void ModelBaker::exportScene() {
auto fbxData = FBXWriter::encodeFBX(_rootNode);
QString bakedModelURL = _bakedModelURL.toString();
QFile bakedFile(bakedModelURL);
if (!bakedFile.open(QIODevice::WriteOnly)) {
handleError("Error opening " + bakedModelURL + " for writing");
return;
}
bakedFile.write(fbxData);
_outputFiles.push_back(bakedModelURL);
#ifdef HIFI_DUMP_FBX
{
FBXToJSON fbxToJSON;
fbxToJSON << _rootNode;
QFileInfo modelFile(_bakedModelURL.toString());
QString outFilename(modelFile.dir().absolutePath() + "/" + modelFile.completeBaseName() + "_FBX.json");
QFile jsonFile(outFilename);
if (jsonFile.open(QIODevice::WriteOnly)) {
jsonFile.write(fbxToJSON.str().c_str(), fbxToJSON.str().length());
jsonFile.close();
}
}
#endif
qCDebug(model_baking) << "Exported" << _modelURL << "with re-written paths to" << bakedModelURL;
}
void HHRImpl::write2Json() {
string outFilename(outputFileLocation);
outFilename += rootName;
outFilename += "/HHR/";
outFilename += "hhr.json";
//cout << outFilename << endl;
ofstream outputFile(outFilename.c_str());
outputFile << "{" << "\n";
for (int i = 0; i < hhrResultVector.size(); i++) {
outputFile << "\"protein" << i << "\":{\n";
outputFile << "\t\"proteinName\":\""
<< hhrResultVector[i].getProteinName() << "\",\n";
outputFile << "\t\"probab\":\"" << hhrResultVector[i].getProbab()
<< "\",\n";
outputFile << "\t\"OriginalSequenceLength\":\"" << proteinSeqLength
<< "\",\n";
outputFile << "\t\"eValue\":\"" << hhrResultVector[i].getExpect()
<< "\",\n";
outputFile << "\t\"score\":\"" << hhrResultVector[i].getScore()
<< "\",\n";
outputFile << "\t\"alignedCols\":\""
<< hhrResultVector[i].getAlignedCols() << "\",\n";
outputFile << "\t\"identities\":\""
<< hhrResultVector[i].getIdentities() << "\",\n";
outputFile << "\t\"QueryStart\":\""
<< hhrResultVector[i].getQueryStart() << "\",\n";
outputFile << "\t\"Query\":\"" << hhrResultVector[i].getQuery()
<< "\",\n";
outputFile << "\t\"QueryEnd\":\"" << hhrResultVector[i].getQueryEnd()
<< "\",\n";
outputFile << "\t\"QueryConsensus\":\""
<< hhrResultVector[i].getQueryConsensus() << "\",\n";
outputFile << "\t\"alignment\":\"" << hhrResultVector[i].getAlignment()
<< "\",\n";
outputFile << "\t\"TargetStart\":\""
<< hhrResultVector[i].getTargetStart() << "\",\n";
outputFile << "\t\"TargetConsensus\":\""
<< hhrResultVector[i].getTargetConsensus() << "\",\n";
outputFile << "\t\"TargetEnd\":\"" << hhrResultVector[i].getTargetEnd()
<< "\",\n";
outputFile << "\t\"target\":\"" << hhrResultVector[i].getTarget()
<< "\",\n";
outputFile << "\t\"targetConf\":\""
<< hhrResultVector[i].getConfidence() << "\",\n";
outputFile << "\t\"tPred\":\"" << hhrResultVector[i].getTargetSsPred()
<< "\"\n";
outputFile << "},\n";
}
outputFile << "\"finish\":\"end\"" << "\n";
outputFile << "}" << "\n";
outputFile.close();
}
void BLAPDBImpl::write2Json() {
string outFilename(outputFileLocation);
outFilename += rootName;
outFilename += "/BLAPDB/";
outFilename += "blaPDB.json";
//cout<<outFilename<<endl;
ofstream outputFile(outFilename.c_str());
outputFile << "{" << "\n";
for (int i = 0; i < blaPDBResultVector.size(); i++) {
outputFile << "\"protein" << i << "\":{\n";
outputFile << "\t\"proteinName\":\""
<< blaPDBResultVector[i].getProteinName() << "\",\n";
outputFile << "\t\"OriginalSequenceLength\":\"" << proteinSeqLength
<< "\",\n";
outputFile << "\t\"Length\":\"" << blaPDBResultVector[i].getLength()
<< "\",\n";
outputFile << "\t\"Score\":\"" << blaPDBResultVector[i].getScore()
<< "\",\n";
outputFile << "\t\"Expect\":\"" << blaPDBResultVector[i].getExpect()
<< "\",\n";
outputFile << "\t\"Identities\":\""
<< blaPDBResultVector[i].getIdentities() << "%\",\n";
outputFile << "\t\"Positives\":\""
<< blaPDBResultVector[i].getPositives() << "%\",\n";
outputFile << "\t\"Gaps\":\"" << blaPDBResultVector[i].getGaps()
<< "%\",\n";
outputFile << "\t\"CoveragePercentage\":\""
<< double((blaPDBResultVector[i].getSubjectEnd()
- blaPDBResultVector[i].getSubjectStart() + 1
- blaPDBResultVector[i].getGapNum()))
/ (proteinSeqLength) << "%\",\n";
outputFile << "\t\"QueyStart\":\""
<< blaPDBResultVector[i].getQueryStart() << "\",\n";
outputFile << "\t\"Query\":\"" << blaPDBResultVector[i].getQuery()
<< "\",\n";
outputFile << "\t\"QueryEnd\":\"" << blaPDBResultVector[i].getQueryEnd()
<< "\",\n";
outputFile << "\t\"Alignment\":\""
<< blaPDBResultVector[i].getAlignment() << "\",\n";
outputFile << "\t\"SubjectStart\":\""
<< blaPDBResultVector[i].getSubjectStart() << "\",\n";
outputFile << "\t\"Subject\":\"" << blaPDBResultVector[i].getSubject()
<< "\",\n";
outputFile << "\t\"SubjectEnd\":\""
<< blaPDBResultVector[i].getSubjectEnd() << "\"\n";
outputFile << "},\n";
}
outputFile << "\"finish\":\"end\"" << "\n";
outputFile << "}" << "\n";
outputFile.close();
}
// Main function (driver).
int main(int argc, char **argv) {
if (argc !=3) {
std::cerr << "# Usage: <execution filename> <input filename> ";
std::cerr << "<output filename> \n";
std::cerr << " Example: $ a.out in.csv out.csv\n";
std::exit(1);
};
// Filenames for input and output csv files.
// (input: puzzle, output: solution)
string inFilename(argv[1]), outFilename(argv[2]);
const short size = 9; // The given size of the board of Sudoku.
try {
// Create a (size x size) sodoku puzzle (default: 9x9).
Sudoku3 puzzle;
cout << "* Created " << size << 'x' << size \
<< " Sodoku puzzle." << endl;
// Reading the file.
cout << "* Reading the input file, " << inFilename << endl;
puzzle.read(inFilename);
cout << "* Solving..." << endl;
if (puzzle.solve()) {
cout << "* Solved, and writing to the output file, " \
<< outFilename << endl;
puzzle.write(outFilename);
}
else
cout << "* Unsolvable puzzle. Nothing is written." << endl;
}
catch(BadSize e) {
std::cerr << "* Bad size of the board (grid) is given.\n";
std::exit(1);
}
catch(BadInput e) {
std::cerr << "* Bad input is given.\n";
std::exit(1);
}
catch(BadValue e) {
std::cerr << "* Bad value is given in the input.\n";
std::exit(1);
}
catch(NoInputFile e) {
std::cerr << "* File, " << inFilename << ", does not exist.\n";
std::exit(1);
}
catch(InvalidPuzzle e) {
std::cerr << "* Given puzzle is invalid.\n";
std::cerr << " Causes: (1) Any given value is not following" \
<< " the rule, or (2) any given value is not in the" \
<< " range.\n";
std::exit(1);
};
return 0;
};
void HHRNR2Json::writeAlignmentResults2JsonFile() {
string outFilename(outputFileLocation);
outFilename += outputJsonFilename;
ofstream outputFile(outFilename.c_str());
outputFile << "{" << "\n";
for (int i = 0; i < HHRNRResultVector.size(); i++) {
outputFile << "\"protein" << i << "\":{\n";
outputFile << "\t\"proteinName\":\""
<< HHRNRResultVector[i].getProteinName() << "\",\n";
outputFile << "\t\"probab\":\"" << HHRNRResultVector[i].getProbab()
<< "\",\n";
outputFile << "\t\"eValue\":\"" << HHRNRResultVector[i].getExpect()
<< "\",\n";
outputFile << "\t\"score\":\"" << HHRNRResultVector[i].getScore()
<< "\",\n";
outputFile << "\t\"alignedCols\":\""
<< HHRNRResultVector[i].getAlignedCols() << "\",\n";
outputFile << "\t\"identities\":\""
<< HHRNRResultVector[i].getIdentities() << "\",\n";
outputFile << "\t\"similarity\":\""
<< HHRNRResultVector[i].getSimilarities() << "\",\n";
outputFile << "\t\"sumProbs\":\"" << HHRNRResultVector[i].getSumProbs()
<< "\",\n";
outputFile << "\t\"QuerySSPred\":\""
<< HHRNRResultVector[i].getQuerySsPred() << "\",\n";
outputFile << "\t\"QueryStart\":\""
<< HHRNRResultVector[i].getQueryStart() << "\",\n";
outputFile << "\t\"Query\":\"" << HHRNRResultVector[i].getQuery()
<< "\",\n";
outputFile << "\t\"QueryEnd\":\"" << HHRNRResultVector[i].getQueryEnd()
<< "\",\n";
outputFile << "\t\"QueryConsensus\":\""
<< HHRNRResultVector[i].getQueryConsensus() << "\",\n";
outputFile << "\t\"alignment\":\""
<< HHRNRResultVector[i].getAlignment() << "\",\n";
outputFile << "\t\"TargetStart\":\""
<< HHRNRResultVector[i].getTargetStart() << "\",\n";
outputFile << "\t\"TargetConsensus\":\""
<< HHRNRResultVector[i].getTargetConsensus() << "\",\n";
outputFile << "\t\"TargetEnd\":\""
<< HHRNRResultVector[i].getTargetEnd() << "\",\n";
outputFile << "\t\"target\":\"" << HHRNRResultVector[i].getTarget()
<< "\",\n";
outputFile << "\t\"tPred\":\"" << HHRNRResultVector[i].getTargetSsPred()
<< "\"\n";
outputFile << "},\n";
}
outputFile << "\"finish\":\"end\"" << "\n";
outputFile << "}" << "\n";
outputFile.close();
}
void BLANR2Json::writeAlignmentResults2JsonFile() {
string outFilename(outputFileLocation);
outFilename += outputJsonFilename;
ofstream outputFile(outFilename.c_str());
outputFile << "{" << "\n";
for (int i = 0; i < BLANRResultVector.size(); i++) {
outputFile << "\"protein" << i << "\":{\n";
outputFile << "\t\"proteinName\":\""
<< BLANRResultVector[i].getProteinName() << "\",\n";
outputFile << "\t\"Length\":\"" << BLANRResultVector[i].getLength()
<< "\",\n";
outputFile << "\t\"Score\":\"" << BLANRResultVector[i].getScore()
<< "\",\n";
outputFile << "\t\"Expect\":\"" << BLANRResultVector[i].getExpect()
<< "\",\n";
outputFile << "\t\"Identities\":\""
<< BLANRResultVector[i].getIdentities() << "\",\n";
outputFile << "\t\"Positives\":\""
<< BLANRResultVector[i].getPositives() << "\",\n";
outputFile << "\t\"Gaps\":\"" << BLANRResultVector[i].getGaps()
<< "\",\n";
outputFile << "\t\"QueyStart\":\""
<< BLANRResultVector[i].getQueryStart() << "\",\n";
outputFile << "\t\"Query\":\"" << BLANRResultVector[i].getQuery()
<< "\",\n";
outputFile << "\t\"QueryEnd\":\"" << BLANRResultVector[i].getQueryEnd()
<< "\",\n";
outputFile << "\t\"Alignment\":\""
<< BLANRResultVector[i].getAlignment() << "\",\n";
outputFile << "\t\"SubjectStart\":\""
<< BLANRResultVector[i].getSubjectStart() << "\",\n";
outputFile << "\t\"Subject\":\"" << BLANRResultVector[i].getSubject()
<< "\",\n";
outputFile << "\t\"SubjectEnd\":\""
<< BLANRResultVector[i].getSubjectEnd() << "\"\n";
outputFile << "},\n";
}
outputFile << "\"finish\":\"end\"" << "\n";
outputFile << "}" << "\n";
outputFile.close();
}
void ModelBaker::exportScene() {
// save the relative path to this FBX inside our passed output folder
auto fileName = _modelURL.fileName();
auto baseName = fileName.left(fileName.lastIndexOf('.'));
auto bakedFilename = baseName + BAKED_FBX_EXTENSION;
_bakedModelFilePath = _bakedOutputDir + "/" + bakedFilename;
auto fbxData = FBXWriter::encodeFBX(_rootNode);
QFile bakedFile(_bakedModelFilePath);
if (!bakedFile.open(QIODevice::WriteOnly)) {
handleError("Error opening " + _bakedModelFilePath + " for writing");
return;
}
bakedFile.write(fbxData);
_outputFiles.push_back(_bakedModelFilePath);
#ifdef HIFI_DUMP_FBX
{
FBXToJSON fbxToJSON;
fbxToJSON << _rootNode;
QFileInfo modelFile(_bakedModelFilePath);
QString outFilename(modelFile.dir().absolutePath() + "/" + modelFile.completeBaseName() + "_FBX.json");
QFile jsonFile(outFilename);
if (jsonFile.open(QIODevice::WriteOnly)) {
jsonFile.write(fbxToJSON.str().c_str(), fbxToJSON.str().length());
jsonFile.close();
}
}
#endif
qCDebug(model_baking) << "Exported" << _modelURL << "with re-written paths to" << _bakedModelFilePath;
}
//==============================================================================
// InitializeReporting PUBLIC STATIC
//==============================================================================
//
OSCL_EXPORT_REF void
UT::CM::InitializeReporting
(
const char* a_pszTestname,
OSCL_HeapString<OsclMemAllocator>& a_filename,
FILE* a_pFileStreamParent,
FILE*& a_pFileStreamChild
)
{
a_pFileStreamChild = a_pFileStreamParent;
if (0 == a_pszTestname || 0 >= a_filename.get_size() || 0 == a_pFileStreamParent)
return;
Oscl_FileServer fs;
fs.Connect();
Oscl_File f;
if (0 == f.Open(a_filename.get_cstr(), Oscl_File::MODE_READWRITE | Oscl_File::MODE_TEXT, fs))
{
_STRING xfr = xml_test_interpreter::unexpected_termination_interpretation(a_pszTestname);
f.Write(xfr.c_str(), sizeof(char), oscl_strlen(xfr.c_str()));
f.Close();
}
else
{
fprintf(a_pFileStreamParent, "ERROR: Failed to open XML test summary log file (%s).\n", a_filename.get_cstr());
}
fs.Close();
OSCL_HeapString<OsclMemAllocator> outFilename(a_filename);
outFilename += ".out";
// open a new stream to file and return it to client
a_pFileStreamChild = fopen(outFilename.get_cstr(), "w");
}
//==============================================================================
// FinalizeReporting PUBLIC STATIC
//==============================================================================
//
OSCL_EXPORT_REF void
UT::CM::FinalizeReporting
(
const char* a_pszTestname,
OSCL_HeapString<OsclMemAllocator> &a_filename,
const test_result& a_tr,
FILE* a_pFileStreamParent,
FILE* a_pFileStreamChild
)
{
if (0 == a_pFileStreamChild)
return;
// report the textual representation of the test results
text_test_interpreter interp;
_STRING rs = interp.interpretation(a_tr);
fprintf(a_pFileStreamChild, "%s", rs.c_str());
if (0 == a_pszTestname || 0 >= a_filename.get_size() || 0 == a_pFileStreamParent)
return;
_STRING strChild;
fclose(a_pFileStreamChild); // close the stream
OSCL_HeapString<OsclMemAllocator> outFilename(a_filename);
outFilename += ".out";
FILE* pFile = fopen(outFilename.get_cstr(), "rb");
if (0 == pFile)
fprintf(a_pFileStreamParent, "ERROR: Failed to open file (%s) for capturing test output!\n", outFilename.get_cstr());
else
{
fseek(pFile, 0, SEEK_END);
long lSize = ftell(pFile);
rewind(pFile);
char* buffer = new char[lSize];
fread(buffer, 1, lSize, pFile);
strChild = _STRING(buffer, lSize);
fprintf(a_pFileStreamParent, "%s", strChild.c_str()); // send the captured output back out the parent stream
delete [] buffer;
fclose(pFile);
}
Oscl_FileServer fs;
fs.Connect();
Oscl_File f;
if (0 == f.Open(a_filename.get_str(), Oscl_File::MODE_READWRITE | Oscl_File::MODE_TEXT, fs))
{
_STRING xfr = xml_test_interpreter::interpretation(a_tr, a_pszTestname, &strChild);
fprintf(a_pFileStreamParent, "\nWrote xml-formatted test results to file: %s\n", a_filename.get_cstr());
f.Write(xfr.c_str(), sizeof(char), oscl_strlen(xfr.c_str()));
f.Close();
}
else
{
fprintf(a_pFileStreamParent, "\nERROR: Failed to open file (%s) for xml-formatted test results\n", a_filename.get_cstr());
}
fs.Close();
}
