void convertHitsToASQG(const std::string& indexPrefix, const StringVector& hitsFilenames, std::ostream* pASQGWriter)
{
// Load the suffix array index and the reverse suffix array index
// Note these are not the full suffix arrays
SuffixArray* pFwdSAI = new SuffixArray(indexPrefix + SAI_EXT);
SuffixArray* pRevSAI = new SuffixArray(indexPrefix + RSAI_EXT);
// Load the ReadInfoTable for the queries to look up the ID and lengths of the hits
ReadInfoTable* pQueryRIT = new ReadInfoTable(opt::readsFile);
// If the target file is not the query file, load its ReadInfoTable
ReadInfoTable* pTargetRIT;
if(!opt::targetFile.empty() && opt::targetFile != opt::readsFile)
pTargetRIT = new ReadInfoTable(opt::targetFile);
else
pTargetRIT = pQueryRIT;
bool bIsSelfCompare = pTargetRIT == pQueryRIT;
// Convert the hits to overlaps and write them to the asqg file as initial edges
for(StringVector::const_iterator iter = hitsFilenames.begin(); iter != hitsFilenames.end(); ++iter)
{
printf("[%s] parsing file %s\n", PROGRAM_IDENT, iter->c_str());
std::istream* pReader = createReader(*iter);
// Read each hit sequentially, converting it to an overlap
std::string line;
while(getline(*pReader, line))
{
size_t readIdx;
size_t totalEntries;
bool isSubstring;
OverlapVector ov;
OverlapCommon::parseHitsString(line, pQueryRIT, pTargetRIT, pFwdSAI, pRevSAI, bIsSelfCompare, readIdx, totalEntries, ov, isSubstring);
for(OverlapVector::iterator iter = ov.begin(); iter != ov.end(); ++iter)
{
ASQG::EdgeRecord edgeRecord(*iter);
edgeRecord.write(*pASQGWriter);
}
}
delete pReader;
// delete the hits file
unlink(iter->c_str());
}
// Deallocate data
if(pTargetRIT != pQueryRIT)
delete pTargetRIT;
delete pFwdSAI;
delete pRevSAI;
delete pQueryRIT;
}
void RegistryComponent::SetComponentInfo(const ComponentInfo &info)
{
std::string KeyComponentClassId = Key_ComponentClassIDs;
KeyComponentClassId += "/";
StringVector ClassIDs = info.GetClassIDs();
for (StringVector::const_iterator i = ClassIDs.begin() ; i != ClassIDs.end() ; ++i)
{
std::string ClassId = KeyComponentClassId;
ClassId += *i;
Reg.CreateKey(ClassId);
Reg.SetValue(ClassId, info.GetModuleGuid().c_str());
}
std::string KeyComponentInformation = Key_ComponentInformation;
KeyComponentInformation += "/";
KeyComponentInformation += info.GetModuleGuid();
KeyComponentInformation += "/";
std::string Key = KeyComponentInformation;
Key += Key_Type;
Reg.CreateKey(Key);
Reg.SetValue(Key, info.GetTypeAsStr().c_str());
Key = KeyComponentInformation;
Key += Key_ModuleName;
Reg.CreateKey(Key);
Reg.SetValue(Key, info.GetModuleName().c_str());
Key = KeyComponentInformation;
Key += Key_Location;
Reg.CreateKey(Key);
Reg.SetValue(Key, info.GetLocation().c_str());
Key = KeyComponentInformation;
Key += Key_Description;
Reg.CreateKey(Key);
Reg.SetValue(Key, info.GetDescription().c_str());
Key = KeyComponentInformation;
Key += Key_ClassIDs;
Reg.CreateKey(Key);
unsigned Index = 0;
for (StringVector::const_iterator i = ClassIDs.begin() ; i != ClassIDs.end() ; ++i)
{
std::stringstream Io;
Io << Key_ClassId << Index++;
std::string ClassIdKey = Key + "/" + Io.str();
Reg.CreateKey(ClassIdKey);
Reg.SetValue(ClassIdKey, static_cast<const char*>(i->c_str()));
}
}
//-----------------------------------------------------------------------
void CgProgram::buildArgs(void)
{
StringVector args;
if (!mCompileArgs.empty())
args = StringUtil::split(mCompileArgs);
StringVector::const_iterator i;
if (mSelectedCgProfile == CG_PROFILE_VS_1_1)
{
// Need the 'dcls' argument whenever we use this profile
// otherwise compilation of the assembler will fail
bool dclsFound = false;
for (i = args.begin(); i != args.end(); ++i)
{
if (*i == "dcls")
{
dclsFound = true;
break;
}
}
if (!dclsFound)
{
args.push_back("-profileopts");
args.push_back("dcls");
}
}
// Now split args into that god-awful char** that Cg insists on
freeCgArgs();
mCgArguments = new char*[args.size() + 1];
int index = 0;
for (i = args.begin(); i != args.end(); ++i, ++index)
{
mCgArguments[index] = new char[i->length() + 1];
strcpy(mCgArguments[index], i->c_str());
}
// Null terminate list
mCgArguments[index] = 0;
}
