void AsyncCopy::Run(void* data)
{
START_KROLL_THREAD;
Logger* logger = Logger::Get("Filesystem.AsyncCopy");
AsyncCopy* ac = static_cast<AsyncCopy*>(data);
std::vector<std::string>::iterator iter = ac->files.begin();
Poco::Path to(ac->destination);
Poco::File tof(to.toString());
logger->Debug("Job started: dest=%s, count=%i", ac->destination.c_str(), ac->files.size());
if (!tof.exists())
{
tof.createDirectory();
}
int c = 0;
while (!ac->stopped && iter!=ac->files.end())
{
bool err_copy = false;
std::string file = (*iter++);
c++;
logger->Debug("File: path=%s, count=%i\n", file.c_str(), c);
try
{
Poco::Path from(file);
Poco::File f(file);
if (f.isDirectory())
{
ac->Copy(from,to);
}
else
{
Poco::Path dest(to,from.getFileName());
ac->Copy(from,dest);
}
logger->Debug("File copied");
KValueRef value = Value::NewString(file);
ValueList args;
args.push_back(value);
args.push_back(Value::NewInt(c));
args.push_back(Value::NewInt(ac->files.size()));
args.push_back(Value::NewBool(true));
RunOnMainThread(ac->callback, args, false);
logger->Debug("Callback executed");
}
catch (ValueException &ex)
{
err_copy = true;
SharedString ss = ex.DisplayString();
logger->Error(std::string("Error: ") + *ss + " for file: " + file);
}
catch (Poco::Exception &ex)
{
err_copy = true;
logger->Error(std::string("Error: ") + ex.displayText() + " for file: " + file);
}
catch (std::exception &ex)
{
err_copy = true;
logger->Error(std::string("Error: ") + ex.what() + " for file: " + file);
}
catch (...)
{
err_copy = true;
logger->Error(std::string("Unknown error during copy: ") + file);
}
try
{
if(err_copy)
{
KValueRef value = Value::NewString(file);
ValueList args;
args.push_back(value);
args.push_back(Value::NewInt(c));
args.push_back(Value::NewInt(ac->files.size()));
args.push_back(Value::NewBool(false));
RunOnMainThread(ac->callback, args, false);
}
}
catch(...)
{
err_copy = true;
logger->Error(std::string("Unknown error during copy: ") + file);
}
}
ac->Set("running",Value::NewBool(false));
ac->stopped = true;
logger->Debug(std::string("Job finished"));
END_KROLL_THREAD;
}
int main(int argc, char** argv) {
if(!parseOption(argc, argv)) {
fprintf(stderr, "failed to parse option\n");
return 1;
}
const char *bitcode = NULL;
size_t bitcodeSize = readBitcode(&bitcode);
unsigned int version = 0;
bcinfo::BitcodeWrapper bcWrapper((const char *)bitcode, bitcodeSize);
if (bcWrapper.getBCFileType() == bcinfo::BC_WRAPPER) {
version = bcWrapper.getTargetAPI();
if (verbose) {
printf("Found bitcodeWrapper\n");
}
} else if (translateFlag) {
version = 12;
}
if (verbose) {
printf("targetAPI: %u\n", version);
printf("compilerVersion: %u\n", bcWrapper.getCompilerVersion());
printf("optimizationLevel: %u\n\n", bcWrapper.getOptimizationLevel());
}
llvm::OwningPtr<bcinfo::BitcodeTranslator> BT;
BT.reset(new bcinfo::BitcodeTranslator(bitcode, bitcodeSize, version));
if (!BT->translate()) {
fprintf(stderr, "failed to translate bitcode\n");
return 3;
}
llvm::OwningPtr<bcinfo::MetadataExtractor> ME;
ME.reset(new bcinfo::MetadataExtractor(BT->getTranslatedBitcode(),
BT->getTranslatedBitcodeSize()));
if (!ME->extract()) {
fprintf(stderr, "failed to get metadata\n");
return 4;
}
if (verbose) {
dumpMetadata(ME.get());
const char *translatedBitcode = BT->getTranslatedBitcode();
size_t translatedBitcodeSize = BT->getTranslatedBitcodeSize();
llvm::LLVMContext &ctx = llvm::getGlobalContext();
llvm::llvm_shutdown_obj called_on_exit;
llvm::OwningPtr<llvm::MemoryBuffer> mem;
mem.reset(llvm::MemoryBuffer::getMemBuffer(
llvm::StringRef(translatedBitcode, translatedBitcodeSize),
inFile.c_str(), false));
llvm::OwningPtr<llvm::Module> module;
std::string errmsg;
module.reset(llvm::ParseBitcodeFile(mem.get(), ctx, &errmsg));
if (module.get() != 0 && module->MaterializeAllPermanently(&errmsg)) {
module.reset();
}
if (module.get() == 0) {
if (errmsg.size()) {
fprintf(stderr, "error: %s\n", errmsg.c_str());
} else {
fprintf(stderr, "error: failed to parse bitcode file\n");
}
return 5;
}
llvm::OwningPtr<llvm::tool_output_file> tof(
new llvm::tool_output_file(outFile.c_str(), errmsg,
llvm::sys::fs::F_Binary));
llvm::OwningPtr<llvm::AssemblyAnnotationWriter> ann;
module->print(tof->os(), ann.get());
tof->keep();
}
if (infoFlag) {
if (dumpInfo(ME.get()) != 0) {
fprintf(stderr, "Error dumping info file\n");
return 6;
}
}
releaseBitcode(&bitcode);
return 0;
}
int init(CSOUND *csound) {
int result = OK;
#pragma omp critical (critical_section_fluid_engine)
{
fluid_synth_t *fluidSynth = 0;
fluid_settings_t *fluidSettings = 0;
chorusEnabled = (int) *iChorusEnabled;
reverbEnabled = (int) *iReverbEnabled;
channelCount = (int) *iChannelCount;
voiceCount = (int) *iVoiceCount;
if (channelCount <= 0) {
channelCount = 256;
} else if (channelCount < 16) {
channelCount = 16;
} else if (channelCount > 256) {
channelCount = 256;
}
if (voiceCount <= 0) {
voiceCount = 4096;
} else if (voiceCount < 16) {
voiceCount = 16;
} else if (voiceCount > 4096) {
voiceCount = 4096;
}
//csound_global_mutex_lock();
fluidSettings = new_fluid_settings();
if (fluidSettings != NULL) {
fluid_settings_setnum(fluidSettings,
(char *)"synth.sample-rate",
(double) csound->GetSr(csound));
fluid_settings_setint(fluidSettings,
(char *)"synth.midi-channels", channelCount);
fluid_settings_setint(fluidSettings,
(char *)"synth.polyphony", voiceCount);
fluidSynth = new_fluid_synth(fluidSettings);
}
//csound_global_mutex_unlock();
if (!fluidSynth) {
if (fluidSettings) {
delete_fluid_settings(fluidSettings);
}
result = csound->InitError(csound,
Str("error allocating fluid engine\n"));
} else {
//csound_global_mutex_lock();
fluid_synth_set_chorus_on(fluidSynth, chorusEnabled);
fluid_synth_set_reverb_on(fluidSynth, reverbEnabled);
//csound_global_mutex_unlock();
log(csound, "Created fluidEngine 0x%p with sampling rate = %f, "
"chorus %s, reverb %s, channels %d, voices %d.\n",
fluidSynth, (double) csound->GetSr(csound),
chorusEnabled ? "on" : "off",
reverbEnabled ? "on" : "off",
channelCount,
voiceCount);
tof(fluidSynth, iFluidSynth);
getFluidSynthsForCsoundInstances()[csound].push_back(fluidSynth);
}
}
return result;
}
void AlignChimeLocal3(const string &Q3, const string &A3, const string &B3,
const string &QLabel, const string &ALabel, const string &BLabel,
ChimeHit2 &Hit)
{
Hit.Clear();
const byte *Q3Seq = (const byte *) Q3.c_str();
const byte *A3Seq = (const byte *) A3.c_str();
const byte *B3Seq = (const byte *) B3.c_str();
const unsigned ColCount = SIZE(Q3);
asserta(SIZE(A3) == ColCount && SIZE(B3) == ColCount);
vector<float> ColScoresA(ColCount, 0.0f);
vector<float> ColScoresB(ColCount, 0.0f);
float ScoreN = -(float) opt_xn;
unsigned QL = 0;
for (unsigned Col = 0; Col < ColCount; ++Col)
{
char q = Q3Seq[Col];
char a = A3Seq[Col];
char b = B3Seq[Col];
if (!isgap(q))
++QL;
if (q == a && q == b && a == b)
continue;
if (isgap(q) || isgap(a) || isgap(b))
continue;
if (Col > 0 && (isgap(Q3Seq[Col-1]) || isgap(A3Seq[Col-1]) || isgap(B3Seq[Col-1])))
continue;
if (Col + 1 < ColCount && (isgap(Q3Seq[Col+1]) || isgap(A3Seq[Col+1]) || isgap(B3Seq[Col+1])))
continue;
if (q == a && q != b)
ColScoresA[Col] = 1;
else
ColScoresA[Col] = ScoreN;
if (q == b && q != a)
ColScoresB[Col] = 1;
else
ColScoresB[Col] = ScoreN;
}
vector<float> LVA(ColCount, 0.0f);
vector<float> LVB(ColCount, 0.0f);
LVA[0] = ColScoresA[0];
LVB[0] = ColScoresB[0];
for (unsigned Col = 1; Col < ColCount; ++Col)
{
LVA[Col] = max(LVA[Col-1], 0.0f) + ColScoresA[Col];
LVB[Col] = max(LVB[Col-1], 0.0f) + ColScoresB[Col];
}
vector<float> RVA(ColCount, 0.0f);
vector<float> RVB(ColCount, 0.0f);
RVA[ColCount-1] = ColScoresA[ColCount-1];
RVB[ColCount-1] = ColScoresB[ColCount-1];
for (int Col = ColCount-2; Col >= 0; --Col)
{
RVA[Col] = max(RVA[Col+1], 0.0f) + ColScoresA[Col];
RVB[Col] = max(RVB[Col+1], 0.0f) + ColScoresB[Col];
}
bool FirstA = true;
float MaxSum = 0.0;
unsigned ColX = UINT_MAX;
for (unsigned Col = 1; Col < ColCount-1; ++Col)
{
float Sum = LVA[Col] + RVB[Col+1];
if (Sum > MaxSum)
{
FirstA = true;
MaxSum = Sum;
ColX = Col;
}
}
for (unsigned Col = 1; Col < ColCount-1; ++Col)
{
float Sum = LVB[Col] + RVA[Col+1];
if (Sum > MaxSum)
{
FirstA = false;
MaxSum = Sum;
ColX = Col;
}
}
if (ColX == UINT_MAX)
return;
unsigned ColLo = UINT_MAX;
unsigned ColHi = UINT_MAX;
if (FirstA)
{
float Sum = 0.0f;
for (int Col = ColX; Col >= 0; --Col)
{
Sum += ColScoresA[Col];
if (Sum >= LVA[ColX])
{
ColLo = Col;
break;
}
}
asserta(Sum >= LVA[ColX]);
Sum = 0.0f;
for (unsigned Col = ColX+1; Col < ColCount; ++Col)
{
Sum += ColScoresB[Col];
if (Sum >= RVB[ColX])
{
ColHi = Col;
break;
}
}
asserta(Sum >= RVB[ColX]);
}
else
{
float Sum = 0.0f;
for (int Col = ColX; Col >= 0; --Col)
{
Sum += ColScoresB[Col];
if (Sum >= LVB[ColX])
{
ColLo = Col;
break;
}
}
asserta(Sum >= LVB[ColX]);
Sum = 0.0f;
for (unsigned Col = ColX+1; Col < ColCount; ++Col)
{
Sum += ColScoresA[Col];
if (Sum >= RVA[ColX])
{
ColHi = Col;
break;
}
}
asserta(Sum >= RVA[ColX]);
}
unsigned ColXHi = ColX;
for (unsigned Col = ColX + 1; Col < ColCount; ++Col)
{
char q = Q3Seq[Col];
char a = A3Seq[Col];
char b = B3Seq[Col];
if (q == a && q == b && !isgap(q))
ColXHi = Col;
else
break;
}
unsigned ColXLo = ColX;
for (int Col = (int) ColX - 1; Col >= 0; --Col)
{
char q = Q3Seq[Col];
char a = A3Seq[Col];
char b = B3Seq[Col];
if (q == a && q == b && !isgap(q))
ColXLo = Col;
else
break;
}
unsigned IdQA = 0;
unsigned IdQB = 0;
unsigned IdAB = 0;
unsigned NQA = 0;
unsigned NQB = 0;
unsigned NAB = 0;
for (unsigned Col = 0; Col < ColCount; ++Col)
{
char q = Q3Seq[Col];
char a = A3Seq[Col];
char b = B3Seq[Col];
if (!isgap(q) && !isgap(a))
{
++NQA;
if (q == a)
++IdQA;
}
if (!isgap(q) && !isgap(b))
{
++NQB;
if (q == b)
++IdQB;
}
if (!isgap(a) && !isgap(b))
{
++NAB;
if (a == b)
++IdAB;
}
}
Hit.PctIdQA = Pct(IdQA, NQA);
Hit.PctIdQB = Pct(IdQB, NQB);
Hit.PctIdAB = Pct(IdAB, NAB);
unsigned LIdQA = 0;
unsigned LIdQB = 0;
for (unsigned Col = ColLo; Col < ColXLo; ++Col)
{
char q = Q3Seq[Col];
char a = A3Seq[Col];
char b = B3Seq[Col];
if (!isgap(q) && !isgap(a))
{
if (q == a)
++LIdQA;
}
if (!isgap(q) && !isgap(b))
{
if (q == b)
++LIdQB;
}
}
unsigned RIdQA = 0;
unsigned RIdQB = 0;
for (unsigned Col = ColXHi+1; Col <= ColHi; ++Col)
{
char q = Q3Seq[Col];
char a = A3Seq[Col];
char b = B3Seq[Col];
if (!isgap(q) && !isgap(a))
{
if (q == a)
++RIdQA;
}
if (!isgap(q) && !isgap(b))
{
if (q == b)
++RIdQB;
}
}
unsigned IdDiffL = max(LIdQA, LIdQB) - min(LIdQA, LIdQB);
unsigned IdDiffR = max(RIdQA, RIdQB) - min(RIdQA, RIdQB);
unsigned MinIdDiff = min(IdDiffL, IdDiffR);
unsigned ColRange = ColHi - ColLo + 1;
if (opt_queryfract > 0.0f && float(ColRange)/float(QL) < opt_queryfract)
return;
// double Div = Pct(MinIdDiff, QSD.L);
#if TRACE
{
Log(" Col A Q B ScoreA ScoreB LVA LVB RVA RVB\n");
Log("----- - - - ------- ------- ------- ------- ------- -------\n");
for (unsigned Col = 0; Col < ColCount; ++Col)
{
if (ColScoresA[Col] == 0.0 && ColScoresB[Col] == 0.0)
continue;
char q = Q3Seq[Col];
char a = A3Seq[Col];
char b = B3Seq[Col];
Log("%5u %c %c %c", Col, a, q, b);
if (ColScoresA[Col] == 0.0)
Log(" %7.7s", "");
else
Log(" %7.1f", ColScoresA[Col]);
if (ColScoresB[Col] == 0.0)
Log(" %7.7s", "");
else
Log(" %7.1f", ColScoresB[Col]);
Log(" %7.1f %7.1f %7.1f %7.1f", LVA[Col], LVB[Col], RVA[Col], RVB[Col]);
Log("\n");
}
Log("\n");
Log("MaxSum %.1f, ColLo %u, ColXLo %u, ColX %u, ColXHi %u, ColHi %u, AF %c\n",
MaxSum, ColLo, ColXLo, ColX, ColXHi, ColHi, tof(FirstA));
Log(" LIdQA %u, LIdQB %u, RIdQA %u, RIdQB %u\n", LIdQA, LIdQB, RIdQA, RIdQB);
}
#endif
string Q3L;
string A3L;
string B3L;
for (unsigned Col = ColLo; Col <= ColHi; ++Col)
{
char q = Q3[Col];
char a = A3[Col];
char b = B3[Col];
Q3L += q;
A3L += a;
B3L += b;
}
AlignChimeGlobal3(Q3L, A3L, B3L, QLabel, ALabel, BLabel, Hit);
#if 0
// CS SNPs
Hit.CS_LY = 0;
Hit.CS_LN = 0;
Hit.CS_RY = 0;
Hit.CS_RN = 0;
Hit.CS_LA = 0;
Hit.CS_RA = 0;
for (unsigned Col = ColLo; Col <= ColHi; ++Col)
{
char q = Q3Seq[Col];
char a = A3Seq[Col];
char b = B3Seq[Col];
if (q == a && q == b && a == b)
continue;
if (isgap(q) || isgap(a) || isgap(b))
continue;
if (Col > 0 && (isgap(Q3Seq[Col-1]) || isgap(A3Seq[Col-1]) || isgap(B3Seq[Col-1])))
continue;
if (Col + 1 < ColCount && (isgap(Q3Seq[Col+1]) || isgap(A3Seq[Col+1]) || isgap(B3Seq[Col+1])))
continue;
if (!FirstA)
swap(a, b);
if (Col < ColXLo)
{
if (q == a && q != b)
++Hit.CS_LY;
else if (q == b && q != a)
++Hit.CS_LN;
else
++Hit.CS_LA;
}
else if (Col > ColXHi)
{
if (q == b && q != a)
++Hit.CS_RY;
else if (q == a && q != b)
++Hit.CS_RN;
else
++Hit.CS_RA;
}
}
double ScoreL = GetScore2(Hit.CS_LY, Hit.CS_LN, Hit.CS_LA);
double ScoreR = GetScore2(Hit.CS_RY, Hit.CS_RN, Hit.CS_RA);
Hit.Score = ScoreL*ScoreR;
//Hit.QSD = QSD;
//if (FirstA)
// {
// Hit.ASD = ASD;
// Hit.BSD = BSD;
// Hit.PathQA = PathQA;
// Hit.PathQB = PathQB;
// }
//else
// {
// Hit.ASD = BSD;
// Hit.BSD = ASD;
// }
//Hit.ColLo = ColLo;
//Hit.ColXLo = ColXLo;
//Hit.ColXHi = ColXHi;
//Hit.ColHi = ColHi;
//Hit.Div = Div;
// Hit.LogMe();
#endif
}
