void PeakMatchingResults::GetMatches(std::vector<int> &vectFeatureIndices, std::vector<int> &vectMassTagIndices,
std::vector<int> &vectProteinIndices , const std::vector<MultiAlignEngine::MassTags::Protein>* &vectProteins,
const std::vector<MultiAlignEngine::MassTags::MassTag>* &vectMasstags) const
{
// The mass tag database has stored in it all the proteins and mass tags corresponding to the matches.
// So thats where we need to get all the data from.
int numMatches = (int) mvectPeakMatches.size();
std::set <int> massTagID;
stdext::hash_map <int, int > massTagSeen;
// first get all mass tags in the matches into the set of mass tags.
for (int matchNum = 0; matchNum < numMatches; matchNum++)
{
PeakMatch match = mvectPeakMatches[matchNum];
massTagSeen.insert(std::pair<int,int>(match.mintMasstagID, matchNum));
}
// copy hash to mass tag vector
std::vector<int> vectMassTagIDs;
vectMassTagIDs.reserve(massTagSeen.size());
for (stdext::hash_map <int, int >::iterator massTagIter = massTagSeen.begin();
massTagIter != massTagSeen.end(); massTagIter++)
{
vectMassTagIDs.push_back((*massTagIter).first);
}
vectMasstags = mobjMasstagDB.GetMassTagVector();
vectProteins = mobjMasstagDB.GetProteinVector();
const std::multimap<int,int> mapMassTagId2ProteinIndex = mobjMasstagDB.GetMassTagId2ProteinIndexMap();
const stdext::hash_map <int, int > hashMapMassTagId2Index = mobjMasstagDB.GetMassTagId2IndexHash();
// now the relevant mass tags are copied, their ids are copied, the protein names are copied.
// So lets create the table of matches using the three vectors vectFeatureIndices, vectMassTagIndices and
// vectProteinIndices. Basically, vectFeatureIndices will have the index of the ms feature in a peak match.
// the vectMassTagIndices will have the corresponding massTagID, and vectProteinIndices will have the corresponding
// parent protein.
for (std::multimap<int,int>::const_iterator featureIter = mmapFeatureIndex2PeakMatch.begin(); featureIter != mmapFeatureIndex2PeakMatch.end();
featureIter++)
{
int featureIndex = (*featureIter).first;
int peakMatchIndex = (*featureIter).second;
PeakMatch pkMatch = mvectPeakMatches[peakMatchIndex];
int massTagID = pkMatch.mintMasstagID;
stdext::hash_map <int, int>::const_iterator massTagIterHash = hashMapMassTagId2Index.find(massTagID);
int massTagIndex = (*massTagIterHash).second;
// now go through each of the parent proteins of this massTagID and push the triplet into their
// corresponding vectors
for (std::multimap<int,int>::const_iterator massTagIter = mapMassTagId2ProteinIndex.find(massTagID);
massTagIter != mapMassTagId2ProteinIndex.end();
massTagIter++)
{
if ((*massTagIter).first != massTagID)
break;
vectFeatureIndices.push_back(featureIndex);
vectMassTagIndices.push_back(massTagIndex);
vectProteinIndices.push_back((*massTagIter).second);
}
}
}
virtual void ProcessingMaterial(GLMmodel* model, KScene& scene, const stdext::hash_map<UINT32, UINT32>& nodeToMtl)
{
// Create material
KMaterialLibrary* pML = KMaterialLibrary::GetInstance();
for (UINT32 mi = 0; mi < model->nummaterials; ++mi) {
ISurfaceShader* pSurfShader = pML->CreateMaterial("simple_phong_default.template", model->materials[mi].name);
pSurfShader->SetParam("diffuse_color", model->materials[mi].diffuse, sizeof(float)*3);
if (model->materials[mi].shininess > 3.0f) {
pSurfShader->SetParam("specular_color", model->materials[mi].specular, sizeof(float)*3);
pSurfShader->SetParam("power", &model->materials[mi].shininess, sizeof(float));
}
else {
float specular[3] = {0,0,0};
float pow = 0;
pSurfShader->SetParam("specular_color", specular, sizeof(float)*3);
pSurfShader->SetParam("power", &pow, sizeof(float));
}
pSurfShader->SetParam("opacity", model->materials[mi].transparency, sizeof(float)*3);
if (mUseTexMap && model->materials[mi].diffuse_map) {
pSurfShader->SetParam("diffuse_map", model->materials[mi].diffuse_map, 0);
}
}
for (UINT32 i = 0; i < scene.GetNodeCnt(); ++i) {
KNode* pNode = scene.GetNode(i);
stdext::hash_map<UINT32, UINT32>::const_iterator it = nodeToMtl.find(i);
assert(it != nodeToMtl.end());
pNode->mpSurfShader = pML->OpenMaterial(model->materials[it->second].name);
}
}
/**********************************************************************************************************************
CConvertibleEnum::Convert_Internal -- internal function to convert from an integer value to a string
value -- integer to convert from
entry_name -- output parameter for the string value
Returns: success/failure
**********************************************************************************************************************/
bool CConvertibleEnum::Convert_Internal( uint64 value, std::string &entry_name ) const
{
auto iter = ValueToNameTable.find( value );
if ( iter == ValueToNameTable.end() )
{
return false;
}
entry_name = iter->second;
return true;
}
/**********************************************************************************************************************
CConvertibleEnum::Convert_Internal -- internal function to convert from a string to an integer value
entry_name -- string value to convert from
output_value -- output parameter for the integer to convert to
Returns: success/failure
**********************************************************************************************************************/
bool CConvertibleEnum::Convert_Internal( const std::string &entry_name, uint64 &output_value ) const
{
std::string upper_entry_name;
NStringUtils::To_Upper_Case( entry_name, upper_entry_name );
auto iter = NameToValueTable.find( upper_entry_name );
if ( iter == NameToValueTable.end() )
{
return false;
}
output_value = iter->second;
return true;
}
/**********************************************************************************************************************
CConvertibleEnum::Register_Entry -- registers a string and integer value pair as convertible
entry_name -- corresponding string value
value -- integer to convert to/from
**********************************************************************************************************************/
void CConvertibleEnum::Register_Entry( const std::string &entry_name, uint64 value )
{
std::string upper_entry_name;
NStringUtils::To_Upper_Case( entry_name, upper_entry_name );
auto name_iter = NameToValueTable.find( upper_entry_name );
FATAL_ASSERT( name_iter == NameToValueTable.end() );
auto value_iter = ValueToNameTable.find( value );
FATAL_ASSERT( value_iter == ValueToNameTable.end() );
NameToValueTable[ upper_entry_name ] = value;
ValueToNameTable[ value ] = upper_entry_name;
}
HRESULT __wrapper_FilterGetMessage(
HANDLE hPort,
PFILTER_MESSAGE_HEADER lpMessageBuffer,
DWORD dwMessageBufferSize,
LPOVERLAPPED lpOverlapped )
{
Chess::SyncVarAccess(GetWin32SyncManager()->GetSyncVarFromHandle(hPorte), SVOP::FLT_RW);
if(qsize.find(hPorte) == qsize.end())
qsize[hPorte] = 0;
if(lpOverlapped != NULL){
HRESULT ret = Real_FilterGetMessage(hPort, lpMessageBuffer, dwMessageBufferSize, lpOverlapped);
if(ret == ERROR_IO_PENDING)
qsize[hPorte]++;
return ret;
}
LPOVERLAPPED myOverlapped;
OVERLAPPED tempOverlapped;
memset(&tempOverlapped, 0, sizeof(OVERLAPPED));
myOverlapped = &tempOverlapped;
myOverlapped->hEvent = CreateEvent(NULL, FALSE, FALSE, NULL);
HRESULT ret = Real_FilterGetMessage(hPort, lpMessageBuffer, dwMessageBufferSize, myOverlapped);
//if(ret != S_OK || ret != ERROR_IO_PENDING)
// return ret;
assert(ret != S_OK);
qsize[hPorte]++;
Chess::SyncVarAccess(GetWin32SyncManager()->GetSyncVarFromHandle(hPorte), SVOP::FLT_RW);
while(true){
HRESULT retVal = WaitForSingleObject(myOverlapped->hEvent, 0);
switch(retVal){
case WAIT_OBJECT_0 :
CloseHandle(myOverlapped->hEvent);
return S_OK;
case WAIT_TIMEOUT :
Chess::LocalBacktrack();
break;
default:
fprintf(stderr, "Waiting for event failed in Wrapper FilterGetMessage");
return retVal;
}
}
assert(false);
return S_OK;
}
HRESULT __wrapper_FilterSendMessage(
HANDLE hPort,
LPVOID lpInBuffer,
DWORD dwInBufferSize,
LPVOID lpOutBuffer,
DWORD dwOutBufferSize,
LPDWORD lpBytesReturned )
{
Chess::SyncVarAccess(GetWin32SyncManager()->GetSyncVarFromHandle(hPorte), SVOP::FLT_RW);
if(qsize.find(hPorte) == qsize.end())
qsize[hPorte] = 0;
while(qsize[hPorte] == 0){
Chess::LocalBacktrack();
}
qsize[hPorte]--;
return Real_FilterSendMessage(hPort, lpInBuffer, dwInBufferSize, lpOutBuffer, dwOutBufferSize, lpBytesReturned);
}
static void push( lua_State* lua_state, const stdext::hash_map<Key, Data, Traits, Allocator>& value )
{
lua_push( lua_state, value.begin(), value.end() );
}
DWORD _stdcall AIGetLastTarget(DWORD source) {
iter itr=targets.find(source);
if(itr==targets.end()) return 0;
else return itr->second;
}
DWORD _stdcall AIGetLastAttacker(DWORD target) {
iter itr=sources.find(target);
if(itr==sources.end()) return 0;
else return itr->second;
}
bool LoadDIASymbols(const wxString &strPDBFile,
wxInt32 modulenum,
std::list<CFunctionDescription> & llFuncs,
stdext::hash_map<BasedAddress,int> & addressmap
)
{
// Create DIA80 Data Source Object
IDiaDataSource *pDataSource;
HRESULT hr = NoRegCoCreate( L"msdia80.dll", _uuidof( DiaSource ), _uuidof( IDiaDataSource ), (void **) &(pDataSource));
if(!SUCCEEDED(hr))
{
return false;
}
/*
HMODULE mod=LoadLibrary(L"msdia80.dll");
if(!mod)
{
return false;
}
TYPEOF_DllGetClassObject *pGetClassObject=(TYPEOF_DllGetClassObject *)GetProcAddress(mod,"DllGetClassObject");
if(!pGetClassObject)
{
FreeLibrary(mod);
return false;
}
IClassFactory *pcf;
HRESULT hr=(*pGetClassObject)(CLSID_DiaSource,IID_IClassFactory,(void **)&pcf);
if(!SUCCEEDED(hr))
{
FreeLibrary(mod);
return false;
}
IDiaDataSource *pDataSource;
hr=pcf->CreateInstance(NULL,_uuidof(IDiaDataSource),(void **)&pDataSource);
if(!SUCCEEDED(hr))
{
pcf->Release();
FreeLibrary(mod);
return false;
}
pcf->Release();
*/
// Load the executable's debug symbols
hr=pDataSource->loadDataFromPdb(strPDBFile);
if(!SUCCEEDED(hr))
{
pDataSource->Release();
return false;
}
// Open a symbol session
IDiaSession *pDIASession;
hr=pDataSource->openSession(&pDIASession);
if(!SUCCEEDED(hr))
{
pDataSource->Release();
return false;
}
// Set the UNBASED address on the session, for resolving BasedAddress addrs
hr=pDIASession->put_loadAddress(0);
if(!SUCCEEDED(hr))
{
pDIASession->Release();
pDataSource->Release();
return false;
}
// Get addresses for this module
std::list<BasedAddress> addresses;
for(stdext::hash_map<BasedAddress,int>::iterator iter=addressmap.begin();iter!=addressmap.end();iter++)
{
if(iter->first.nModule==modulenum)
{
addresses.push_back(iter->first);
}
}
stdext::hash_map<DWORD,wxInt32> functions;
int curidx=(int)llFuncs.size();
for(std::list<BasedAddress>::iterator itera=addresses.begin();itera!=addresses.end();itera++)
{
// Get the symbol for this thing
IDiaSymbol* pFunc;
if(FAILED(pDIASession->findSymbolByVA(itera->nAddr, SymTagFunction, &pFunc)) || pFunc==NULL)
{
continue;
}
// Get the unique symbol index id
DWORD indexId;
if(FAILED(pFunc->get_symIndexId(&indexId)))
{
pFunc->Release();
continue;
}
// See if we have this function already
stdext::hash_map<DWORD,int>::iterator iterf=functions.find(indexId);
if(iterf!=functions.end())
{
addressmap[*itera]=iterf->second;
}
else
{
CFunctionDescription func;
//////
ULONGLONG addr;
if(FAILED(pFunc->get_virtualAddress(&addr)))
{
pFunc->Release();
continue;
}
//////
ULONGLONG length;
if(FAILED(pFunc->get_length(&length)))
{
pFunc->Release();
continue;
}
/////////
BSTR pName;
if(FAILED(pFunc->get_name(&pName)))
{
pFunc->Release();
continue;
}
func.strMangledName=(const LPWSTR)pName;
LocalFree(pName);
char mangled[512];
WideCharToMultiByte(CP_UTF8,0,func.strMangledName,-1,mangled,512,NULL,NULL);
/////////
char outbase[512];
__unDName(outbase,mangled,512,&malloc,&free,0x1000);
wchar_t outbasew[512];
MultiByteToWideChar(CP_UTF8,0,outbase,-1,outbasew,512);
func.strBaseName=(const wchar_t *)(outbasew);
/////////
char outfull[512];
__unDName(outfull,mangled,512,&malloc,&free,0);
wchar_t outfullw[512];
MultiByteToWideChar(CP_UTF8,0,outfull,-1,outfullw,512);
func.strFullName=(const wchar_t *)(outfullw);
//////////
func.nAddress=BasedAddress(addr,modulenum);
func.nByteLength=length;
/////////
IDiaEnumLineNumbers *pdeln;
func.strSourceFile=wxT("<unknown>");
func.nFirstSourceLine=0;
func.nLastSourceLine=0;
bool bGotFile=false;
if(SUCCEEDED(pDIASession->findLinesByVA(addr,length,&pdeln)))
{
IDiaLineNumber *pdln;
int nLineItem=0;
while(SUCCEEDED(pdeln->Item(nLineItem,&pdln)))
{
DWORD dwLineNumber;
IDiaSourceFile *pdsf;
if(SUCCEEDED(pdln->get_lineNumber(&dwLineNumber)) &&
SUCCEEDED(pdln->get_sourceFile(&pdsf)))
{
BSTR filename;
if(SUCCEEDED(pdsf->get_fileName(&filename)))
{
if(bGotFile)
{
if(filename==func.strSourceFile)
{
if(dwLineNumber<func.nFirstSourceLine)
{
func.nFirstSourceLine=dwLineNumber;
}
if(dwLineNumber>func.nLastSourceLine)
{
func.nLastSourceLine=dwLineNumber;
}
}
}
else
{
bGotFile=true;
func.strSourceFile=filename;
func.nFirstSourceLine=dwLineNumber;
func.nLastSourceLine=dwLineNumber;
}
LocalFree(filename);
}
pdsf->Release();
}
pdln->Release();
nLineItem++;
}
pdeln->Release();
}
llFuncs.push_back(func);
functions[indexId]=curidx;
addressmap[*itera]=curidx;
curidx++;
}
}
pDIASession->Release();
pDataSource->Release();
// FreeLibrary(mod);
return true;
}
