samUser* samHive::getSamUser(int rid) {
string userNKPath = stringPrintf("\\SAM\\Domains\\Account\\Users\\%08X", rid);
reg_off userNKOffset = this->travPath(0, (char*)userNKPath.c_str(), 0) + 4;
string vValuePath = stringPrintf("\\SAM\\Domains\\Account\\Users\\%08X\\V",rid);
ntreg::keyval *vValue = this->copyValueToBuffer(NULL, 0, (char*)vValuePath.c_str(), REG_BINARY, TPF_VK_EXACT);
string fValuePath = stringPrintf("\\SAM\\Domains\\Account\\Users\\%08X\\F",rid);
ntreg::keyval *fValue = this->copyValueToBuffer(NULL, 0, (char*)fValuePath.c_str(), REG_BINARY, TPF_VK_EXACT);
// this should be null for local accounts, and set for microsoft accounts
string internetUserNamePath = stringPrintf("\\SAM\\Domains\\Account\\Users\\%08X\\InternetUserName",rid);
ntreg::keyval *internetUserNameValue = this->copyValueToBuffer(NULL, 0, (char*)internetUserNamePath.c_str(), REG_BINARY, TPF_VK_EXACT);
string internetUserName = "";
if(internetUserNameValue != NULL) {
int inetUserNameLen = internetUserNameValue->len;
char* inetUserNameCString = new char[inetUserNameLen + 1];
inetUserNameCString[inetUserNameLen] = '\0';
binaryManip::unicodeToAscii((char*)&internetUserNameValue->data, inetUserNameCString, internetUserNameValue->len);
internetUserName = inetUserNameCString;
delete[] inetUserNameCString;
free(internetUserNameValue);
internetUserNameValue = NULL;
}
samUser *newSamUser;
try{
newSamUser = new samUser(rid, userNKOffset, vValue, vValuePath, fValue, fValuePath, this->hashedBootKey, internetUserName);
}catch(owpException e) {
cerr << e.formattedMessage;
newSamUser = NULL;
}
return newSamUser;
}
char* getEntryNumber( int number, int pairType, int readNum ) {
int flag=0;
Stringa str=stringCreate(10);
switch ( pairType ) {
case GFR_PAIR_TYPE_EXONIC_EXONIC:
case GFR_PAIR_TYPE_EXONIC_INTRONIC:
case GFR_PAIR_TYPE_INTRONIC_EXONIC:
case GFR_PAIR_TYPE_INTRONIC_INTRONIC:
break;
case GFR_PAIR_TYPE_INTRONIC_JUNCTION:
case GFR_PAIR_TYPE_EXONIC_JUNCTION:
if( readNum==2 ) flag=1;
break;
case GFR_PAIR_TYPE_JUNCTION_EXONIC:
case GFR_PAIR_TYPE_JUNCTION_INTRONIC:
if( readNum==1 ) flag=1;
break;
case GFR_PAIR_TYPE_JUNCTION_JUNCTION:
flag=1;
}
if( flag==1 ) {
int rem = number % 2;
if( rem == 0 )
stringPrintf(str, "%d right", number/2);
else
stringPrintf(str, "left %d", number/2+1);
} else {
stringPrintf(str, "%d", number);
}
return string(str);
}
static void addSubstitution (Alteration *currAlteration, char* proteinSequenceBeforeIndel, char *proteinSequenceAfterIndel, int indelOffset)
{
int lengthBefore,lengthAfter;
static Stringa buffer = NULL;
int i;
int diff;
int index;
stringCreateClear (buffer,100);
index = ((currAlteration->relativePosition - 1) / 3);
lengthBefore = strlen (proteinSequenceBeforeIndel);
lengthAfter = strlen (proteinSequenceAfterIndel);
diff = abs (lengthBefore - lengthAfter);
if (lengthBefore < lengthAfter) {
stringPrintf (buffer,"%d_%c->",index + 1,proteinSequenceBeforeIndel[index]);
for (i = 0; i <= diff; i++) {
stringAppendf (buffer,"%c",proteinSequenceAfterIndel[index + i]);
}
}
else if (lengthBefore > lengthAfter) {
stringPrintf (buffer,"%d_",index + 1);
for (i = 0; i <= diff; i++) {
stringAppendf (buffer,"%c",proteinSequenceBeforeIndel[index + i]);
}
stringAppendf (buffer,"->%c",proteinSequenceAfterIndel[index]);
}
else {
stringPrintf (buffer,"%d_%s->",index,subString (proteinSequenceBeforeIndel,index - 1,index + (int)ceil ((double)indelOffset / 3)));
stringAppendf (buffer,"%s",subString (proteinSequenceAfterIndel,index - 1,index + (int)ceil ((double)indelOffset / 3)));
}
currAlteration->substitution = hlr_strdup (string (buffer));
}
void TextMgr::statusDraw() {
char *statusTextPtr = NULL;
charAttrib_Push();
charPos_Push();
if (_statusEnabled) {
clearLine(_statusRow, 15);
charAttrib_Set(0, 15);
charPos_Set(_statusRow, 1);
statusTextPtr = stringPrintf(_systemUI->getStatusTextScore());
displayText(statusTextPtr);
charPos_Set(_statusRow, 30);
if (_vm->getFlag(VM_FLAG_SOUND_ON)) {
statusTextPtr = stringPrintf(_systemUI->getStatusTextSoundOn());
} else {
statusTextPtr = stringPrintf(_systemUI->getStatusTextSoundOff());
}
displayText(statusTextPtr);
}
charPos_Pop();
charAttrib_Pop();
}
/**
* Merges changes made with samUser objects back into the hive in memory
* @return bool Whether or not all changes were merged
*/
bool samHive::mergeChangesToHive() {
bool allSuccessful = true;
for(unsigned int i = 0; i < userList.size(); i++) {
if(userList.at(i)->hasChanges()) {
ntreg::keyval *keyValue = userList.at(i)->getVStructRegValue();
string path = userList.at(i)->getVStructPath().c_str();
int size = copyBufferToValue(keyValue, 0, (char*)path.c_str(), VAL_TYPE_REG_BINARY, TPF_VK_EXACT);
if(size < 1) {
allSuccessful = false;
}
cout << stringPrintf("Merging into %s: wrote %d bytes", path.c_str(), size) << endl;
keyValue = userList.at(i)->getFStructRegValue();
path = userList.at(i)->getFStructPath().c_str();
size = copyBufferToValue(keyValue, 0, (char*)path.c_str(), VAL_TYPE_REG_BINARY, TPF_VK_EXACT);
if(size < 1 || allSuccessful == false) {
allSuccessful = false;
} else {
userList.at(i)->hasSaved();
}
cout << stringPrintf("Merging into %s: wrote %d bytes", path.c_str(), size) << endl;
}
}
regHive->state |= HMODE_DIRTY;
return allSuccessful;
}
/**
* Prints currSeq to char*.
*/
char* fastq_printOneSequence (Fastq* currFQ)
{
static Stringa buffer=NULL;
stringCreateClear( buffer, 100 );
stringPrintf( buffer, "@%s\n%s\n+\n%s", currFQ->seq->name, currFQ->seq->sequence, currFQ->quality );
return string( buffer );
}
String BufferedReader::dumpCurrentContext ()
{
String context;
stringPrintf ( context, "at file='%s', line %llu, char %llu : ",
getCurrentURI().c_str(),
totalLinesParsed, totalParsed );
if ( buffer )
{
static const __ui64 MaxBufferDumpSize = 256;
char _dumpBuff[MaxBufferDumpSize];
__ui64 _dumpBuffStart, _dumpBuffSize = 0;
_dumpBuffStart = bufferIdx;
while ( _dumpBuffStart && buffer[_dumpBuffStart] != '\n' &&
( bufferIdx - _dumpBuffStart < MaxBufferDumpSize / 2 ) )
_dumpBuffStart--;
if ( _dumpBuffStart ) _dumpBuffStart++;
while ( _dumpBuffSize < bufferSz && buffer[_dumpBuffStart + _dumpBuffSize] != '\n' )
_dumpBuffSize++;
if ( _dumpBuffSize > MaxBufferDumpSize )
_dumpBuffSize = MaxBufferDumpSize;
memcpy ( _dumpBuff, &(buffer[_dumpBuffStart]), _dumpBuffSize );
_dumpBuff[_dumpBuffSize-1] = '\0';
context += _dumpBuff;
context += "\n";
}
else
{
context += "(Unknown context)";
}
return context;
}
static void sslGenerateCertificate(const char *certificate,
const char *serverName) {
debug("Auto-generating missing certificate \"%s\" for \"%s\"",
certificate, serverName);
pid_t pid = fork();
if (pid == -1) {
warn("Failed to generate self-signed certificate \"%s\"", certificate);
} else if (pid == 0) {
int fd = NOINTR(open("/dev/null", O_RDONLY));
check(fd != -1);
check(NOINTR(dup2(fd, STDERR_FILENO)) == STDERR_FILENO);
check(NOINTR(close(fd)) == 0);
fd = NOINTR(open("/dev/null", O_WRONLY));
check(fd != -1);
check(NOINTR(dup2(fd, STDIN_FILENO)) == STDIN_FILENO);
check(NOINTR(close(fd)) == 0);
umask(077);
check(setenv("PATH", "/usr/bin:/usr/sbin", 1) == 0);
execlp("openssl", "openssl", "req", "-x509", "-nodes", "-days", "7300",
"-newkey", "rsa:2048", "-keyout", certificate, "-out", certificate,
"-subj", stringPrintf(NULL, "/CN=%s/", serverName),
(char *)NULL);
check(0);
} else {
int status;
check(NOINTR(waitpid(pid, &status, 0)) == pid);
if (!WIFEXITED(status) || WEXITSTATUS(status) != 0)
warn("Failed to generate self-signed certificate \"%s\"", certificate);
}
}
void samHive::loadUserList() {
reg_off regKeyOffset = this->travPath(0,(char*)"\\SAM\\Domains\\Account\\Users\\Names\\",0);
if(!regKeyOffset) {
throw(new owpException("loadUserList: could not find usernames in registry!"));
} else {
cout << stringPrintf("regKeyOffset: %d\n", regKeyOffset) << endl;
}
int subKeyCount = 0;
int subKeyCountRI = 0;
struct ntreg::ex_data exData;
string adminUser;
while((this->getNextSubKey(regKeyOffset+4, &subKeyCount, &subKeyCountRI, &exData) > 0)) {
//get the RID
int rid = this->getUserRID(exData.name);
if(rid == 500) {
adminUser = exData.name;
}
samUser* newSamUser = this->getSamUser(rid);
if(newSamUser != NULL) {
this->userList.push_back(newSamUser);
}
FREE(exData.name);
}
}
int main (int argc, char *argv[])
{
LineStream ls;
char *line;
char *pos;
Stringa buffer;
if (argc != 2) {
usage ("%s <file.intraOffsets>");
}
TH1 *his = new TH1D ("","Intra-read distribution",1000,0,1000);
TCanvas *canv = new TCanvas("","canvas",1200,400);
ls = ls_createFromFile (argv[1]);
while (line = ls_nextLine (ls)) {
his->Fill (atoi (line));
}
ls_destroy (ls);
his->Draw();
his->GetXaxis()->SetLabelSize (0.04);
his->GetYaxis()->SetLabelSize (0.04);
buffer = stringCreate (100);
pos = strchr (argv[1],'.');
if (pos == NULL) {
die ("Expected <file.intraOffsets>: %s",argv[1]);
}
*pos = '\0';
stringPrintf (buffer,"%s_intraDistribution.jpg",argv[1]);
canv->Print (string (buffer),"jpg");
stringDestroy (buffer);
return 0;
}
void PersistenceModule::functionGetCurrentRevisionId ( __XProcFunctionArgs__ )
{
BranchRevId branchRevId = node.getDocument().getBranchRevId();
String revisionId;
stringPrintf ( revisionId, "%llu", branchRevId.revisionId );
result.setSingleton ( revisionId );
}
llvm::Function* FunctionAST::codegen() {
debug_info_helper->emitLocation(getLoc());
llvm::Function* function = prototype_->codegen();
CHECK(function != nullptr);
CurFunctionGuard guard(function);
debug_info_helper->createFunction(function, getLoc(), false);
std::string body_label = stringPrintf("%s.entry", function->getName().data());
llvm::BasicBlock* basic_block = llvm::BasicBlock::Create(*context, body_label, function);
llvm::IRBuilder<>::InsertPointGuard InsertPointGuard(*cur_builder);
cur_builder->SetInsertPoint(basic_block);
// Don't allow to break on argument initialization.
// global_debug_info.emitLocation(nullptr);
auto arg_it = function->arg_begin();
for (size_t i = 0; i < function->arg_size(); ++i, ++arg_it) {
llvm::Value* variable = createVariable(arg_it->getName(), getLoc(), i + 1);
cur_builder->CreateStore(&*arg_it, variable);
}
// global_debug_info.emitLocation(nullptr);
llvm::Value* ret_val = body_->codegen();
CHECK(ret_val != nullptr);
cur_builder->CreateRet(ret_val);
debug_info_helper->endFunction();
return function;
}
/**
* Generates a link to Rat Genome Database (RGD) gene description page.
* Example: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=727972
* @note The rgdId must be numeric.
*/
char* htmlLinker_generateLinkToRatGeneDescriptionPage (char* rgdId)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=%s",rgdId);
return string (buffer);
}
/**
* Generates a link to Saccharomyces Genome Database (SGD) gene description page.
* Both the SGD gene ID or the gene symbol can be used.
* Example: http://db.yeastgenome.org/cgi-bin/locus.pl?locus=AAC3 or
http://db.yeastgenome.org/cgi-bin/locus.pl?locus=S000000289
*/
char* htmlLinker_generateLinkToYeastGeneDescriptionPage (char* sgdId)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://db.yeastgenome.org/cgi-bin/locus.pl?locus=%s",sgdId);
return string (buffer);
}
/**
* Generates a link to InterPro.
* Example: http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001922
*/
char* htmlLinker_generateLinkToInterPro (char* interProId)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=%s",interProId);
return string (buffer);
}
/**
* Generates a link to FlyBase gene description page.
* Example: http://flybase.bio.indiana.edu/reports/FBgn0033837.html
*/
char* htmlLinker_generateLinkToFlyBaseGeneDescriptionPage (char* flyBaseId)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://flybase.bio.indiana.edu/reports/%s.html",flyBaseId);
return string (buffer);
}
/**
* Generates a link to WormBase gene description page.
* Both the WormBase gene ID or the gene symbol can be used.
* Example: http://www.wormbase.org/db/gene/gene?name=WBGene00002239 or
http://www.wormbase.org/db/gene/gene?name=ksr-1
*/
char* htmlLinker_generateLinkToWormBaseGeneDescriptionPage (char* wormBaseGeneId)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://www.wormbase.org/db/gene/gene?name=%s",wormBaseGeneId);
return string (buffer);
}
/**
* Generates a link to AmiGO.
* Example: http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0051240
*/
char* htmlLinker_generateLinkToAmiGO (char* goId)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=%s",goId);
return string (buffer);
}
/**
* Generates a link to the PDB.
* Example: http://www.rcsb.org/pdb/explore/explore.do?structureId=1HDC
*/
char* htmlLinker_generateLinkToPDB (char* pdbId)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://www.rcsb.org/pdb/explore/explore.do?structureId=%s",pdbId);
return string (buffer);
}
/**
* Generates a link to PubMed.
* Example: http://www.ncbi.nlm.nih.gov/pubmed/18276894
*/
char* htmlLinker_generateLinkToPubmed (char* pmid)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://www.ncbi.nlm.nih.gov/pubmed/%s",pmid);
return string (buffer);
}
/**
* Generates a link to EntrezGene.
* Example: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=NP_001069323 or
http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=1812
*/
char* htmlLinker_generateLinkToEntrezGene (char* term)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=%s",term);
return string (buffer);
}
char* htmlLinker_generateLinkToMouseGeneDescriptionPage (char* mgiId)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://www.informatics.jax.org/searches/accession_report.cgi?id=%s",mgiId);
return string (buffer);
}
/**
* Generates a link to Pfam.
* Example: http://pfam.sanger.ac.uk/family?acc=PF09582
*/
char* htmlLinker_generateLinkToPfam (char* pfamId)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://pfam.sanger.ac.uk/family?acc=%s",pfamId);
return string (buffer);
}
/**
* Generates a link to the Yale human pseudogene site.
* Example: http://tables.pseudogene.org/human/200550
*/
char* htmlLinker_generateLinkToHumanPseudogenePageAtYale (char* pseudogeneId)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://tables.pseudogene.org/human/%s",pseudogeneId);
return string (buffer);
}
/**
* Generates a link to Uniprot.
* Example: http://www.pir.uniprot.org/cgi-bin/upEntry?id=Q91V24 or
http://www.pir.uniprot.org/cgi-bin/upEntry?id=ADA1A_BOVIN
*/
char* htmlLinker_generateLinkToUniProt (char* uniProtId)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://www.pir.uniprot.org/cgi-bin/upEntry?id=%s",uniProtId);
return string (buffer);
}
static char* getBreakPointSequence (char *tileCoordinate1, char *tileCoordinate2)
{
Stringa buffer;
Stringa targetsFile;
FILE *fp;
Array targetSeqs;
int i;
Seq *currSeq;
static Stringa sequence = NULL;
buffer = stringCreate (100);
targetsFile = stringCreate (100);
stringPrintf (targetsFile,"targets_%d.txt",getpid ());
if (!(fp = fopen (string (targetsFile),"w")) ){
die ("Unable to open target file: %s",string (targetsFile));
}
fprintf (fp,"%s\n%s",tileCoordinate1,tileCoordinate2);
fclose (fp);
stringPrintf (buffer,"%s %s/%s stdout -noMask -seqList=%s",
confp_get(Conf, "BLAT_TWO_BIT_TO_FA"),
confp_get(Conf, "BLAT_DATA_DIR"),
confp_get(Conf, "BLAT_TWO_BIT_DATA_FILENAME"),
string (targetsFile));
fasta_initFromPipe (string (buffer));
targetSeqs = fasta_readAllSequences (0);
fasta_deInit ();
if (arrayMax (targetSeqs) != 2) {
die ("Expected only two target sequences");
}
stringCreateClear (sequence,100);
for (i = 0; i < arrayMax (targetSeqs); i++) {
currSeq = arrp (targetSeqs,i,Seq);
stringAppendf (sequence,"%s",currSeq->sequence);
hlr_free (currSeq->name);
hlr_free (currSeq->sequence);
}
arrayDestroy (targetSeqs);
stringPrintf (buffer,"rm -rf %s",string (targetsFile));
hlr_system (string (buffer),0);
stringDestroy (targetsFile);
stringDestroy (buffer);
return string (sequence);
}
/**
* Generates a link to KnownGene description page.
* Example: http://genome.ucsc.edu/cgi-bin/hgGene?db=rn4&hgg_gene=NM_012824&hgg_chrom=chr1&hgg_start=78996678&hgg_end=78999875
*/
char* htmlLinker_generateLinkToGeneDescriptionPageAtUCSC (char* database, char* geneName,
char* chromosome, int start, int end)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://genome.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d",
database,geneName,chromosome,start,end);
return string (buffer);
}
/**
* Generates a link to the UCSC track element description page.
* Example: http://genome.ucsc.edu/cgi-bin/hgc?db=hg18&g=intronEst&i=BI755927&c=chrX&l=149673899&r=152783129
*/
char* htmlLinker_generateLinkToTrackElementDescriptionPageAtUCSC (char* database, char* trackName, char* elementName,
char* chromosome, int start, int end)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://genome.ucsc.edu/cgi-bin/hgc?db=%s&g=%s&i=%s&c=%s&l=%d&r=%d",
database,trackName,elementName,chromosome,start,end);
return string (buffer);
}
/**
* Generates a link to the UCSC genome browser.
* Example: http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&clade=vertebrate&org=Mouse&position=chr12:10000-20000
*/
char* htmlLinker_generateLinkToGenomeBrowserAtUCSC (char* database, char* clade, char* organism,
char* chromosome, int start, int end)
{
static Stringa buffer = NULL;
stringCreateClear (buffer,100);
stringPrintf (buffer,"http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&clade=%s&org=%s&position=%s:%d-%d",
database,clade,organism,chromosome,start,end);
return string (buffer);
}
/**
* writes circos configuration file
*/
int write_circosConf (char* prefix,
Locus locus,
Array regions,
Chrdata_t *chromosomes,
SVCfg_t *settings)
{
float rpos = 0.99;
FILE *fp;
Stringa buffer = stringCreate(50);
int scale = getScale (regions);
stringPrintf (buffer, "%s/test/circos_%s_%s_%d_%d.conf",
confp_get(Conf, "WEB_CIRCOS_DIR"),
prefix,
locus.chromosome,
locus.start,
locus.end);
if (!(fp = fopen (string (buffer), "w"))) {
die ("Unable to open target file");
return -1;
};
printf ("<h2>%i</h2>", scale);
// write conf file
conf_printHeader (fp,
confp_get(Conf, "WEB_CIRCOS_DIR"),
confp_get(Conf, "WEB_DATA_DIR"),
confp_get(Conf, "WEB_SDATA_DIR"),
chromosomes,
prefix,
locus,
scale);
conf_printUnits (fp, regions, chromosomes, scale);
if (scale <= 10000) {
conf_printDataTracks (fp,
prefix,
locus,
confp_get(Conf, "WEB_SDATA_DIR"),
confp_get(Conf, "WEB_DATA_DIR"),
&rpos,
regions,
chromosomes,
settings);
}
conf_printLinks (fp, confp_get(Conf, "WEB_DATA_DIR"), &rpos, prefix, locus, settings->readlim);
conf_printFooter (fp);
fclose (fp);
stringDestroy (buffer);
return 0;
}
