int main(int argc, char *argv[])
{
char *ortho1;
char *ortho2;
char *consensus;
char *err;
struct sizeList *ortho1List=NULL;
struct sizeList *ortho2List=NULL;
struct sizeList *consensusList=NULL;
FILE *consensusFile=NULL;
FILE *errFile=NULL;
if(argc != 5)
usage();
ortho1 = cloneString(argv[1]); // liftOver
ortho2 = cloneString(argv[2]); // Mercator
consensus = cloneString(argv[3]); // Consensus
err = cloneString(argv[4]); // errors
ortho1List = getRegions(ortho1, FALSE); // liftOver - include random chroms
ortho2List = getRegions(ortho2, TRUE ); // Mercator - exclude random chroms
consensusFile = mustOpen(consensus, "w");
errFile = mustOpen(err, "w");
consensusList = unionSizeLists(ortho1List, ortho2List, errFile);
consensusList = unionSizeLists(consensusList, ortho1List, errFile);
consensusList = unionSizeLists(consensusList, ortho2List, errFile);
writeSizeListToBedFile(consensusFile, consensusList);
return 0;
}
TilePosition Commander::findUnfortifiedChokePoint()
{
double bestDist = 0;
Chokepoint* bestChoke = NULL;
for(set<BWTA::Region*>::const_iterator i=getRegions().begin();i!=getRegions().end();i++)
{
if (isOccupied((*i)))
{
for(set<Chokepoint*>::const_iterator c=(*i)->getChokepoints().begin();c!=(*i)->getChokepoints().end();c++)
{
if (isEdgeChokepoint((*c)))
{
if (!chokePointFortified(TilePosition((*c)->getCenter())))
{
double cDist = Broodwar->self()->getStartLocation().getDistance(TilePosition((*c)->getCenter()));
if (cDist > bestDist)
{
bestDist = cDist;
bestChoke = (*c);
}
}
}
}
}
}
TilePosition buildPos = TilePosition(-1, -1);
if (bestChoke != NULL)
{
buildPos = TilePosition(bestChoke->getCenter());
}
return buildPos;
}
FEM_Partition::~FEM_Partition() {
if (elem2chunk) {delete[] elem2chunk;elem2chunk=NULL;}
for (int i=0;i<getRegions();i++) {
delete regions[i].layer;
delete regions[i].stencil;
}
}
void doGenePredPal(struct sqlConnection *conn)
/* Output genePred protein alignment. */
{
if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
{
sendParamsToGalaxy(hgtaDoPalOut, "submit");
return;
}
/* get rid of pesky cookies that would bring us back here */
cartRemove(cart, hgtaDoPal);
cartRemove(cart, hgtaDoPalOut);
if (anyIntersection() && intersectionIsBpWise())
errAbort("Can't do CDS FASTA output when bit-wise intersection is on. "
"Please go back and select another output type, or clear the intersection.");
checkNoGenomeDisabled(database, curTable);
struct lm *lm = lmInit(64*1024);
int fieldCount;
struct bed *bedList = cookedBedsOnRegions(conn, curTable, getRegions(),
lm, &fieldCount);
//lmCleanup(&lm);
textOpen();
int outCount = palOutPredsInBeds(conn, cart, bedList, curTable);
/* Do some error diagnostics for user. */
if (outCount == 0)
explainWhyNoResults(NULL);
}
int bammer_main(args *pars){
gf=(getFasta *) allMethods[1];
func = pars->callback;
std::vector<char *> nams;
//read bamfiles
if(pars->inputfiles)
nams = angsd::getFilenames(pars->inputfiles,pars->nInd);
else
nams.push_back(strdup(pars->inputfile));//if only one file just push bamfile
bufReader *rd = initializeBufReaders2(nams);
//read regions
std::vector<char *> regionsRaw;
if(pars->regionfile)
regionsRaw = getRegions(pars->regionfile);
else if(pars->region!=NULL){
regionsRaw.push_back(strdup(pars->region));//if only one file just push bamfile
}
std::vector<regs> regions;
for(size_t i=0;i<regionsRaw.size();i++){
regs tmpRegs;
if(parse_region(regionsRaw[i],*rd[0].hd,tmpRegs.refID,tmpRegs.start,tmpRegs.stop)<0||tmpRegs.stop<tmpRegs.start){
fprintf(stderr,"[%s] problems with indexing: %s\n",__FUNCTION__,regionsRaw[i]);
exit(0);
}else
regions.push_back(tmpRegs);
}
//printReg(stderr,regions)
//each filereader contains a filename for a bam, if we try to read remote files, then we need to download the bai file, and update the filename
if(regions.size()!=0)
modNames(rd,nams.size());
extern int maxThreads;
if(pars->jobtype==2)
uppile(pars->show,maxThreads,rd,pars->nLines,nams.size(),regions);
else if(pars->jobtype==1)
while(motherView(rd,nams.size(),regions));
else{
fprintf(stderr,"nothing to do? what should program do?\n");
}
//cleanup stuff
for(int i=0;i<(int)nams.size();i++){
free(nams[i]);
dalloc_bufReader(rd[i]);
}
for(size_t i=0;i<regions.size();i++)
free(regionsRaw[i]);
delete [] rd;
free(pars->inputfiles);free(pars->inputfile);free(pars->region);
delete pars;
return 0;
}
TilePosition Commander::findChokePoint()
{
//First, check the DefenseLocator
//for a stored defense position.
DefenseLocator* df = DefenseLocator::getInstance();
TilePosition storedPos = df->getBaseDefensePos(Broodwar->mapHash());
if (storedPos.x() != -1) return storedPos;
double bestPrio = -1;
Chokepoint* bestChoke = NULL;
for(set<BWTA::Region*>::const_iterator i=getRegions().begin();i!=getRegions().end();i++)
{
if (isOccupied((*i)))
{
for(set<Chokepoint*>::const_iterator c=(*i)->getChokepoints().begin();c!=(*i)->getChokepoints().end();c++)
{
if (isEdgeChokepoint((*c)))
{
double cPrio = getChokepointPrio(TilePosition((*c)->getCenter()));
if (cPrio > bestPrio)
{
bestPrio = cPrio;
bestChoke = (*c);
}
}
}
}
}
TilePosition guardPos = Broodwar->self()->getStartLocation();
if (bestChoke != NULL)
{
guardPos = findDefensePos(bestChoke);
//guardPos = TilePosition(bestChoke->getCenter());
//Pre-calculate path
TilePosition b = ExplorationManager::getInstance()->getClosestSpottedBuilding(guardPos);
if (b.x() >= 0)
{
Pathfinder::getInstance()->requestPath(guardPos, b);
}
}
return guardPos;
}
ExplorationManager::ExplorationManager()
{
active = true;
ownForce.reset();
enemyForce.reset();
//Add the regions for this map
for(set<BWTA::Region*>::const_iterator i=getRegions().begin();i!=getRegions().end();i++)
{
exploreData.push_back(ExploreData((*i)->getCenter()));
}
siteSetFrame = 0;
lastCallFrame = Broodwar->getFrameCount();
expansionSite = TilePosition(-1, -1);
}
void doOutGff(char *table, struct sqlConnection *conn, boolean outputGtf)
/* Save as GFF/GTF. */
{
struct hTableInfo *hti = getHti(database, table, conn);
struct bed *bedList;
struct hash *chromHash = NULL;
struct slName *exonFramesList = NULL;
char source[HDB_MAX_TABLE_STRING];
int itemCount;
struct region *region, *regionList = getRegions();
textOpen();
int efIdx = -1;
safef(source, sizeof(source), "%s_%s", database, table);
if (conn)
{
boolean simpleTableExists = sqlTableExists(conn, table);
// simpleTable means not split table, not custom track
// However it still can include bbi table with bam fileName path
if (simpleTableExists) // no tables having exonFrames are split tables anyway
efIdx = sqlFieldIndex(conn, table, "exonFrames");
itemCount = 0;
int regionCount = slCount(regionList);
// regionList can have many thousands of items e.g. rheMac3 has 34000 chroms!
// This regionCount threshold should be just above the # chroms in the latest human assembly
if (simpleTableExists && (regionCount > 500))
{
chromHash = makeChromHashForTable(conn, table);
}
}
// Note: code could be added here to extract exonFrames from bigGenePred
// Process each region
for (region = regionList; region != NULL; region = region->next)
{
if (chromHash && (!hashFindVal(chromHash, region->chrom)))
continue;
struct lm *lm = lmInit(64*1024);
int fieldCount;
bedList = cookedBedList(conn, table, region, lm, &fieldCount);
// Use exonFrames field if available for better accuracy instead of calculating from coordinates
if (efIdx != -1)
exonFramesList = getExonFrames(table, conn, bedList);
itemCount += bedToGffLines(bedList, exonFramesList, hti, fieldCount, source, outputGtf);
lmCleanup(&lm);
}
if (itemCount == 0)
hPrintf(NO_RESULTS);
}
bool CSMWorld::Data::hasId (const std::string& id) const
{
return
getGlobals().searchId (id)!=-1 ||
getGmsts().searchId (id)!=-1 ||
getSkills().searchId (id)!=-1 ||
getClasses().searchId (id)!=-1 ||
getFactions().searchId (id)!=-1 ||
getRaces().searchId (id)!=-1 ||
getSounds().searchId (id)!=-1 ||
getScripts().searchId (id)!=-1 ||
getRegions().searchId (id)!=-1 ||
getBirthsigns().searchId (id)!=-1 ||
getSpells().searchId (id)!=-1 ||
getTopics().searchId (id)!=-1 ||
getJournals().searchId (id)!=-1 ||
getCells().searchId (id)!=-1 ||
getReferenceables().searchId (id)!=-1;
}
void doGenomicDna(struct sqlConnection *conn)
/* Get genomic sequence (UI has already told us how). */
{
struct region *region, *regionList = getRegions();
struct hTableInfo *hti = getHti(database, curTable, conn);
int fieldCount;
textOpen();
int resultCount = 0;
for (region = regionList; region != NULL; region = region->next)
{
struct lm *lm = lmInit(64*1024);
struct bed *bedList = cookedBedList(conn, curTable, region, lm, &fieldCount);
if (bedList != NULL)
resultCount += hgSeqBed(database, hti, bedList);
lmCleanup(&lm);
}
if (!resultCount)
hPrintf(NO_RESULTS);
}
void doHalMaf(struct trackDb *parentTrack, char *table, struct sqlConnection *conn)
/* Output regions as MAF. maf tables look bed-like enough for
* cookedBedsOnRegions to handle intersections. */
{
#ifdef USE_HAL
struct region *region = NULL, *regionList = getRegions();
struct trackDb *tdb;
if ((tdb = findTrackDb(parentTrack, table)) == NULL)
errAbort("cannot find track named %s under %s\n", table, parentTrack->table);
char *fileName = trackDbSetting(tdb, "bigDataUrl");
char *otherSpecies = trackDbSetting(tdb, "otherSpecies");
int handle = halOpenLOD(fileName);
struct hal_species_t *speciesList = halGetSpecies(handle);
for(; speciesList; speciesList = speciesList->next)
{
if (sameString(speciesList->name, otherSpecies))
break;
}
if (speciesList == NULL)
errAbort("cannot find species %s in hal file %s\n",
otherSpecies, fileName);
speciesList->next = NULL;
textOpen();
for (region = regionList; region != NULL; region = region->next)
{
halGetMAF(stdout, handle, speciesList,
trackHubSkipHubName(database), region->chrom,
region->start, region->end, FALSE);
}
#else // USE_HAL
errAbort("hgTables not compiled with HAL support.");
#endif // USE_HAL
}
LayoutRegion *FormatterDeviceRegion::cloneRegion() {
LayoutRegion *cloneRegion;
vector<LayoutRegion*> *childRegions;
cloneRegion = new FormatterDeviceRegion(id);
cloneRegion->setTitle(getTitle());
cloneRegion->setLeft(left, false);
cloneRegion->setTop(top, false);
cloneRegion->setWidth(width, false);
cloneRegion->setHeight(height, false);
cloneRegion->setDecorated(false);
cloneRegion->setMovable(false);
cloneRegion->setResizable(false);
childRegions = getRegions();
vector<LayoutRegion*>::iterator it;
for (it = childRegions->begin(); it != childRegions->end(); ++it) {
cloneRegion->addRegion(*it);
}
return cloneRegion;
}
void Channel::frameAssemble( const eq::uint128_t& )
{
const bool composeOnly = (_drawRange == eq::Range::ALL);
_startAssemble();
const eq::Frames& frames = getInputFrames();
eq::PixelViewport coveredPVP;
eq::Frames dbFrames;
eq::Zoom zoom( eq::Zoom::NONE );
// Make sure all frames are ready and gather some information on them
for( eq::Frames::const_iterator i = frames.begin();
i != frames.end(); ++i )
{
eq::Frame* frame = *i;
{
eq::ChannelStatistics stat( eq::Statistic::CHANNEL_FRAME_WAIT_READY,
this );
frame->waitReady( );
}
const eq::Range& range = frame->getRange();
if( range == eq::Range::ALL ) // 2D frame, assemble directly
eq::Compositor::assembleFrame( frame, this );
else
{
dbFrames.push_back( frame );
zoom = frame->getZoom();
_expandPVP( coveredPVP, frame->getImages(), frame->getOffset() );
}
}
coveredPVP.intersect( getPixelViewport( ));
if( dbFrames.empty( ))
{
resetAssemblyState();
return;
}
// calculate correct frames sequence
eq::FrameDataPtr data = _frame.getFrameData();
if( !composeOnly && coveredPVP.hasArea( ))
{
_frame.clear();
data->setRange( _drawRange );
dbFrames.push_back( &_frame );
}
_orderFrames( dbFrames );
// Update range
eq::Range newRange( 1.f, 0.f );
for( size_t i = 0; i < dbFrames.size(); ++i )
{
const eq::Range range = dbFrames[i]->getRange();
if( newRange.start > range.start ) newRange.start = range.start;
if( newRange.end < range.end ) newRange.end = range.end;
}
_drawRange = newRange;
// check if current frame is in proper position, read back if not
if( !composeOnly )
{
if( _bgColor == eq::Vector3f::ZERO && dbFrames.front() == &_frame )
dbFrames.erase( dbFrames.begin( ));
else if( coveredPVP.hasArea())
{
eq::util::ObjectManager& glObjects = getObjectManager();
_frame.setOffset( eq::Vector2i( 0, 0 ));
_frame.setZoom( zoom );
data->setPixelViewport( coveredPVP );
_frame.readback( glObjects, getDrawableConfig(), getRegions( ));
clearViewport( coveredPVP );
// offset for assembly
_frame.setOffset( eq::Vector2i( coveredPVP.x, coveredPVP.y ));
}
}
// blend DB frames in order
try
{
eq::Compositor::assembleFramesSorted( dbFrames, this, 0,
true /*blendAlpha*/ );
}
catch( const co::Exception& e )
{
LBWARN << e.what() << std::endl;
}
resetAssemblyState();
}
int main(int argc, char **argv)
{
P_STR *P;
SEQ_STR *SEQ;
int i,j;
int type;
char *path;
if (argc!=3) {
printf(" Usage: %s seqfile type \n",argv[0]);
printf(" where type stands for one of the options of \n");
printf(" \"long\", \"short\" or \"glob\"\n");
exit(1);
}
/*if ((path=getenv("IUPred_PATH"))==NULL) {
fprintf(stderr,"IUPred_PATH environment variable is not set\n");
path="./";
} */
path="lib/disorder_apps/iupred";
printf("# IUPred \n");
printf("# Copyright (c) Zsuzsanna Dosztanyi, 2005\n");
printf("#\n");
printf("# Z. Dosztanyi, V. Csizmok, P. Tompa and I. Simon\n");
printf("# J. Mol. Biol. (2005) 347, 827-839. \n");
printf("#\n");
printf("#\n");
if ((strncmp(argv[2],"long",4))==0) {
type=0;
}
else if ((strncmp(argv[2],"short",5))==0) {
type=1;
}
else if ((strncmp(argv[2],"glob",4))==0) {
type=2;
}
else {
printf("Wrong argument\n");exit(1);
}
SEQ=malloc(sizeof(SEQ_STR));
Get_Seq(argv[1],SEQ);
if (SEQ->le==0) {printf(" Sequence length 0\n");exit(1);}
#ifdef DEBUG
printf("%s %d\n%s\n",SEQ->name,SEQ->le,SEQ->seq);
#endif
P=malloc(sizeof(P_STR));
P->CC= DMatrix(AAN,AAN);
if (type==0) {
LC=1;
UC=100;
WS=10;
Flag_EP=0;
read_ref(path,"ss",P->CC);
Get_Histo(P, path, "histo");
IUPred(SEQ,P);
printf("# Prediction output \n");
printf("# %s\n",SEQ->name);
for (i=0;i<SEQ->le;i++)
printf("%5d %c %10.4f\n",i+1,SEQ->seq[i],SEQ->en[i]);
}
if (type==1) {
LC=1;
UC=25;
WS=10;
Flag_EP=1;
EP=-1.26;
read_ref(path,"ss_casp",P->CC);
Get_Histo(P, path, "histo_casp");
IUPred(SEQ,P);
printf("# Prediction output \n");
printf("# %s\n",SEQ->name);
for (i=0;i<SEQ->le;i++)
printf("%5d %c %10.4f\n",i+1,SEQ->seq[i],SEQ->en[i]);
}
if (type==2) {
char *globseq;
LC=1;
UC=100;
WS=15;
Flag_EP=0;
read_ref(path,"ss",P->CC);
Get_Histo(P,path,"histo");
IUPred(SEQ,P);
Min_Ene=DMin_Ene;
JOIN=DJOIN;
DEL=DDEL;
getRegions(SEQ);
globseq=malloc((SEQ->le+1)*sizeof(char));
for (i=0;i<SEQ->le;i++) globseq[i]=tolower(SEQ->seq[i]);
printf("# Prediction output \n");
printf("# %s\n",SEQ->name);
printf("Number of globular domains: %5d \n",SEQ->ngr);
for (i=0;i<SEQ->ngr;i++) {
printf(" globular domain %5d. %d - %d \n",
i+1,SEQ->gr[i][0]+1,SEQ->gr[i][1]+1);
for (j=SEQ->gr[i][0];j<SEQ->gr[i][1]+1;j++) {
globseq[j]=toupper(globseq[j]);
}
}
printf(">%s\n",SEQ->name);
for (i=0;i<SEQ->le;i++) {
if ((i>0)&&(i%60==0)) printf("\n");
else if ((i>0)&&(i%10==0)) printf(" ");
printf("%c",globseq[i]);
}
printf("\n");
free(globseq);
#ifdef DEBUG
for (i=0;i<SEQ->le;i++)
printf("%5d %c %10.4f\n",i,SEQ->seq[i],SEQ->en[i]);
#endif
}
free(SEQ->seq);
free(SEQ->eprof);free(SEQ->en);free(SEQ->smp);
free(SEQ);
return 0;
}
void bigBedTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f)
/* Print out selected fields from Big Bed. If fields is NULL, then print out all fields. */
{
if (f == NULL)
f = stdout;
/* Convert comma separated list of fields to array. */
int fieldCount = chopByChar(fields, ',', NULL, 0);
char **fieldArray;
AllocArray(fieldArray, fieldCount);
chopByChar(fields, ',', fieldArray, fieldCount);
/* Get list of all fields in big bed and turn it into a hash of column indexes keyed by
* column name. */
struct hash *fieldHash = hashNew(0);
struct slName *bb, *bbList = bigBedGetFields(table, conn);
int i;
for (bb = bbList, i=0; bb != NULL; bb = bb->next, ++i)
hashAddInt(fieldHash, bb->name, i);
// If bigBed has name column, look up pasted/uploaded identifiers if any:
struct hash *idHash = NULL;
if (slCount(bbList) >= 4)
idHash = identifierHash(db, table);
/* Create an array of column indexes corresponding to the selected field list. */
int *columnArray;
AllocArray(columnArray, fieldCount);
for (i=0; i<fieldCount; ++i)
{
columnArray[i] = hashIntVal(fieldHash, fieldArray[i]);
}
/* Output row of labels */
fprintf(f, "#%s", fieldArray[0]);
for (i=1; i<fieldCount; ++i)
fprintf(f, "\t%s", fieldArray[i]);
fprintf(f, "\n");
/* Open up bigBed file. */
char *fileName = bigBedFileName(table, conn);
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct asObject *as = bigBedAsOrDefault(bbi);
struct asFilter *filter = NULL;
if (anyFilter())
{
filter = asFilterFromCart(cart, db, table, as);
if (filter)
{
fprintf(f, "# Filtering on %d columns\n", slCount(filter->columnList));
}
}
/* Loop through outputting each region */
struct region *region, *regionList = getRegions();
for (region = regionList; region != NULL; region = region->next)
{
struct lm *lm = lmInit(0);
struct bigBedInterval *iv, *ivList = bigBedIntervalQuery(bbi, region->chrom,
region->start, region->end, 0, lm);
char *row[bbi->fieldCount];
char startBuf[16], endBuf[16];
for (iv = ivList; iv != NULL; iv = iv->next)
{
bigBedIntervalToRow(iv, region->chrom, startBuf, endBuf, row, bbi->fieldCount);
if (asFilterOnRow(filter, row))
{
if ((idHash != NULL) && (hashLookup(idHash, row[3]) == NULL))
continue;
int i;
fprintf(f, "%s", row[columnArray[0]]);
for (i=1; i<fieldCount; ++i)
fprintf(f, "\t%s", row[columnArray[i]]);
fprintf(f, "\n");
}
}
lmCleanup(&lm);
}
/* Clean up and exit. */
bbiFileClose(&bbi);
hashFree(&fieldHash);
freeMem(fieldArray);
freeMem(columnArray);
}
boolean doGetBedOrCt(struct sqlConnection *conn, boolean doCt,
boolean doCtFile, boolean redirectToGb)
/* Actually output bed or custom track. Return TRUE unless no results. */
{
char *db = cloneString(database);
char *table = curTable;
struct hTableInfo *hti = getHti(db, table, conn);
struct featureBits *fbList = NULL, *fbPtr;
struct customTrack *ctNew = NULL;
boolean doCtHdr = (cartUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE)
|| doCt || doCtFile);
char *ctWigOutType = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
char *fbQual = fbOptionsToQualifier();
char fbTQ[128];
int fields = hTableInfoBedFieldCount(hti);
boolean gotResults = FALSE;
struct region *region, *regionList = getRegions();
boolean isBedGr = isBedGraph(curTable);
boolean isBgWg = isBigWigTable(curTable);
boolean needSubtrackMerge = anySubtrackMerge(database, curTable);
boolean doDataPoints = FALSE;
boolean isWig = isWiggle(database, table);
struct wigAsciiData *wigDataList = NULL;
struct dataVector *dataVectorList = NULL;
boolean doRgb = bedItemRgb(hTrackDbForTrack(db, curTable));
if (!cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE) && !doCt)
{
textOpen();
}
if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE))
fputs("#", stdout);
if ((isWig || isBedGr || isBgWg) && sameString(outWigData, ctWigOutType))
doDataPoints = TRUE;
for (region = regionList; region != NULL; region = region->next)
{
struct bed *bedList = NULL, *bed;
struct lm *lm = lmInit(64*1024);
struct dataVector *dv = NULL;
if (isWig && doDataPoints)
{
if (needSubtrackMerge)
{
dv = wiggleDataVector(curTrack, curTable, conn, region);
if (dv != NULL)
slAddHead(&dataVectorList, dv);
}
else
{
int count = 0;
struct wigAsciiData *wigData = NULL;
struct wigAsciiData *asciiData;
struct wigAsciiData *next;
wigData = getWiggleAsData(conn, curTable, region);
for (asciiData = wigData; asciiData; asciiData = next)
{
next = asciiData->next;
if (asciiData->count)
{
slAddHead(&wigDataList, asciiData);
++count;
}
}
slReverse(&wigDataList);
}
}
else if (isBedGr && doDataPoints)
{
dv = bedGraphDataVector(curTable, conn, region);
if (dv != NULL)
slAddHead(&dataVectorList, dv);
}
else if (isBgWg && doDataPoints)
{
dv = bigWigDataVector(curTable, conn, region);
if (dv != NULL)
slAddHead(&dataVectorList, dv);
}
else if (isWig || isBgWg)
{
dv = wiggleDataVector(curTrack, curTable, conn, region);
bedList = dataVectorToBedList(dv);
dataVectorFree(&dv);
}
else if (isBedGr)
{
bedList = getBedGraphAsBed(conn, curTable, region);
}
else
{
bedList = cookedBedList(conn, curTable, region, lm, &fields);
}
/* this is a one-time only initial creation of the custom track
* structure to receive the results. gotResults turns it off after
* the first time.
*/
if (doCtHdr && !gotResults &&
((bedList != NULL) || (wigDataList != NULL) ||
(dataVectorList != NULL)))
{
ctNew = beginCustomTrack(table, fields,
doCt, (isWig || isBedGr || isBgWg), doDataPoints);
}
if (doDataPoints && (wigDataList || dataVectorList))
gotResults = TRUE;
else
{
if ((fbQual == NULL) || (fbQual[0] == 0))
{
for (bed = bedList; bed != NULL; bed = bed->next)
{
if (bed->name != NULL)
{
subChar(bed->name, ' ', '_');
}
if (doCt)
{
struct bed *dupe = cloneBed(bed); /* Out of local memory. */
slAddHead(&ctNew->bedList, dupe);
}
else
{
if (doRgb)
bedTabOutNitemRgb(bed, fields, stdout);
else
bedTabOutN(bed, fields, stdout);
}
gotResults = TRUE;
}
}
else
{
safef(fbTQ, sizeof(fbTQ), "%s:%s", hti->rootName, fbQual);
fbList = fbFromBed(db, fbTQ, hti, bedList, 0, 0, FALSE, FALSE);
if (fields >= 6)
fields = 6;
else if (fields >= 4)
fields = 4;
else
fields = 3;
if (doCt && ctNew)
{
ctNew->fieldCount = fields;
safef(ctNew->tdb->type, strlen(ctNew->tdb->type)+1,
"bed %d", fields);
}
for (fbPtr=fbList; fbPtr != NULL; fbPtr=fbPtr->next)
{
if (fbPtr->name != NULL)
{
char *ptr = strchr(fbPtr->name, ' ');
if (ptr != NULL)
*ptr = 0;
}
if (doCt)
{
struct bed *fbBed = fbToBedOne(fbPtr);
slAddHead(&ctNew->bedList, fbBed );
}
else
{
if (fields >= 6)
hPrintf("%s\t%d\t%d\t%s\t%d\t%c\n",
fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name,
0, fbPtr->strand);
else if (fields >= 4)
hPrintf("%s\t%d\t%d\t%s\n",
fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name);
else
hPrintf("%s\t%d\t%d\n",
fbPtr->chrom, fbPtr->start, fbPtr->end);
}
gotResults = TRUE;
}
featureBitsFreeList(&fbList);
}
}
bedList = NULL;
lmCleanup(&lm);
}
if (!gotResults)
{
hPrintf(NO_RESULTS);
}
else if (doCt)
{
int wigDataSize = 0;
/* Load existing custom tracks and add this new one: */
struct customTrack *ctList = getCustomTracks();
removeNamedCustom(&ctList, ctNew->tdb->table);
if (doDataPoints)
{
if (needSubtrackMerge || isBedGr || isBgWg)
{
slReverse(&dataVectorList);
wigDataSize = dataVectorWriteWigAscii(dataVectorList, ctNew->wigAscii, 0, NULL);
// TODO: see if can make prettier wig output here that
// doesn't necessarily have one value per base
}
else
{
struct wiggleDataStream *wds = NULL;
/* create an otherwise empty wds so we can print out the list */
wds = wiggleDataStreamNew();
wds->ascii = wigDataList;
wigDataSize = wds->asciiOut(wds, db, ctNew->wigAscii, TRUE, FALSE);
#if defined(DEBUG) /* dbg */
/* allow file readability for debug */
chmod(ctNew->wigAscii, 0666);
#endif
wiggleDataStreamFree(&wds);
}
}
else
slReverse(&ctNew->bedList);
slAddHead(&ctList, ctNew);
/* Save the custom tracks out to file (overwrite the old file): */
customTracksSaveCart(db, cart, ctList);
/* Put up redirect-to-browser page. */
if (redirectToGb)
{
char browserUrl[256];
char headerText[512];
int redirDelay = 3;
safef(browserUrl, sizeof(browserUrl),
"%s?%s&db=%s", hgTracksName(), cartSidUrlString(cart), database);
safef(headerText, sizeof(headerText),
"<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"%d;URL=%s\">",
redirDelay, browserUrl);
webStartHeader(cart, database, headerText,
"Table Browser: %s %s: %s", hOrganism(database),
freezeName, "get custom track");
if (doDataPoints)
{
hPrintf("There are %d data points in custom track. ", wigDataSize);
}
else
{
hPrintf("There are %d items in custom track. ",
slCount(ctNew->bedList));
}
hPrintf("You will be automatically redirected to the genome browser in\n"
"%d seconds, or you can \n"
"<A HREF=\"%s\">click here to continue</A>.\n",
redirDelay, browserUrl);
}
}
else if (doDataPoints)
{
if (needSubtrackMerge || isBedGr || isBgWg)
{
slReverse(&dataVectorList);
dataVectorWriteWigAscii(dataVectorList, "stdout", 0, NULL);
}
else
{
/* create an otherwise empty wds so we can print out the list */
struct wiggleDataStream *wds = NULL;
wds = wiggleDataStreamNew();
wds->ascii = wigDataList;
wds->asciiOut(wds, db, "stdout", TRUE, FALSE);
wiggleDataStreamFree(&wds);
}
}
return gotResults;
}
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) */
static void doOutWig(struct trackDb *track, char *table, struct sqlConnection *conn,
enum wigOutputType wigOutType)
{
struct region *regionList = getRegions(), *region;
int maxOut = 0, outCount, curOut = 0;
char *shortLabel = table, *longLabel = table;
if (track == NULL)
errAbort("Sorry, can't find necessary track information for %s. "
"If you reached this page by selecting \"All tables\" as the "
"group, please go back and select the same table via a regular "
"track group if possible.",
table);
maxOut = bigFileMaxOutput();
if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE))
fputs("#", stdout);
else
textOpen();
if (track != NULL)
{
if (!sameString(track->table, table) && track->subtracks != NULL)
{
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(track->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
struct trackDb *tdb = tdbRef->val;
if (sameString(tdb->table, table))
{
track = tdb;
break;
}
}
slFreeList(&tdbRefList);
}
shortLabel = track->shortLabel;
longLabel = track->longLabel;
}
wigDataHeader(shortLabel, longLabel, NULL, wigOutType);
for (region = regionList; region != NULL; region = region->next)
{
int curMaxOut = maxOut - curOut;
if (anySubtrackMerge(database, table))
outCount = mergedWigOutRegion(table, conn, region, curMaxOut,
wigOutType);
else if (startsWithWord("bedGraph", track->type))
outCount = bedGraphOutRegion(table, conn, region, curMaxOut,
wigOutType);
else if (startsWithWord("mathWig", track->type))
outCount = mathWigOutRegion(track, table, conn, region, curMaxOut, wigOutType);
else if (startsWithWord("bigWig", track->type))
outCount = bigWigOutRegion(table, conn, region, curMaxOut, wigOutType);
else
outCount = wigOutRegion(table, conn, region, curMaxOut,
wigOutType, NULL, 0);
curOut += outCount;
if (curOut >= maxOut)
break;
}
if (curOut >= maxOut)
errAbort("Reached output limit of %d data values, please make region smaller,\n\tor set a higher output line limit with the filter settings.", curOut);
}
void bamTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f)
/* Print out selected fields from BAM. If fields is NULL, then print out all fields. */
{
struct hTableInfo *hti = NULL;
hti = getHti(db, table, conn);
struct hash *idHash = NULL;
char *idField = getIdField(db, curTrack, table, hti);
int idFieldNum = 0;
/* if we know what field to use for the identifiers, get the hash of names */
if (idField != NULL)
idHash = identifierHash(db, table);
if (f == NULL)
f = stdout;
/* Convert comma separated list of fields to array. */
int fieldCount = chopByChar(fields, ',', NULL, 0);
char **fieldArray;
AllocArray(fieldArray, fieldCount);
chopByChar(fields, ',', fieldArray, fieldCount);
/* Get list of all fields in big bed and turn it into a hash of column indexes keyed by
* column name. */
struct hash *fieldHash = hashNew(0);
struct slName *bb, *bbList = bamGetFields();
int i;
for (bb = bbList, i=0; bb != NULL; bb = bb->next, ++i)
{
/* if we know the field for identifiers, save it away */
if ((idField != NULL) && sameString(idField, bb->name))
idFieldNum = i;
hashAddInt(fieldHash, bb->name, i);
}
/* Create an array of column indexes corresponding to the selected field list. */
int *columnArray;
AllocArray(columnArray, fieldCount);
for (i=0; i<fieldCount; ++i)
{
columnArray[i] = hashIntVal(fieldHash, fieldArray[i]);
}
/* Output row of labels */
fprintf(f, "#%s", fieldArray[0]);
for (i=1; i<fieldCount; ++i)
fprintf(f, "\t%s", fieldArray[i]);
fprintf(f, "\n");
struct asObject *as = bamAsObj();
struct asFilter *filter = NULL;
if (anyFilter())
{
filter = asFilterFromCart(cart, db, table, as);
if (filter)
{
fprintf(f, "# Filtering on %d columns\n", slCount(filter->columnList));
}
}
/* Loop through outputting each region */
struct region *region, *regionList = getRegions();
int maxOut = bigFileMaxOutput();
for (region = regionList; region != NULL && (maxOut > 0); region = region->next)
{
struct lm *lm = lmInit(0);
char *fileName = bamFileName(table, conn, region->chrom);
struct samAlignment *sam, *samList = bamFetchSamAlignment(fileName, region->chrom,
region->start, region->end, lm);
char *row[SAMALIGNMENT_NUM_COLS];
char numBuf[BAM_NUM_BUF_SIZE];
for (sam = samList; sam != NULL && (maxOut > 0); sam = sam->next)
{
samAlignmentToRow(sam, numBuf, row);
if (asFilterOnRow(filter, row))
{
/* if we're looking for identifiers, check if this matches */
if ((idHash != NULL)&&(hashLookup(idHash, row[idFieldNum]) == NULL))
continue;
int i;
fprintf(f, "%s", row[columnArray[0]]);
for (i=1; i<fieldCount; ++i)
fprintf(f, "\t%s", row[columnArray[i]]);
fprintf(f, "\n");
maxOut --;
}
}
freeMem(fileName);
lmCleanup(&lm);
}
if (maxOut == 0)
warn("Reached output limit of %d data values, please make region smaller,\n\tor set a higher output line limit with the filter settings.", bigFileMaxOutput());
/* Clean up and exit. */
hashFree(&fieldHash);
freeMem(fieldArray);
freeMem(columnArray);
}
CoverMap::CoverMap()
{
w = Broodwar->mapWidth();
h = Broodwar->mapHeight();
range = 30;
Unit* worker = findWorker();
cover_map = new int*[w];
for(int i = 0 ; i < w ; i++)
{
cover_map[i] = new int[h];
//Fill from static map and Region connectability
for (int j = 0; j < h; j++)
{
int ok = BUILDABLE;
if (!Broodwar->isBuildable(i, j))
{
ok = BLOCKED;
}
cover_map[i][j] = ok;
}
}
//Fill from current agents
vector<BaseAgent*> agents = AgentManager::getInstance()->getAgents();
for (int i = 0; i < (int)agents.size(); i++)
{
BaseAgent* agent = agents.at(i);
if (agent->isBuilding())
{
Corners c = getCorners(agent->getUnit());
fill(c);
}
}
//Fill from minerals
for(set<Unit*>::iterator m = Broodwar->getMinerals().begin(); m != Broodwar->getMinerals().end(); m++)
{
Corners c;
c.x1 = (*m)->getTilePosition().x() - 1;
c.y1 = (*m)->getTilePosition().y() - 1;
c.x2 = (*m)->getTilePosition().x() + 2;
c.y2 = (*m)->getTilePosition().y() + 1;
fill(c);
cover_map[c.x1+2][c.y1+2] = MINERAL;
}
//Fill from gas
for(set<Unit*>::iterator m = Broodwar->getGeysers().begin(); m != Broodwar->getGeysers().end(); m++)
{
Corners c;
c.x1 = (*m)->getTilePosition().x() - 2;
c.y1 = (*m)->getTilePosition().y() - 2;
c.x2 = (*m)->getTilePosition().x() + 5;
c.y2 = (*m)->getTilePosition().y() + 3;
fill(c);
cover_map[c.x1+2][c.y1+2] = GAS;
}
//Fill from narrow chokepoints
if (analyzed)
{
for(set<Region*>::const_iterator i=getRegions().begin();i!=getRegions().end();i++)
{
for(set<Chokepoint*>::const_iterator c=(*i)->getChokepoints().begin();c!=(*i)->getChokepoints().end();c++)
{
if ((*c)->getWidth() <= 4 * 32)
{
TilePosition center = TilePosition((*c)->getCenter());
Corners c;
c.x1 = center.x() - 1;
c.x2 = center.x() + 1;
c.y1 = center.y() - 1;
c.y2 = center.y() + 1;
fill(c);
}
}
}
}
mapData = MapDataReader();
mapData.readMap();
}
TilePosition ExplorationManager::getNextToExplore(Squad* squad)
{
TilePosition curPos = squad->getCenter();
TilePosition goal = squad->getGoal();
//Special case: No goal set
if (goal.x() == -1 || goal.y() == -1)
{
BWTA::Region* startRegion = getRegion(curPos);
goal = TilePosition(startRegion->getCenter());
return goal;
}
double dist = curPos.getDistance(goal);
double acceptDist = 4;
if (squad->isGround())
{
acceptDist = 6;
}
if (dist <= acceptDist)
{
//Squad is close to goal
//1. Set region to explored
setExplored(goal);
//2. Find new region to explore
BWTA::Region* startRegion = getRegion(goal);
BWTA::Region* bestRegion = startRegion;
if (bestRegion != NULL)
{
int bestLastVisitFrame = getLastVisitFrame(bestRegion);
if (!squad->isAir())
{
//Ground explorers
for(set<BWTA::Region*>::const_iterator i=startRegion->getReachableRegions().begin();i!=startRegion->getReachableRegions().end();i++)
{
int cLastVisitFrame = getLastVisitFrame((*i));
TilePosition c = TilePosition((*i)->getCenter());
if (cLastVisitFrame <= bestLastVisitFrame)
{
bestLastVisitFrame = cLastVisitFrame;
bestRegion = (*i);
}
}
}
else
{
//Air explorers
double bestDist = 100000;
for(set<BWTA::Region*>::const_iterator i=getRegions().begin();i!=getRegions().end();i++)
{
int cLastVisitFrame = getLastVisitFrame((*i));
TilePosition c = TilePosition((*i)->getCenter());
double dist = c.getDistance(curPos);
if (cLastVisitFrame < bestLastVisitFrame)
{
bestLastVisitFrame = cLastVisitFrame;
bestRegion = (*i);
bestDist = dist;
}
if (cLastVisitFrame == bestLastVisitFrame && dist < bestDist)
{
bestLastVisitFrame = cLastVisitFrame;
bestRegion = (*i);
bestDist = dist;
}
}
}
TilePosition newGoal = TilePosition(bestRegion->getCenter());
return newGoal;
//Broodwar->printf("Explorer: new goal (%d,%d) I am at (%d,%d) agentGoal (%d,%d)", newGoal.x(), newGoal.y(), curPos.x(), curPos.y(), agent->getGoal().x(), agent->getGoal().y());
}
}
return TilePosition(-1, -1);
}
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();
}
void doSummaryStatsBigWig(struct sqlConnection *conn)
/* Put up page showing summary stats for bigWig track. */
{
struct trackDb *track = curTrack;
char *table = curTable;
char *shortLabel = (track == NULL ? table : track->shortLabel);
char *fileName = bigWigFileName(table, conn);
long startTime = clock1000();
htmlOpen("%s (%s) Big Wig 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);
struct bbiFile *bwf = bigWigFileOpen(fileName);
struct region *region, *regionList = getRegions();
double sumData = 0, sumSquares = 0, minVal = 0, maxVal = 0;
bits64 validCount = 0;
if (!anyFilter() && !anyIntersection())
{
for (region = regionList; region != NULL; region = region->next)
{
struct bbiSummaryElement sum;
if (bbiSummaryArrayExtended(bwf, region->chrom, region->start, region->end,
bigWigIntervalQuery, 1, &sum))
{
if (validCount == 0)
{
minVal = sum.minVal;
maxVal = sum.maxVal;
}
else
{
if (sum.minVal < minVal)
minVal = sum.minVal;
if (sum.maxVal > maxVal)
maxVal = sum.maxVal;
}
sumData += sum.sumData;
sumSquares += sum.sumSquares;
validCount += sum.validCount;
}
}
}
else
{
double ll, ul;
enum wigCompare cmp;
getWigFilter(database, curTable, &cmp, &ll, &ul);
for (region = regionList; region != NULL; region = region->next)
{
struct lm *lm = lmInit(0);
struct bbiInterval *iv, *ivList;
ivList = intersectedFilteredBbiIntervalsOnRegion(conn, bwf, region, cmp, ll, ul, lm);
for (iv = ivList; iv != NULL; iv = iv->next)
{
double val = iv->val;
double size = iv->end - iv->start;
if (validCount == 0)
minVal = maxVal = val;
else
{
if (val < minVal)
minVal = val;
if (val > maxVal)
maxVal = val;
}
sumData += size*val;
sumSquares += size*val*val;
validCount += size;
}
lmCleanup(&lm);
}
}
hTableStart();
floatStatRow("mean", sumData/validCount);
floatStatRow("min", minVal);
floatStatRow("max", maxVal);
floatStatRow("standard deviation", calcStdFromSums(sumData, sumSquares, validCount));
numberStatRow("bases with data", validCount);
long long regionSize = basesInRegion(regionList,0);
long long gapTotal = gapsInRegion(conn, regionList,0);
numberStatRow("bases with sequence", regionSize - gapTotal);
numberStatRow("bases in region", regionSize);
wigFilterStatRow(conn);
stringStatRow("intersection", cartUsualString(cart, hgtaIntersectTable, "off"));
long wigFetchTime = clock1000() - startTime;
floatStatRow("load and calc time", 0.001*wigFetchTime);
hTableEnd();
bbiFileClose(&bwf);
htmlClose();
}
void tabOutSelectedFields(
char *primaryDb, /* The primary database. */
char *primaryTable, /* The primary table. */
FILE *f, /* file for output, null for stdout */
struct slName *fieldList) /* List of db.table.field */
/* Do tab-separated output on selected fields, which may
* or may not include multiple tables. */
{
struct joinerDtf *dtfList = NULL;
struct joinerDtf *filterTables = NULL;
boolean doJoin = joinRequired(primaryDb, primaryTable,
fieldList, &dtfList, &filterTables);
if (! doJoin)
{
struct sqlConnection *conn = hAllocConn(dtfList->database);
struct dyString *dy = dyStringNew(0);
if (hIsBigBed(database, dtfList->table, NULL, ctLookupName))
makeBigBedOrderedCommaFieldList(dtfList, dy);
else if (isCustomTrack(dtfList->table))
makeCtOrderedCommaFieldList(dtfList, dy);
else
makeDbOrderedCommaFieldList(conn, dtfList->table, dtfList, dy);
doTabOutTable(dtfList->database, dtfList->table, f, conn, dy->string);
hFreeConn(&conn);
}
else
{
struct joiner *joiner = allJoiner;
struct joinedTables *joined = joinedTablesCreate(joiner,
primaryDb, primaryTable, dtfList, filterTables, 1000000, getRegions());
if (f == NULL)
joinedTablesTabOut(joined);
else
joinedTablesTabOutFile(joined, f);
joinedTablesFree(&joined);
}
joinerDtfFreeList(&dtfList);
joinerDtfFreeList(&filterTables);
}
static DetectedFace *postProcessing(DetectedFace *faces, int size, int *newsize)
{
int size1 = 0;
DetectedFace *trueFaces1 = malloc(size * sizeof(DetectedFace));
int *regionsInfos;
DetectedFace **regions = getRegions(faces, size, ®ionsInfos);
int nbRegions = *regionsInfos;
double *confidenceVals = malloc(nbRegions * sizeof(double));
for(int i = 0; i < nbRegions; ++i)
{
DetectedFace *region = regions[i];
int nbFacesInRegion = regionsInfos[i+1];
double confidence = (double)nbFacesInRegion / (double)region->w;
if(confidence > CONFIDENCE_THRESHOLD)
{
trueFaces1[size1] = region[nbFacesInRegion/2];
confidenceVals[size1++] = confidence;
}
}
sortFacesBySize(trueFaces1, size1);
DetectedFace *trueFaces2 = malloc(size1 * sizeof(DetectedFace));
int size2 = 0;
for(int i = 0; i < size1; ++i)
{
DetectedFace face = trueFaces1[i];
int faceX = face.x + face.w/2;
int faceY = face.y + face.h/2;
for(int j = i+1; j < size1; ++j)
{
DetectedFace face2 = trueFaces1[j];
if(face2.x >= 0
&& faceX > face2.x && faceX < face2.x + face2.w
&& faceY > face2.y && faceY < face2.y + face2.h)
{
if(confidenceVals[i] > confidenceVals[j])
{
trueFaces1[j].x = -1;
}
else
{
trueFaces1[i].x = -1;
break;
}
}
}
}
for(int i = 0; i < size1; ++i)
{
if(trueFaces1[i].x >= 0)
trueFaces2[size2++] = trueFaces1[i];
}
*newsize = size2;
return trueFaces2;
}
void doGenePredNongenomic(struct sqlConnection *conn, int typeIx)
/* Get mrna or protein associated with selected genes. */
{
/* Note this does do the whole genome at once rather than one
* chromosome at a time, but that's ok because the gene prediction
* tracks this serves are on the small side. */
char *typeWords[3];
char *table;
struct lm *lm = lmInit(64*1024);
int fieldCount;
struct bed *bed, *bedList = cookedBedsOnRegions(conn, curTable, getRegions(),
lm, &fieldCount);
int typeWordCount;
textOpen();
/* Figure out which table to use. */
if (isRefGeneTrack(curTable))
{
if (typeIx == 1) /* Protein */
doRefGeneProteinSequence(conn, bedList);
else
doRefGeneMrnaSequence(conn, bedList);
}
else
{
char *dupType = cloneString(findTypeForTable(database, curTrack, curTable, ctLookupName));
typeWordCount = chopLine(dupType, typeWords);
if (typeIx >= typeWordCount)
internalErr();
table = typeWords[typeIx];
if (sqlTableExists(conn, table))
{
struct sqlResult *sr;
char **row;
char query[256];
struct hash *hash = newHash(18);
boolean gotResults = FALSE;
/* Make hash of all id's passing filters. */
for (bed = bedList; bed != NULL; bed = bed->next)
hashAdd(hash, bed->name, NULL);
/* Scan through table, outputting ones that match. */
sqlSafef(query, sizeof(query), "select name, seq from %s", table);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
if (hashLookup(hash, row[0]))
{
hPrintf(">%s\n", row[0]);
writeSeqWithBreaks(stdout, row[1], strlen(row[1]), 60);
gotResults = TRUE;
}
}
sqlFreeResult(&sr);
hashFree(&hash);
if (!gotResults)
hPrintf(NO_RESULTS);
}
else
{
internalErr();
}
freez(&dupType);
}
lmCleanup(&lm);
}
void vcfTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f,
boolean isTabix)
/* Print out selected fields from VCF. If fields is NULL, then print out all fields. */
{
struct hTableInfo *hti = NULL;
hti = getHti(db, table, conn);
struct hash *idHash = NULL;
char *idField = getIdField(db, curTrack, table, hti);
int idFieldNum = 0;
/* if we know what field to use for the identifiers, get the hash of names */
if (idField != NULL)
idHash = identifierHash(db, table);
if (f == NULL)
f = stdout;
/* Convert comma separated list of fields to array. */
int fieldCount = chopByChar(fields, ',', NULL, 0);
char **fieldArray;
AllocArray(fieldArray, fieldCount);
chopByChar(fields, ',', fieldArray, fieldCount);
/* Get list of all fields in big bed and turn it into a hash of column indexes keyed by
* column name. */
struct hash *fieldHash = hashNew(0);
struct slName *bb, *bbList = vcfGetFields();
int i;
for (bb = bbList, i=0; bb != NULL; bb = bb->next, ++i)
{
/* if we know the field for identifiers, save it away */
if ((idField != NULL) && sameString(idField, bb->name))
idFieldNum = i;
hashAddInt(fieldHash, bb->name, i);
}
/* Create an array of column indexes corresponding to the selected field list. */
int *columnArray;
AllocArray(columnArray, fieldCount);
for (i=0; i<fieldCount; ++i)
{
columnArray[i] = hashIntVal(fieldHash, fieldArray[i]);
}
// If we are outputting a subset of fields, invalidate the VCF header.
boolean allFields = (fieldCount == VCFDATALINE_NUM_COLS);
if (!allFields)
fprintf(f, "# Only selected columns are included below; output is not valid VCF.\n");
struct asObject *as = vcfAsObj();
struct asFilter *filter = NULL;
if (anyFilter())
filter = asFilterFromCart(cart, db, table, as);
/* Loop through outputting each region */
struct region *region, *regionList = getRegions();
int maxOut = bigFileMaxOutput();
struct trackDb *tdb = hashFindVal(fullTableToTdbHash, table);
// Include the header, absolutely necessary for VCF parsing.
boolean printedHeader = FALSE;
// Temporary storage for row-ification:
struct dyString *dyAlt = newDyString(1024);
struct dyString *dyFilter = newDyString(1024);
struct dyString *dyInfo = newDyString(1024);
struct dyString *dyGt = newDyString(1024);
struct vcfRecord *rec;
for (region = regionList; region != NULL && (maxOut > 0); region = region->next)
{
char *fileName = vcfFileName(tdb, conn, table, region->chrom);
struct vcfFile *vcff;
if (isTabix)
vcff = vcfTabixFileMayOpen(fileName, region->chrom, region->start, region->end,
100, maxOut);
else
vcff = vcfFileMayOpen(fileName, region->chrom, region->start, region->end,
100, maxOut, TRUE);
if (vcff == NULL)
noWarnAbort();
// If we are outputting all fields, but this VCF has no genotype info, omit the
// genotype columns from output:
if (allFields && vcff->genotypeCount == 0)
fieldCount = VCFDATALINE_NUM_COLS - 2;
if (!printedHeader)
{
fprintf(f, "%s", vcff->headerString);
if (filter)
fprintf(f, "# Filtering on %d columns\n", slCount(filter->columnList));
if (!allFields)
{
fprintf(f, "#%s", fieldArray[0]);
for (i=1; i<fieldCount; ++i)
fprintf(f, "\t%s", fieldArray[i]);
fprintf(f, "\n");
}
printedHeader = TRUE;
}
char *row[VCFDATALINE_NUM_COLS];
char numBuf[VCF_NUM_BUF_SIZE];
for (rec = vcff->records; rec != NULL && (maxOut > 0); rec = rec->next)
{
vcfRecordToRow(rec, region->chrom, numBuf, dyAlt, dyFilter, dyInfo, dyGt, row);
if (asFilterOnRow(filter, row))
{
/* if we're looking for identifiers, check if this matches */
if ((idHash != NULL) && (hashLookup(idHash, row[idFieldNum]) == NULL))
continue;
// All fields output: after asFilter'ing, preserve original VCF chrom
if (allFields && !sameString(rec->chrom, region->chrom))
row[0] = rec->chrom;
int i;
fprintf(f, "%s", row[columnArray[0]]);
for (i=1; i<fieldCount; ++i)
{
fprintf(f, "\t%s", row[columnArray[i]]);
}
fprintf(f, "\n");
maxOut --;
}
}
vcfFileFree(&vcff);
freeMem(fileName);
}
if (maxOut == 0)
warn("Reached output limit of %d data values, please make region smaller,\n\tor set a higher output line limit with the filter settings.", bigFileMaxOutput());
/* Clean up and exit. */
dyStringFree(&dyAlt); dyStringFree(&dyFilter); dyStringFree(&dyInfo); dyStringFree(&dyGt);
hashFree(&fieldHash);
freeMem(fieldArray);
freeMem(columnArray);
}
