RPTreeNode* RPTree::readRPTreeNode(std::ifstream* fis, uint64_t fileOffset, bool forceDescend) {
RPTreeNode* thisNode = NULL;
typedef int8_t byte;
try {
// Read node format into a buffer
fis->clear();
fis->seekg(fileOffset);
// find node type
byte type;
fis->read( reinterpret_cast<char*>(&type) , sizeof(byte) );
type=endian::LittleByte(type);
bool isLeaf;
uint32_t itemSize;
//TODO Check the creator of RPTreeNodes, make sure parent value is called and whatbnot
if (type == 1) {
isLeaf = true;
itemSize = RPTREE_NODE_LEAF_ITEM_SIZE;
RPTreeLeafNode* tempP= new RPTreeLeafNode();
thisNode = tempP ;
} else {
isLeaf = false;
itemSize = RPTREE_NODE_CHILD_ITEM_SIZE;
thisNode = new RPTreeChildNode();
}
//nodeCount++;
uint16_t itemCount;
byte empty_b;
fis->read( reinterpret_cast<char*>(&empty_b) , sizeof(byte) );
empty_b=endian::LittleByte(empty_b);
fis->read( reinterpret_cast<char*>(&itemCount) , sizeof(uint16_t) );
itemCount=endian::LittleShort(itemCount);
// uint32_t itemBlockSize = itemCount * itemSize;
// buffer = new byte[itemBlockSize]; // allocate buffer for item sisze
// get the node items - leaves or child nodes
uint32_t startChromID, endChromID;
uint32_t startBase, endBase;
int itemBlockSize = itemCount * itemSize;
//Readitems into buffer and set to stringstream
std::vector<char> buffer(itemBlockSize);
fis->read(&buffer[0],itemBlockSize);
std::stringstream itemStream(std::string(buffer.begin(), buffer.end()));
//Set string stream, does not copy buffer
//itemStream.rdbuf()->pubsetbuf(&buffer[0],itemBlockSize);
//TODO make item reading work with buffer
for (uint32_t item = 0; item < itemCount; ++item) {
// always extract the bounding rectangle
//Read from buffer
itemStream.read( reinterpret_cast<char*>(&startChromID) , sizeof(uint32_t) );
startChromID=endian::LittleLong(startChromID);
itemStream.read( reinterpret_cast<char*>(&startBase) , sizeof(uint32_t) );
startBase=endian::LittleLong(startBase);
itemStream.read( reinterpret_cast<char*>(&endChromID) , sizeof(uint32_t) );
endChromID=endian::LittleLong(endChromID);
itemStream.read( reinterpret_cast<char*>(&endBase) , sizeof(uint32_t) );
endBase=endian::LittleLong(endBase);
if (isLeaf) {
uint64_t dataOffset;
uint64_t dataSize;
itemStream.read( reinterpret_cast<char*>(&dataOffset) , sizeof(uint64_t) );
dataOffset=endian::LittleDouble(dataOffset);
itemStream.read( reinterpret_cast<char*>(&dataSize) , sizeof(uint64_t) );
dataSize=endian::LittleDouble(dataSize);
//TODO Check creation here, it was incorrect.
thisNode->insertItem(new RPTreeLeafNodeItem(startChromID, startBase, endChromID, endBase,
dataOffset, dataSize));
} else {
// get the child node pointed to in the node item
uint64_t nodeOffset=0;
itemStream.read( reinterpret_cast<char*>(&nodeOffset) , sizeof(uint64_t) );
nodeOffset=endian::LittleDouble(nodeOffset);
// Recursive call to read next child node
// The test on chromIds is designed to stop the descent when the tree reaches the level of an
// individual chromosome. These are loaded later on demand.
RPTreeNode* childNode;
if (startChromID != endChromID || forceDescend) {
childNode = readRPTreeNode(fis, nodeOffset, forceDescend);
} else {
childNode = new RPTreeNodeProxy(*fis, nodeOffset, startChromID);
}
// insert child node item
thisNode->insertItem(new RPTreeChildNodeItem(startChromID, startBase, endChromID,
endBase, childNode));
}
fileOffset += itemSize;
}
} catch (...) {
throw new std::runtime_error("Error reading R+ tree nodes: \n");
}
// return success
return thisNode;
}
void IOHandler::loadDatasetsAndQuestionsFromFile(string FilePath)
{
int nDatasets,datasetSize,questionsSize;
string action;
string question;
char ch;
string str;
int index;
vector<string> dataset;
vector<string> questions;
vector <string> answers;
ifstream inFile(FilePath.c_str());
while(1)
{
inFile>>ch;
inFile>>index;
inFile>>ch;
//read dataset
inFile>>datasetSize;
getline(inFile, action); //to avoid "\n"
for(int j=0;j<datasetSize;j++){
getline(inFile, action);
dataset.push_back(action);
}
//read questions and answers
inFile>>questionsSize;
if(!getline(inFile, action)) break; //to avoid "\n"
for(int j=0;j<questionsSize;j++){
question = "";
getline(inFile, action);
istringstream itemStream(action);
string item;
while(!itemStream.eof())
{
itemStream>>item;
if(question == "") question = item;
else question = question +" "+item;
}
for(int k=(question.size()-1);;k--)
{
if(question[k] == ' ') {question.erase(k,1); break;}
question.erase(k,1);
}
answers.push_back(item);
questions.push_back(question);
}
//save
memory->addDatasetQuestionsAnswers(dataset,questions,answers);
dataset.clear();
questions.clear();
answers.clear();
}
inFile.close();
}
