void HashTable::loadActionValueTable(const string& fileName)
{
// fprintf(stream, "Q-Hash Table\n");
double maxDiscreteBin = 0.;
ifstream inFile(fileName.c_str());
if (!inFile.is_open())
{
cerr << "ERROR: Cannot open Q Table file <" << fileName << ">!" << endl;
exit(1);
}
_valueTable.clear();
nor_utils::StreamTokenizer lineToken(inFile, "\n\r");
while (lineToken.has_token())
{
string line = lineToken.next_token();
if (line.size() == 0)
continue;
stringstream ssLine(line);
nor_utils::StreamTokenizer itemToken(ssLine, " \n\r\t");
ValueKey key;
string item = itemToken.next_token();
// assert(tmp.compare("(") == 0);
int pointer = 0;
while (itemToken.has_token()) {
item = itemToken.next_token();
if (item.size() == 0)
continue;
if (item.compare(")") == 0)
break;
stringstream ssItem(item);
double k;
ssItem >> k;
key.push_back(k);
// if it points to the bin index and if it's not the max yet
if (pointer == (_numWinnerClasses + 1) && k > maxDiscreteBin) {
maxDiscreteBin = k;
}
++pointer;
}
while (itemToken.has_token())
{
item = itemToken.next_token();
if (item.size() == 0)
continue;
stringstream ssItem(item);
AlphaReal q;
ssItem >> q;
_valueTable[key].push_back(q);
}
assert(_valueTable[key].size() == _numberOfActions);
}
++maxDiscreteBin; //starts at 0
if ((1./maxDiscreteBin) != _stepResolution) {
cout << "[!] Warning: the score resolution used (" << 1/_stepResolution << ") seems to be different in the Q table file (" << (int)maxDiscreteBin << ")." << endl;
}
}
bool BedValidator::validate()
{
dumpmessage(DEBUG, __FILE__, " In BedValidator::validate()");
bool isValid = true;
int colCount = -1;
int trackCount = 1;
string line, token;
string traceChromName = "";
string trackName = "track1";
string dumpMsg;
const string TRACK = "track";
const char lineDelim = '\n';
if(mBamChromNames.size() != mBamChromSizes.size())
{
dumpmessage(ERROR, __FILE__, " Validation failed. Size of input chrom names is not the same as the chrom sizes.");
return false;
}
ifstream bedStream;
// Open BED file for validation
bedStream.open(mBedFn.c_str(), ifstream::in);
if( !bedStream.is_open() )
{
dumpMsg = " BED file: " + mBedFn + ". BED file can not be opened";
dumpmessage(ERROR, __FILE__, dumpMsg);
return false;
}
dumpMsg = " BED file: " + mBedFn;
dumpmessage(INFO, __FILE__, dumpMsg);
while( getline(bedStream, line, lineDelim) )
{
size_t pos = line.find(TRACK);
if (pos < line.length())
{ //Track is present
if(!getTrackName(trackName, line, trackCount))
{
dumpmessage(ERROR, __FILE__, " ERROR while reading track name.");
}
// Reset column count as new track starting
colCount = -1;
//Increment track count for every track
++trackCount;
}
else
{ // Process BED file data
bool dataLineFound = false;
int colIdx = 1;
int64 chromStart = -1, chromEnd = -1, score = -1;
string chromName, strand;
const char colDelim = '\t';
// push the line into stringstream line for another round of getline
stringstream ssLine(line);
for(; getline(ssLine, token, colDelim); ++colIdx)
{
stringstream ssToken(token);
dataLineFound = true;
switch(colIdx)
{ // Validate Column data from BED file
case CHROM_IDX:
chromName = token;
break;
case CHROMSTART_IDX:
ssToken >> chromStart;
if(chromStart < 0 || ssToken.fail())
{
dumpMsg = " Track: " + trackName + " Chrom: " + chromName + " chromStart:"+ token + " Error: chromStart can not be less than 0";
dumpmessage(ERROR, __FILE__, dumpMsg);
isValid = false;
}
break;
case CHROMEND_IDX:
ssToken >> chromEnd;
if(chromEnd < 1 || ssToken.fail())
{
dumpMsg = " Track: " + trackName + " Chrom: " + chromName + " chromEnd:" + token + " Error: chromEnd can not be less than 1";
dumpmessage(ERROR, __FILE__, dumpMsg);
isValid = false;
}
if( chromStart > chromEnd)
{
stringstream ssValue;
ssValue << " ChromStart: " << chromStart << ", ChromEnd: " << chromEnd;
dumpMsg = " Track: " + trackName + " Chrom: " + chromName + ssValue.str() + " Error: chromStart can not be greater than chromEnd";
dumpmessage(ERROR, __FILE__, dumpMsg);
isValid = false;
}
break;
case SCORE_IDX:
ssToken >> score;
if(score < SCORE_MIN || score > SCORE_MAX || ssToken.fail())
{
stringstream ssValue;
ssValue << " ChromStart: " << chromStart;
dumpMsg = " Track: " + trackName + " Chrom: " + chromName + ssValue.str() + " score:" + token + " Error: Score is not in 0 to 1000 limit";
dumpmessage(ERROR, __FILE__, dumpMsg);
isValid = false;
}
break;
case STRAND_IDX:
strand = token;
if(token[0] != STRAND_PLUS && token[0] != STRAND_MINUS)
{
stringstream ssValue;
ssValue << " ChromStart: " << chromStart;
dumpMsg = " Track: " + trackName + " Chrom: " + chromName + ssValue.str() + " strand:" + token + " Error: Strand value is not + or -";
dumpmessage(ERROR, __FILE__, dumpMsg);
isValid = false;
}
break;
case NAME_IDX:
case THICKSTART_IDX:
case THICKEND_IDX:
case ITEMRGB_IDX:
case BLOCKCOUNT_IDX:
case BLOCKSIZES_IDX:
case BLOCKSTARTS_IDX:
default:
break;
} // switch()
} // for()
if( colCount > 0 )
{ // Verify the column count with the previous column count
if( dataLineFound )
{
--colIdx;
if(colCount < MIN_COLUMNS)
{ // Minimum three columns must be present
dumpMsg = " Track: " + trackName + " Chrom: " + chromName + " ERROR - Do not match the minimum three columns criteria";
dumpmessage(ERROR, __FILE__, dumpMsg);
isValid = false;
}
if( colCount != colIdx )
{ // If the column count do not match
stringstream ssValue;
ssValue << " ChromStart: " << chromStart;
dumpMsg = " Track: " + trackName + " Chrom: " + chromName + ssValue.str() + " ERROR - Columns do not match from same track";
dumpmessage(ERROR, __FILE__, dumpMsg);
isValid = false;
}
}
}
else
{ // Initialize Column count for current Track
stringstream ssColcount;
colCount = --colIdx;
ssColcount << colCount;
dumpMsg = " Track: " + trackName + " - Column count: " + ssColcount.str();
dumpmessage(INFO, __FILE__, dumpMsg);
}
// Validating Bam Header data if present otherwise return the validation of BED file
if( dataLineFound && mBamChromNames.size() > 0)
{
bool retVal;
retVal = checkWithBAMHeader(trackName, chromName, chromStart, chromEnd);
if(!retVal)
isValid = retVal;
}
} // else{} process BED data
} // while()
//Close the BED file
bedStream.close();
dumpmessage(DEBUG, __FILE__, " Out BedValidator::validate()");
return isValid;
}
int KGTestMapDisuseResource::FindResInMDL(const char cszResourceName[], set<string>& setResList)
{
//参照KG3DModelST::LoadMDLContent
int nResult = false;
char szFilePath[MAX_PATH] = {0};
IFile* pFile = NULL;
unsigned long uSize = 0;
unsigned long uFileSize = 0;
char* pBuffer = NULL;
std::stringstream ss;
std::string strBuffer;
std::string strFilePath;
MDLFileContent Content;
KG_ASSERT_EXIT(cszResourceName);
KGLOG_PROCESS_ERROR(cszResourceName[0] != '\0');
Content.dwNumModels = 0;
pFile = g_OpenFile(cszResourceName);
KG_PROCESS_ERROR(pFile);
uFileSize = pFile->Size();
pBuffer = (char*)malloc(uFileSize + 1);
KG_PROCESS_ERROR(pBuffer);
uSize = pFile->Read(pBuffer, uFileSize);
KG_PROCESS_ERROR(uSize == uFileSize);
pBuffer[uSize] = '\0'; // TODO : text 文件没有使用'\0'作结束，不能作为字符串处理，特别麻烦，建议使用binary
ss << pBuffer;
std::getline(ss, strBuffer);
strBuffer.erase(strBuffer.find_last_not_of("\n\r") + 1);
KG_PROCESS_ERROR(!strBuffer.empty());
g_ExtractFilePath(szFilePath, cszResourceName);
strFilePath = szFilePath;
strFilePath += "\\";
if (strBuffer[0] == '\\')
{
Content.strBipFile = strBuffer;
}
else
{
Content.strBipFile = std::string(strFilePath + strBuffer);
}
FindResource(Content.strBipFile.c_str(), setResList);
while (std::getline(ss, strBuffer))
{
strBuffer.erase(strBuffer.find_last_not_of("\n\r") + 1);
if (strBuffer.empty())
break;
std::stringstream ssLine(strBuffer);
std::string strMesh, strMtl;
ssLine >> strMesh >> strMtl;
if (strMtl.size())
{
Content.strMaterialFile[Content.dwNumModels] = strMtl;
}
FindResource(Content.strMaterialFile[Content.dwNumModels].c_str(), setResList);
if (strMesh.size())
{
if (strMesh[0] == '\\')
{
Content.strMeshFile[Content.dwNumModels] = strMesh;
}
else
{
Content.strMeshFile[Content.dwNumModels] = strFilePath + strMesh;
}
FindResource(Content.strMeshFile[Content.dwNumModels].c_str(), setResList);
Content.dwNumModels++;
}
}
nResult = true;
Exit0:
SAFE_FREE(pBuffer);
KG_COM_RELEASE(pFile);
if (!nResult && cszResourceName)
{
KGLogPrintf(KGLOG_ERR, "Find Res In MDL %s failed.\n", cszResourceName);
}
return nResult;
}
SceneManager::SceneManager(GLint width, GLint height)
#endif
{
Log << Function << endl;
// The projection matrix is represented by the perspective matrix given by glm, assign it to each one of the objects
GLfloat aspect = static_cast<GLfloat>(width) / static_cast<GLfloat>(height);
projectionMatrix = glm::perspective(
45.0f, // Field of view, is the amount of zoom. A wide angle is 90 and a narrow angle is 30
aspect, // Depends on the size of the window
0.1f, // Near clipping plane
500.0f // Far clipping plane
);
// Read the resources.txt file to obtain the valid configuration for the engine
string resourcesFileName = "resources.txt";
#if defined(__ANDROID__)
AAssetManager* mgr = AAssetManager_fromJava(*env, assetManager);
AAsset* pFile = AAssetManager_open(mgr, resourcesFileName.c_str(), AASSET_MODE_UNKNOWN);
if (!pFile)
#else
ifstream resourcesFile(resourcesFileName, ios::in);
if (!resourcesFile.is_open())
#endif
{
Log << Error << "Unable to read the resources file: " << resourcesFileName << endl;
terminate();
}
#if defined(__ANDROID__)
// Get the file size
size_t fileSize = AAsset_getLength(pFile);
// Read data from the file
char* pData = (char*)calloc(fileSize + 1, sizeof(char));
AAsset_read(pFile, pData, fileSize);
// fix the string to be zero-terminated
pData[fileSize] = 0;
// Copy the data to a stringstream
stringstream resourcesFile(pData);
AAsset_close(pFile);
free(pData);
#endif
Log << Debug << "Parsing the resources.txt file." << endl;
string line, name, vertex, fragment, object, texture, projection, modelview;
vector<string> cubeTextures{ NumCubeFaces };
GLuint size, bufferType;
vec3 pos, scl, rot;
char token;
bool finished = true;
while (getline(resourcesFile, line))
{
stringstream ssLine(line);
// Ignore empty lines on the configuration file
if(line.size() == 0)
continue;
ssLine >> token;
switch (token)
{
// If the line is a comment get the next token
case '#':
continue;
// Start of object definition
case '.':
// Create a new scene object
Log << Debug << "Starting an object definition." << endl;
sceneobjects.push_back(make_unique<SceneObject>());
finished = false;
break;
// End of an object definition
case '-':
Log << Debug << "End an object definition." << endl;
finished = true;
break;
// Attributes used on the shaders
case 'A':
ssLine >> name >> size >> bufferType;
Log << Debug << "Adding the attribute: " << name << endl;
attributes.push_back(make_unique<Variable>(name, size, (BufferType)bufferType));
break;
// Uniforms used on the shaders
case 'U':
ssLine >> name;
Log << Debug << "Adding the uniform: " << name << endl;
uniforms.push_back(make_unique<Variable>(name));
break;
// Shaders creation
case 'S':
ssLine >> vertex >> fragment;
Log << Debug << "Creating the shaders." << endl;
#if defined (__ANDROID__)
sceneobjects.back()->SetShader(make_shared<Shader>(&mgr, vertex, fragment, attributes, uniforms));
#else
sceneobjects.back()->SetShader(make_shared<Shader>(vertex, fragment, attributes, uniforms));
#endif
break;
// Object definitions
case 'O':
ssLine >> object;
Log << Debug << "Loading a model." << endl;
#if defined (__ANDROID__)
sceneobjects.back()->SetMesh(make_unique<Mesh>(&mgr, object, sceneobjects.back()->GetShader()));
#else
sceneobjects.back()->SetMesh(make_unique<Mesh>(object, sceneobjects.back()->GetShader()));
#endif
break;
// Textures
case 'T':
ssLine >> texture;
Log << Debug << "Loading a texture." << endl;
#if defined(__ANDROID__)
sceneobjects.back()->SetTexture(make_unique<Texture>(&mgr, texture, sceneobjects.back()->GetShader()));
#else
sceneobjects.back()->SetTexture(make_unique<Texture>(texture, sceneobjects.back()->GetShader()));
#endif
break;
// Initial coordinates
case 'C':
Log << Debug << "Adding coordinates to the object." << endl;
ssLine >> pos.x >> pos.y >> pos.z >> scl.x >> scl.y >> scl.z >> rot.x >> rot.y >> rot.z >> angle;
sceneobjects.back()->SetCoordinates(pos, scl, rot, angle);
break;
// Projection matrix
case 'P':
ssLine >> projection;
break;
// Modelview matrix
case 'M':
ssLine >> modelview;
break;
// Skybox
case 'B':
Log << Debug << "Adding a skybox." << endl;
ssLine >> cubeTextures[0] >> cubeTextures[1] >> cubeTextures[2] >> cubeTextures[3] >> cubeTextures[4] >> cubeTextures[5];
sceneobjects.back()->SetSkymap();
#if defined(__ANDROID__)
sceneobjects.back()->SetMesh(make_unique<Mesh>(&mgr, string(""), sceneobjects.back()->GetShader()));
sceneobjects.back()->SetTexture(make_unique<Texture>(&mgr, cubeTextures, sceneobjects.back()->GetShader()));
#else
sceneobjects.back()->SetMesh(make_unique<Mesh>(string(""), sceneobjects.back()->GetShader()));
sceneobjects.back()->SetTexture(make_unique<Texture>(cubeTextures, sceneobjects.back()->GetShader()));
#endif
break;
// Terrain Heightmap
case 'H':
Log << Debug << "Loading the terrain." << endl;
ssLine >> texture >> object;
#if defined(__ANDROID__)
sceneobjects.back()->SetTexture(make_unique<Texture>(&mgr, texture, sceneobjects.back()->GetShader()));
sceneobjects.back()->SetMesh(make_unique<Mesh>(&mgr, object, sceneobjects.back()->GetShader(), &sceneobjects.back()->GetTexture()));
#else
sceneobjects.back()->SetTexture(make_unique<Texture>(texture, sceneobjects.back()->GetShader()));
sceneobjects.back()->SetMesh(make_unique<Mesh>(object, sceneobjects.back()->GetShader(), &sceneobjects.back()->GetTexture()));
#endif
break;
default:
continue;
}
// Check if the definition of an object is complete or if more lines are needed
if (finished)
{
// Get the projection and modelview uniforms
if (!projection.empty())
{
sceneobjects.back()->SetProjectionUni(glGetUniformLocation(sceneobjects.back()->GetShader()->getProgramObject(), "Projection"));
projection.clear();
}
if (!modelview.empty())
{
sceneobjects.back()->SetModelviewUni(glGetUniformLocation(sceneobjects.back()->GetShader()->getProgramObject(), "Modelview"));
modelview.clear();
}
// Clear the attributes and uniforms in order to load the next object
attributes.clear();
uniforms.clear();
}
}
#if !defined(__ANDROID__)
// Close de the resources file
resourcesFile.close();
#endif
// Set the initial position of the camera
camera = vec3(2.5f, -1.0f, -5.0f);
// Initial value of the rotation angle
angle = 0.0f;
}
