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Parser.cpp
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Parser.cpp
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#include "Parser.h"
#include <string>
#include <fstream>
#include <iostream>
using namespace std;
const char Parser::PAIR_SEPARATOR[] = "************************************"
"************************************";
Parser::Parser() {
scoreCombination = BOUNDARIES_SUMMED;
windowLength = 20;
printAll = false;
scoreMatrix = NULL;
}
int Parser::parse(string intputFile, string outputFile) {
inputStream.open(intputFile.c_str());
if (!inputStream) {
cerr << "error: Failed to open file \"" << intputFile << "\"" << endl;
return OPEN_FAIL;
}
IntronStorage storage;
int status = parseNext();
while (status != NO_MORE_ALIGNMENTS) {
if (scoreCombination == BOUNDARIES_SUMMED) {
alignment.scoreIntrons(windowLength, false, scoreMatrix, kernel);
} else {
alignment.scoreIntrons(windowLength, true, scoreMatrix, kernel);
}
alignment.storeIntrons(storage);
status = parseNext();
}
storage.normalizeScores(0, maxScore());
storage.printIntrons(outputFile, printAll);
inputStream.close();
return READ_SUCCESS;
}
int Parser::parseNext() {
int consecutiveSeparators = 0;
string line;
while (getline(inputStream, line)) {
if (line == PAIR_SEPARATOR) {
consecutiveSeparators++;
if (consecutiveSeparators == NUM_SEPARATORS) {
return alignment.parse(inputStream);
}
} else {
consecutiveSeparators = 0;
}
}
return NO_MORE_ALIGNMENTS;
}
double Parser::maxScore() {
if (scoreMatrix == NULL) {
return COMPLETE_MATCH;
} else {
return scoreMatrix->getMaxScore();
}
}
void Parser::setScoringCombination(int combination) {
scoreCombination = combination;
}
void Parser::setWindowLegth(int length) {
windowLength = length;
}
void Parser::printAllSites() {
printAll = true;
}
void Parser::printCanonicalsites() {
printAll = false;
}
void Parser::setScoringMatrix(const ScoreMatrix * scoreMatrix) {
this->scoreMatrix = scoreMatrix;
}
void Parser::setKernel(Kernel* kernel) {
this->kernel = kernel;
}