bool IO_UncertSimResults::ReadUncertResults(DC_UncertSimResults& results)
{
try
{
ReadFileHeader(results, true);
ReadNextRecord();
ReadInt(); // skip next rec
SC_IntArray runStartRecs;
ReadIntArray(runStartRecs);
results.AllocAndSetSize(runStartRecs.Size());
for (int i = 0; i < results.Size(); i++)
{
ReadAbsolute(runStartRecs[i]);
ReadOneRun(results[i]);
}
CloseFile();
return true;
}
catch (BufFileC::BufferFileError& err) {
GenAppErrorMsg("ReadUncertResults", err.errMsg);
CloseFile();
}
return false;
}
uint64 FastqParser::ParseFrom(const FastqDataChunk& chunk_, std::vector<FastqRecord>& records_, uint64& rec_count_)
{
ASSERT(buffer == NULL);
memory = (byte*)chunk_.data.Pointer();
memoryPos = 0;
memorySize = chunk_.size;
rec_count_ = 0;
while (memoryPos < memorySize && ReadNextRecord(records_[rec_count_]))
{
rec_count_++;
if (records_.size() < rec_count_ + 1)
records_.resize(records_.size() + REC_EXTENSION_FACTOR(records_.size()));
}
ASSERT(rec_count_ > 0);
return chunk_.size - skippedBytes;
}
void IO_ProfileSimResults::ReadOneRun(ProfileSimRunResults& runRes)
{
ReadString(runRes.runID, ProfileSimRunResults::runIDLen);
ReadStringArray(runRes.caseValDesc);
ReadStringArray(runRes.caseValShortDesc);
ReadStringArray(runRes.caseSeqData.sequenceIDs);
ReadDoubleArray(runRes.caseSeqData.sequenceStartTimes);
// next record contains case start records
ReadNextRecord();
SC_IntArray caseStartRecs;
ReadIntArray(caseStartRecs);
runRes.AllocAndSetSize(caseStartRecs.Size());
// individual case results
for (int i = 0; i < runRes.Size(); i++)
{
ReadAbsolute(caseStartRecs[i]);
ReadOneCase(runRes[i]);
}
}
uint64 FastqParserExt::ParseFrom(const FastqDataChunk &chunk_, std::vector<FastqRecord> &records_, uint64 &rec_count_, uint64 tagPreserveFlags_)
{
ASSERT(buffer == NULL);
ASSERT(tagPreserveFlags_ != 0);
uchar tagBuffer[MaxTagBufferSize];
totalBytesCut = 0;
memory = (byte*)chunk_.data.Pointer();
memoryPos = 0;
memorySize = chunk_.size;
rec_count_ = 0;
while (memoryPos < memorySize && ReadNextRecord(records_[rec_count_], tagBuffer, tagPreserveFlags_))
{
rec_count_++;
if (records_.size() < rec_count_ + 1)
records_.resize(records_.size() + REC_EXTENSION_FACTOR(records_.size()));
}
ASSERT(rec_count_ > 0);
ASSERT(chunk_.size >= totalBytesCut + skippedBytes);
return chunk_.size - totalBytesCut - skippedBytes;
}
bool IO_UncertSimResults::AddUncertRun(const DC_UncertSimResults& resultHeader,
const UncertRunResults& results,
bool addExisting)
{
GenAppClearMsgs();
bool openExisting = addExisting && ConvFileC::CFfileExists(fileName);
DC_UncertSimResults currHeader;
if (openExisting)
{
if (!ReadFileHeader(currHeader, false))
{
GenAppErrorMsg("UncertSimResults", "File contents incompatible");
return false;
}
if ((currHeader.IsMultiple() && (!resultHeader.IsMultiple())) ||
((!currHeader.IsMultiple()) && resultHeader.IsMultiple()))
{
GenAppErrorMsg("UncertSimResults", "Cannot combine multiple & not multiple");
return false;
}
if (currHeader.IsMultiple())
{
if (currHeader.multipleRunVariableIDs.Size() != resultHeader.multipleRunVariableIDs.Size())
GenAppErrorMsg("UncertSimResults", "Multiple run results different size??");
}
}
try
{
SC_IntArray runStartRecs;
runStartRecs.SetResizable();
int nextRec, runIndexRecord;
if (openExisting)
{
ReadFileHeader(currHeader, true);
ReadNextRecord();
runIndexRecord = GetCurrentRec();
nextRec = ReadInt();
ReadIntArray(runStartRecs);
}
else
{
OpenFile(fileName, false);
// set up initial header info
nRuns = 0;
WriteFileHeader(resultHeader);
FlushBuffer(nextRec);
runIndexRecord = nextRec;
// initial header
BufferReset(nextRec);
WriteInt(0);
FlushBuffer(nextRec);
// backup and set nextRec
BufferReset(runIndexRecord);
WriteInt(nextRec);
// reflush
FlushBuffer();
}
int runStart = nextRec;
// set to next avail
BufferReset(nextRec);
// add the run to the end
WriteOneRun(results, nextRec);
nRuns++;
// update header
BufferReset(0);
WriteFileHeader(resultHeader);
FlushBuffer();
// update next avail record
BufferReset(runIndexRecord);
WriteInt(nextRec);
// update run start records
runStartRecs += runStart;
WriteIntArray(runStartRecs);
FlushBuffer();
CloseFile();
return true;
}
catch (BufFileC::BufferFileError& err) {
GenAppErrorMsg("WriteUncertResults", err.errMsg);
}
CloseFile();
return false;
}
/*===========================================================================
* ReadContinuousLogData
*---------------------------------------------------------------------------
* Description: Puts the node in continuous mode, reads the sensor data and
* prints to the screen and logs data to user file until the user
* interrupts.
*
* Return: HANDLE - handle to the opened comport
*===========================================================================*/
void ReadContinuousLogData(int portNum)
{
int iCount = 0;
BOOL bStopContinuous = FALSE;
DWORD dwcharsRead = 0;
I3dmgx3Set Record;
BYTE cmd_return;
int Curs_posY = 0;
int Curs_posX = 0;
int status = 0;
int error_record = 0;
int valid_check = 0;
int valid_count = 0;
char consoleBuff[60] = {0};
long valid_rec = 0;
unsigned char error_cmd;
char ComLogFile[256];
FILE *m_logFile;
int LogFlag = 0;
int error_count = 0;
int errorCode =0, i=0;
char fw[20] = {0};
char sn[20] = {0};
char mListSep[4];
char mDecSep[4];
LANGID langId;
char szLanguage[256]; /*MAX_PATH]; */
char idchar[] = {'\x02', '\x00', '\x01', '\x03', '\x04'};
int m_timerconst = 62500;
unsigned long AA_Time_Stamp=0;
unsigned long AA_s_prev =0;
float AA_convert = 0.0;
float AA_prev = 0.0;
struct __timeb64 timebuffer;
char *timeline;
_ftime64( &timebuffer );
timeline = _ctime64( & ( timebuffer.time ) );
while (LogFlag != 1){
printf("Enter Name of LogFile to use:");
scanf("%s", &ComLogFile); // 255);
printf("logFile %s\n", ComLogFile);
if ( ( m_logFile= fopen( ComLogFile, "w")) == NULL){
printf("File: %s not opened\n", ComLogFile);
if(++error_count > 2)
return;
}else LogFlag = 1;
}
fprintf(m_logFile, "[SESSION START TAG]\n");
fprintf(m_logFile, "Session Start Time:%.19s.%hu \n", timeline, timebuffer.millitm );
fprintf(m_logFile, "Time Source: HOST\n");
GetLocaleInfo(LOCALE_SYSTEM_DEFAULT,LOCALE_SLIST,mListSep,4);
fprintf(m_logFile, "List Separator: %s\n", mListSep);
GetLocaleInfo(LOCALE_SYSTEM_DEFAULT,LOCALE_SDECIMAL,mDecSep,4);
fprintf(m_logFile, "Decimal Separator: %s\n", mDecSep);
langId = GetSystemDefaultLangID ();
i = VerLanguageName (langId, szLanguage, 256); //dwSize = MAX_PATH;
fprintf(m_logFile, "Language: %s\n", szLanguage);
while(valid_check == 0)
{
errorCode = i3dmgx3_getFirmwareVersion(portNum, &fw[0]);
if (errorCode < 0){
purge_port(portNum);
printf("Firmware Error %d\n",errorCode);
if (valid_count++ > 6) {
printf("Please Halt Current Data Display and Retry, count %d\n", valid_count);
return;
}
}else if (errorCode >= 0){
valid_check = 1;
}
}
/*------------------------------------------------------------------
* 0xEA get serial information number, model and options (as string)
*-----------------------------------------------------------------*/
valid_count =0;
for ( i=0; i<4; i++){ //cycles through the valid device options
errorCode = i3dmgx3_getDeviceIdentiy(portNum, idchar[i], &sn[0]);
if (errorCode < 0){
purge_port(portNum);
i--;
if (valid_count++ >6){
printf("Error Read Device Identity: %s\n", explainError(errorCode));
}
} else{
switch( i ) {
case 0:
fprintf(m_logFile, "Device Name: %s\n",sn);
break;
case 1:
fprintf(m_logFile, "Device Model: %s\n",sn);
break;
case 2:
fprintf(m_logFile, "Device FirmWare Version: %s\n", fw);
fprintf(m_logFile, "Device Serial Number: %s\n", sn);
break;
case 3:
fprintf(m_logFile, "Device Options: %s\n", sn);
break;
case 4:
default:
break;
}
}
}
fprintf(m_logFile, "Command C2\n[DATA START TAG]\n\t Time%s Accel X%s Accel Y%s Accel Z%s AngRate X%s AngRate Y%s AngRate Z%s Ticks\n", mListSep, mListSep, mListSep, mListSep, mListSep, mListSep, mListSep);
//put the node in continuous mode
status =SetContinuousMode(portNum, 0xC2);
printf("setcontinuous is %d", status);
//set up the output for the data
printf("\n\n");
printf("Reading streaming data (hit s to Stop streaming).\n");
printf("C2___________________________Acceleration_______________________________\n");
printf(" X Y Z \n");
/* acceleration values go here */
printf("\n\n\n");
printf("C2____________________________Angular_Rate______________________________\n");
printf(" X Y Z \n");
/* angle rate values go here */
getConXY(&Curs_posX, &Curs_posY);
printf("\n\n\n\n");
//continue until the user hits the <s>top key
while(!bStopContinuous)
{
if(ReadNextRecord(portNum, &Record, &cmd_return) != SUCCESS)
error_record++;
if (cmd_return == 0xC2){
if (AA_s_prev == 0){
fprintf(m_logFile, "\t 0.00");
AA_s_prev = Record.timer; //AA_Time_Stamp;
}
else
{
AA_convert = ((float)(Record.timer - AA_s_prev)/m_timerconst); //19660800);
AA_s_prev = Record.timer; //AA_Time_Stamp;
AA_prev = AA_prev + AA_convert;
fprintf(m_logFile, "\t%6.2f", AA_prev);
}
//move to the acceleration position and print the data
sprintf(consoleBuff, "\t%2.6f\t\t%2.6f\t\t%2.6f", Record.setA[0], Record.setA[1], Record.setA[2]);
fprintf(m_logFile, "%s %2.6f%s %2.6f%s %2.6f%s ", mListSep, Record.setA[0],mListSep, Record.setA[1], mListSep, Record.setA[2], mListSep);
setConXY(Curs_posX, Curs_posY -5, &consoleBuff[0]);
sprintf(consoleBuff, "\t%2.6f\t\t%2.6f\t\t%2.6f", Record.setB[0], Record.setB[1], Record.setB[2]);
fprintf(m_logFile, "%2.6f%s %2.6f%s %2.6f%s %u\n", Record.setB[0], mListSep, Record.setB[1], mListSep, Record.setB[2], mListSep, Record.timer);
setConXY(Curs_posX, Curs_posY, &consoleBuff[0]);
valid_rec++;
}else if (cmd_return != 0xc4){
if((cmd_return == 0xCB || cmd_return == 0xD3) && error_record == 0)
error_cmd = cmd_return;
else
error_record++;
}
//check for a key every 50 iterations
if(iCount++ > 50) {
int ch = 0;
if(ReadCharNoReturn(&ch)){
bStopContinuous = (ch == 's' || ch == 'S');
}
//reset the counter
iCount = 0;
}
}
printf("\n\n\nStopping Continuous Mode...");
StopContinuousMode(portNum);
printf("stopped.\n");
fclose(m_logFile);
if (error_record > 0)
printf("Number of records received in error were %d and received successfully %d\n", error_record, valid_rec);
else
printf("All %d records read successfully.\n", valid_rec);
}
/*===========================================================================
* ReadContinuousData
*---------------------------------------------------------------------------
* Description: Puts the node in continuous mode, reads the sensor data and
* prints to the screen until the user interrupts.
*
* Return: HANDLE - handle to the opened comport
*===========================================================================*/
void ReadContinuousData(int portNum)
{
int iCount = 0;
BOOL bStopContinuous = FALSE;
DWORD dwcharsRead = 0;
I3dmgx3Set Record;
BYTE cmd_return;
int Curs_posY = 0;
int Curs_posX = 0;
int status = 0;
int error_record = 0;
char consoleBuff[60] = {0};
long valid_rec = 0;
unsigned char error_cmd;
//put the node in continuous mode
status =SetContinuousMode(portNum, 0xC2);
printf("setcontinuous is %d", status);
//set up the output for the data
printf("\n\n");
printf("Reading streaming data (hit s to Stop streaming).\n");
printf("C2___________________________Acceleration_______________________________\n");
printf(" X Y Z \n");
/* acceleration values go here, save the position */
printf("\n\n\n");
printf("C2____________________________Angular_Rate______________________________\n");
printf(" X Y Z \n");
/* angle rate values go here, save the position */
getConXY(&Curs_posX, &Curs_posY);
printf("\n\n\n\n");
//continue until the user hits the s key
while(!bStopContinuous)
{
if(ReadNextRecord(portNum, &Record, &cmd_return) != SUCCESS)
error_record++;
if (cmd_return == 0xC2){
//move to the acceleration position and print the data
sprintf(consoleBuff, "\t%2.6f\t\t%2.6f\t\t%2.6f", Record.setA[0], Record.setA[1], Record.setA[2]);
setConXY(Curs_posX, Curs_posY -5, &consoleBuff[0]);
sprintf(consoleBuff, "\t%2.6f\t\t%2.6f\t\t%2.6f", Record.setB[0], Record.setB[1], Record.setB[2]);
setConXY(Curs_posX, Curs_posY, &consoleBuff[0]);
valid_rec++;
}else if (cmd_return != 0xC4){
if((cmd_return == 0xCB || cmd_return == 0xD3) && error_record == 0)
error_cmd = cmd_return;
else
error_record++;
}
//check for a key every 50 iterations
if(iCount++ > 50) {
int ch = 0;
if(ReadCharNoReturn(&ch)){
bStopContinuous = (ch == 's' || ch == 'S');
}
//reset the counter
iCount = 0;
}
}
printf("\n\n\nStopping Continuous Mode...");
StopContinuousMode(portNum);
printf("stopped.\n");
if (error_record > 0)
printf("Number of records received in error were %d and received successfully %d\n", error_record, valid_rec);
else
printf("All %d records read successfully.\n", valid_rec);
}
bool IO_ProfileSimResults::AddSimRun(const ProfileSimRunResults& results,
bool addExisting)
{
GenAppClearMsgs();
bool fileOK = addExisting && ReadFileHeader(false);
try
{
SC_IntArray runStartRecs;
runStartRecs.SetResizable();
int nextRec, runIndexRecord;
if (fileOK)
{
ReadFileHeader(true);
ReadNextRecord();
runIndexRecord = GetCurrentRec();
nextRec = ReadInt();
ReadIntArray(runStartRecs);
}
else
{
OpenFile(fileName, false);
WriteStdFileHeader(fileHeader, StringLength(fileHeader) + 1, writeVersion, 0);
WriteInt(0); // 0 runs
FlushBuffer(nextRec);
runIndexRecord = nextRec;
// initial header
BufferReset(nextRec);
WriteInt(0);
WriteInt(0);
WriteInt(0);
FlushBuffer(nextRec);
// backup and set nextRec
BufferReset(runIndexRecord);
WriteInt(nextRec);
WriteInt(0);
WriteInt(0);
// reflush
FlushBuffer();
}
int runStart = nextRec;
// set to next avail
BufferReset(nextRec);
// add the run to the end
WriteOneRun(results, nextRec);
nRuns++;
// update header
BufferReset(0);
WriteStdFileHeader(fileHeader, StringLength(fileHeader) + 1, writeVersion, 0);
WriteInt(nRuns);
FlushBuffer();
// update next avail record
BufferReset(runIndexRecord);
WriteInt(nextRec);
// update run start records
runStartRecs += runStart;
WriteIntArray(runStartRecs);
FlushBuffer();
CloseFile();
return true;
}
catch (BufFileC::BufferFileError& err) {
GenAppErrorMsg("WriteSimResults", err.errMsg);
}
CloseFile();
return false;
}
void DnaPacker::UnpackFromBin(const BinaryBinBlock& binBin_, DnaBin& dnaBin_, uint32 minimizerId_, DataChunk& dnaChunk_, bool append_)
{
// calculate global bin properties
//
uint64 recordsCount = 0;
for (uint32 i = 0; i < binBin_.descriptors.size(); ++i)
{
const BinaryBinDescriptor& desc = binBin_.descriptors[i];
recordsCount += desc.recordsCount;
}
ASSERT(recordsCount < (1 << 28));
// initialize
//
uint64 recId = 0;
if (append_)
{
recId = dnaBin_.Size();
recordsCount += recId;
ASSERT(dnaChunk_.data.Size() >= dnaChunk_.size + binBin_.rawDnaSize);
}
else
{
dnaBin_.Clear();
dnaChunk_.size = 0;
if (dnaChunk_.data.Size() < binBin_.rawDnaSize)
dnaChunk_.data.Extend(binBin_.rawDnaSize);
}
dnaBin_.Resize(recordsCount);
if (recordsCount == 0)
return;
// configure settings
//
BinPackSettings settings;
char minString[64] = {0};
if (minimizerId_ != params.TotalMinimizersCount()) // N bin?
{
settings.suffixLen = params.signatureSuffixLen;
params.GenerateMinimizer(minimizerId_, minString);
}
else
{
settings.suffixLen = 0;
}
BitMemoryReader metaReader(binBin_.metaData, binBin_.metaSize);
BitMemoryReader dnaReader(binBin_.dnaData, binBin_.dnaSize);
char* dnaBufferPtr = (char*)dnaChunk_.data.Pointer();
for (uint32 i = 0; i < binBin_.descriptors.size(); ++i)
{
const BinaryBinDescriptor& desc = binBin_.descriptors[i];
const uint64 initialMetaPos = metaReader.Position();
const uint64 initialDnaPos = dnaReader.Position();
// read bin header
//
settings.minLen = metaReader.GetBits(LenBits);
settings.maxLen = metaReader.GetBits(LenBits);
ASSERT(settings.minLen > 0);
ASSERT(settings.maxLen >= settings.minLen);
settings.hasConstLen = (settings.minLen == settings.maxLen);
if (!settings.hasConstLen)
{
settings.bitsPerLen = bit_length(settings.maxLen - settings.minLen);
ASSERT(settings.bitsPerLen > 0);
}
// read bin records
//
if (settings.suffixLen > 0)
{
for (uint32 j = 0; j < desc.recordsCount; ++j)
{
DnaRecord& rec = dnaBin_[recId++];
rec.dna = dnaBufferPtr + dnaChunk_.size;
bool b = ReadNextRecord(metaReader, dnaReader, rec, settings);
ASSERT(b);
ASSERT(dnaChunk_.size + rec.len <= dnaChunk_.data.Size());
std::copy(minString, minString + params.signatureSuffixLen, rec.dna + rec.minimizerPos);
dnaChunk_.size += rec.len;
}
}
else
{
for (uint32 j = 0; j < desc.recordsCount; ++j)
{
DnaRecord& rec = dnaBin_[recId++];
rec.dna = dnaBufferPtr + dnaChunk_.size;
bool b = ReadNextRecord(metaReader, dnaReader, rec, settings);
ASSERT(b);
ASSERT(dnaChunk_.size + rec.len <= dnaChunk_.data.Size());
dnaChunk_.size += rec.len;
}
}
metaReader.FlushInputWordBuffer();
dnaReader.FlushInputWordBuffer();
dnaBin_.SetStats(MIN(settings.minLen, dnaBin_.GetStats().minLen),
MAX(settings.maxLen, dnaBin_.GetStats().maxLen));
ASSERT(metaReader.Position() - initialMetaPos == desc.metaSize);
ASSERT(dnaReader.Position() - initialDnaPos == desc.dnaSize);
}
}
void DnaPacker::UnpackFromBin(const BinaryBinDescriptor& desc_, DnaBin &dnaBin_, DataChunk& dnaChunk_,
BitMemoryReader& metaReader_, BitMemoryReader& dnaReader_, uint32 minimizerId_)
{
const uint64 recordsCount = desc_.recordsCount;
const uint64 initialMetaPos = metaReader_.Position();
const uint64 initialDnaPos = dnaReader_.Position();
ASSERT(recordsCount < (1 << 28));
dnaBin_.Resize(recordsCount);
// initialize settings
//
BinPackSettings settings;
settings.minLen = metaReader_.GetBits(LenBits);
settings.maxLen = metaReader_.GetBits(LenBits);
settings.hasConstLen = (settings.minLen == settings.maxLen);
ASSERT(settings.maxLen > 0);
ASSERT(settings.maxLen >= settings.minLen);
if (minimizerId_ != params.TotalMinimizersCount())
settings.suffixLen = params.signatureSuffixLen;
else
settings.suffixLen = 0;
if (!settings.hasConstLen)
{
settings.bitsPerLen = bit_length(settings.maxLen - settings.minLen);
ASSERT(settings.bitsPerLen > 0);
}
char* dnaBufferPtr = (char*)dnaChunk_.data.Pointer();
uint64 dnaBufferPos = 0;
// unpack records
//
if (settings.suffixLen > 0)
{
char minString[64] = {0};
params.GenerateMinimizer(minimizerId_, minString);
for (uint32 r = 0; r < recordsCount; ++r)
{
DnaRecord& rec = dnaBin_[r];
rec.dna = dnaBufferPtr + dnaChunk_.size + dnaBufferPos;
bool b = ReadNextRecord(metaReader_, dnaReader_, rec, settings);
ASSERT(b);
ASSERT(dnaBufferPos + rec.len <= desc_.rawDnaSize);
std::copy(minString, minString + params.signatureSuffixLen, rec.dna + rec.minimizerPos);
dnaBufferPos += rec.len;
}
}
else
{
for (uint32 r = 0; r < recordsCount; ++r)
{
DnaRecord& rec = dnaBin_[r];
rec.dna = dnaBufferPtr + dnaChunk_.size + dnaBufferPos;
bool b = ReadNextRecord(metaReader_, dnaReader_, rec, settings);
ASSERT(b);
ASSERT(dnaBufferPos + rec.len <= desc_.rawDnaSize);
dnaBufferPos += rec.len;
}
}
dnaChunk_.size += dnaBufferPos;
dnaBin_.SetStats(settings.minLen, settings.maxLen);
metaReader_.FlushInputWordBuffer();
dnaReader_.FlushInputWordBuffer();
ASSERT(metaReader_.Position() - initialMetaPos == desc_.metaSize);
ASSERT(dnaReader_.Position() - initialDnaPos == desc_.dnaSize);
}