void
BaseType::printForm(std::ostream& out) const
{
out << "-Base";
if (qualifier != TQ_None)
{
out << ":";
printQual(out,qualifier);
}
}
void
PtrType::printForm(std::ostream& out) const
{
out << "-Ptr";
if (qualifier != TQ_None)
{
out << ":";
printQual(out,qualifier);
}
if (subType)
subType->printForm(out);
}
// o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o
void
PtrType::printBefore( std::ostream& out, Symbol *name, int level ) const
{
if (subType)
{
subType->printBefore(out,NULL,level);
bool paren = ! (subType->isPointer() || subType->isBaseType());
if (paren)
out << "(" ;
out << "*" ;
printQual(out,qualifier);
}
if (name)
{
out << *name;
}
}
//***************************************************************************************************************
int SummaryQualCommand::execute(){
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
int numSeqs = 0;
vector<int> position;
vector<int> averageQ;
vector< vector<int> > scores;
if (m->control_pressed) { return 0; }
if (namefile != "") { nameMap = m->readNames(namefile); }
else if (countfile != "") {
CountTable ct;
ct.readTable(countfile, false, false);
nameMap = ct.getNameMap();
}
vector<unsigned long long> positions;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(qualfile, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
#else
if (processors == 1) {
lines.push_back(linePair(0, 1000));
}else {
positions = m->setFilePosFasta(qualfile, numSeqs);
if (numSeqs < processors) { processors = numSeqs; }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numSeqs / processors;
for (int i = 0; i < processors; i++) {
int startIndex = i * numSeqsPerProcessor;
if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; }
lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
}
}
#endif
if(processors == 1){ numSeqs = driverCreateSummary(position, averageQ, scores, qualfile, lines[0]); }
else{ numSeqs = createProcessesCreateSummary(position, averageQ, scores, qualfile); }
if (m->control_pressed) { return 0; }
//print summary file
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qualfile));
string summaryFile = getOutputFileName("summary",variables);
printQual(summaryFile, position, averageQ, scores);
if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
//output results to screen
cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
m->mothurOutEndLine();
m->mothurOut("Position\tNumSeqs\tAverageQ"); m->mothurOutEndLine();
for (int i = 0; i < position.size(); i+=100) {
float average = averageQ[i] / (float) position[i];
cout << i << '\t' << position[i] << '\t' << average;
m->mothurOutJustToLog(toString(i) + "\t" + toString(position[i]) + "\t" + toString(average)); m->mothurOutEndLine();
}
m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SummaryQualCommand", "execute");
exit(1);
}
}
void
BaseType::printBase(std::ostream& out, int level) const
{
printQual(out,qualifier);
if (typemask & BT_UnSigned)
out << "unsigned ";
else if (typemask & BT_Signed)
out << "signed ";
if (typemask & BT_Void)
out << "void ";
else if (typemask & BT_Char)
out << "char ";
else if (typemask & BT_Short)
out << "short ";
else if (typemask & BT_LongLong)
out << "long long ";
else if (typemask & BT_Float)
out << "float ";
else if (typemask & BT_Float2)
out << "float2 ";
else if (typemask & BT_Float3)
out << "float3 ";
else if (typemask & BT_Float4)
out << "float4 ";
else if ((typemask & BT_Double) && (typemask & BT_Long))
out << "long double ";
else if (typemask & BT_Double)
out << "double ";
else if (typemask & BT_Ellipsis)
out << "...";
else if (typemask & BT_Long)
out << "long ";
else if (typemask & BT_Struct)
{
if (stDefn != NULL)
{
stDefn->print(out, NULL, level);
}
else
{
out << "struct ";
if (tag)
out << *tag << " ";
}
}
else if (typemask & BT_Union)
{
if (stDefn != NULL)
{
stDefn->print(out, NULL, level);
}
else
{
out << "union ";
if (tag)
out << *tag << " ";
}
}
else if (typemask & BT_Enum)
{
out << "enum ";
if (enDefn != NULL)
{
enDefn->print(out, NULL, level);
}
else
{
if (tag)
out << *tag << " ";
}
}
else if (typemask & BT_UserType)
{
if (typeName)
out << *typeName << " ";
}
else
{
out << "int "; // Default
}
}
bool BaseType::printStructureStreamHelperType( std::ostream& out, const std::string& name ) const
{
printQual(out,qualifier);
if (typemask & BT_UnSigned)
out << "unsigned ";
else if (typemask & BT_Signed)
out << "signed ";
if (typemask & BT_Void)
out << "void ";
else if (typemask & BT_Char)
out << "char ";
else if (typemask & BT_Short)
out << "short ";
else if (typemask & BT_LongLong)
out << "long long ";
else if (typemask & BT_Float)
out << "__BrtFloat1 ";
else if (typemask & BT_Float2)
out << "__BrtFloat2 ";
else if (typemask & BT_Float3)
out << "__BrtFloat3 ";
else if (typemask & BT_Float4)
out << "__BrtFloat4 ";
else if ((typemask & BT_Double) && (typemask & BT_Long))
out << "long double ";
else if (typemask & BT_Double)
out << "double ";
else if (typemask & BT_Ellipsis)
out << "...";
else if (typemask & BT_Long)
out << "long ";
else if (typemask & BT_Struct)
{
if (stDefn != NULL)
{
if( !stDefn->printStructureStreamHelper(out) )
return false;
}
else
{
out << "struct ";
if (tag)
out << "__cpustruct_" << *tag << " ";
}
}
else if (typemask & BT_Union)
{
return false;
}
else if (typemask & BT_Enum)
{
return false;
}
else if (typemask & BT_UserType)
{
if (typeName)
out << "__cpustruct_" << *typeName << " ";
}
else
{
out << "int "; // Default
}
out << name;
return true;
}