up page showing summary stats for track that is in database
* or that is bed-format custom. */
{
struct bed *bedList = NULL;
struct region *regionList = getRegions(), *region;
char *regionName = getRegionName();
long long regionSize = 0, gapTotal = 0, realSize = 0;
long startTime, midTime, endTime;
long loadTime = 0, calcTime = 0, freeTime = 0;
struct covStats *itemCovList = NULL, *blockCovList = NULL, *cov;
int itemCount = 0;
struct hTableInfo *hti = getHti(database, curTable, conn);
int minScore = BIGNUM, maxScore = -BIGNUM;
long long sumScores = 0;
boolean hasBlocks = hti->hasBlocks;
boolean hasScore = (hti->scoreField[0] != 0);
int fieldCount;
htmlOpen("%s (%s) Summary Statistics", curTableLabel(), curTable);
for (region = regionList; region != NULL; region = region->next)
{
struct lm *lm = lmInit(64*1024);
startTime = clock1000();
bedList = cookedBedList(conn, curTable, region, lm, &fieldCount);
if (fieldCount < 12)
hasBlocks = FALSE;
if (fieldCount < 5)
hasScore = FALSE;
midTime = clock1000();
loadTime += midTime - startTime;
if (bedList != NULL)
{
itemCount += slCount(bedList);
regionSize += region->end - region->start;
cov = calcSpanOverRegion(region, bedList);
slAddHead(&itemCovList, cov);
if (hasBlocks)
{
cov = calcBlocksOverRegion(region, bedList);
slAddHead(&blockCovList, cov);
}
if (hti->scoreField[0] != 0)
{
struct bed *bed;
for (bed = bedList; bed != NULL; bed = bed->next)
{
int score = bed->score;
if (score < minScore) minScore = score;
if (score > maxScore) maxScore = score;
sumScores += score;
}
}
}
endTime = clock1000();
calcTime += endTime - midTime;
lmCleanup(&lm);
bedList = NULL;
freeTime += clock1000() - endTime;
}
regionSize = basesInRegion(regionList, 0);
gapTotal = gapsInRegion(conn, regionList, 0);
realSize = regionSize - gapTotal;
hTableStart();
startTime = clock1000();
numberStatRow("item count", itemCount);
if (itemCount > 0)
{
cov = covStatsSum(itemCovList);
percentStatRow("item bases", cov->basesCovered, realSize);
percentStatRow("item total", cov->sumBases, realSize);
numberStatRow("smallest item", cov->minBases);
numberStatRow("average item", round((double)cov->sumBases/cov->itemCount));
numberStatRow("biggest item", cov->maxBases);
}
if (hasBlocks && itemCount > 0)
{
cov = covStatsSum(blockCovList);
hPrintf("<TR><TD>block count</TD><TD ALIGN=RIGHT>");
printLongWithCommas(stdout, cov->itemCount);
hPrintf("</TD></TR>\n");
percentStatRow("block bases", cov->basesCovered, realSize);
percentStatRow("block total", cov->sumBases, realSize);
numberStatRow("smallest block", cov->minBases);
numberStatRow("average block", round((double)cov->sumBases/cov->itemCount));
numberStatRow("biggest block", cov->maxBases);
}
if (hasScore != 0 && itemCount > 0 && sumScores != 0)
{
numberStatRow("smallest score", minScore);
numberStatRow("average score", round((double)sumScores/itemCount));
numberStatRow("biggest score", maxScore);
}
hTableEnd();
/* Show region and time stats part of stats page. */
webNewSection("Region and Timing Statistics");
hTableStart();
stringStatRow("region", regionName);
numberStatRow("bases in region", regionSize);
numberStatRow("bases in gaps", gapTotal);
floatStatRow("load time", 0.001*loadTime);
floatStatRow("calculation time", 0.001*calcTime);
floatStatRow("free memory time", 0.001*freeTime);
stringStatRow("filter", (anyFilter() ? "on" : "off"));
stringStatRow("intersection", (anyIntersection() ? "on" : "off"));
hTableEnd();
covStatsFreeList(&itemCovList);
covStatsFreeList(&blockCovList);
htmlClose();
}
//This function outputs Prno2Vreg after Dex register allocation.
bool DexRegion::process(OptCtx * oc)
{
if (getIRList() == NULL) { return true; }
OC_show_comp_time(*oc) = g_show_comp_time;
g_indent = 0;
if (!g_silence) {
LOG("DexRegion process %s", getRegionName());
}
//note("\n==---- REGION_NAME:%s ----==", getRegionName());
prescan(getIRList());
PassMgr * passmgr = initPassMgr();
HighProcess(*oc);
MiddleProcess(*oc);
ASSERT0(getPassMgr());
PRSSAMgr * ssamgr = (PRSSAMgr*)passmgr->queryPass(PASS_PR_SSA_MGR);
if (ssamgr != NULL && ssamgr->isSSAConstructed()) {
ssamgr->destruction();
}
if (!g_retain_pass_mgr_for_region) {
//Destroy PassMgr.
destroyPassMgr();
}
if (!is_function()) { return true; }
///////////////////////////////////////
//DO NOT REQUEST PASS AFTER THIS LINE//
///////////////////////////////////////
BBList * bbl = getBBList();
if (bbl->get_elem_count() == 0) { return true; }
ASSERT0(verifyIRandBB(bbl, this));
RefineCtx rf;
RC_insert_cvt(rf) = false; //Do not insert cvt for DEX code.
refineBBlist(bbl, rf);
ASSERT0(verifyIRandBB(bbl, this));
if (g_do_dex_ra) {
Prno2Vreg * original_prno2vreg = getDex2IR()->getPR2Vreg();
RA ra(this,
getTypeIndexRep(),
getParamNum(),
getOrgVregNum(),
getDex2IR()->getVreg2PR(),
original_prno2vreg,
&m_var2pr);
LOG("\t\tdo DEX Register Allcation for '%s'", getRegionName());
ra.perform(*oc);
updateRAresult(ra, *getPrno2Vreg());
} else {
//Do not allocate register.
getPrno2Vreg()->clean();
getPrno2Vreg()->copy(*getDex2IR()->getPR2Vreg());
}
return true;
}