//====================================================================
// GeneticsSimDataParser.cpp
// Implementation file for the data parser.
// Author: Dr. Rick Coleman
// Date: December 2009
//====================================================================
#pragma warning(disable : 4996)
#include "pch.h"
#include "GeneticsSimDataParser.h"
#include <string.h>

//-----------------------------------
// Constructor
//-----------------------------------
GeneticsSimDataParser::GeneticsSimDataParser(const char *fileName)
{
	// Initialize everything
	char line[128];
	m_iNumGenes = 0;
	m_iNextGeneNumber = 0;
	m_iNextParentNumber = 0;
	strcpy_s(m_sFileName, fileName);

	// Open the data file for reading
	inFile = new ifstream();				// Create an ifstream object
	inFile->open(fileName, fstream::in);	// Open it
	if (inFile->is_open())					// Make sure it is open
	{
		// Get the basic information
		while (getNextLine(line, 127))
		{
			if (strcmp(line, "<GENE>") == 0)
			{
				m_iNumGenes++;	// Count all wells
			}
			else if (strcmp(line, "<GENUS>") == 0)
			{
				getNextLine(line, 127); // Read the genus string
				strcpy_s(m_sGenus, line); // Save the genus name
			}
			else if (strcmp(line, "<SPECIES>") == 0)
			{
				getNextLine(line, 127); // Read the species string
				strcpy_s(m_sSpecies, line); // Save the species name
			}
			else if (strcmp(line, "<COMMON_NAME>") == 0)
			{
				getNextLine(line, 127); // Read the common name string
				strcpy_s(m_sCommonName, line); // Save the common name
			}
		}
		inFile->close();	// Close the file
		delete inFile;		// Destroy the ifstream object
	}
	else
	{
		cout << "Failed to open file\n";
		cout << "Program terminated.\n\n";
		exit(0);
	}
}

//-----------------------------------
// Destructor
//-----------------------------------
GeneticsSimDataParser::~GeneticsSimDataParser()
{
}

//-----------------------------------
// Get the number of genes
//-----------------------------------
int GeneticsSimDataParser::getGeneCount()
{
	return m_iNumGenes;
}

//-----------------------------------
// Get the genus name
//-----------------------------------
char *GeneticsSimDataParser::getGenus()
{
	return m_sGenus;
}

//-----------------------------------
// Get the species name
//-----------------------------------
char *GeneticsSimDataParser::getSpecies()
{
	return m_sSpecies;
}

//-----------------------------------
// Get the full scientific name
//-----------------------------------
char *GeneticsSimDataParser::getScientificName()
{
	// Build the full name just in case it hasn't been done
	sprintf_s(m_sSciName, "%s %s", m_sGenus, m_sSpecies);
	return m_sSciName;
}

//-----------------------------------
// Get the common name
//-----------------------------------
char *GeneticsSimDataParser::getCommonName()
{
	return m_sCommonName;
}

//--------------------------------------------------------------------------
// Get data on the next gene
// Args:	*trait - pointer to a character array to hold the trait name
//			*domDesc - pointer to a character array to hold the name of the
//						dominant allele name
//			*domSymbol - pointer to a char variable to hold the dominant
//						trait letter symbol
//			*recDesc - pointer to a character array to hold the name of the
//						recessive allele name
//			*recSymbol - pointer to a char variable to hold the recessive
//						trait letter symbol
//--------------------------------------------------------------------------
bool GeneticsSimDataParser::getGeneData(char *trait, char *domDesc, char *domSymbol,
	char *recDesc, char *recSymbol)
{
	int gNum = 0;
	char line[128];
	// Reopen the file
	inFile = new ifstream();
	inFile->open(m_sFileName, fstream::in);
	if (inFile->is_open())
	{
		// Read to the the current Gene count
		while (getNextLine(line, 127))
		{
			if (strcmp(line, "<GENE>") == 0) // Got one
			{
				if (gNum == m_iNextGeneNumber)
				{
					// Get data on this one
					while (getNextLine(line, 127))
					{
						// Get the gene trait name
						if (strcmp(line, "<GENE_TRAIT>") == 0)
						{
							if (getNextLine(line, 127))
							{
								strcpy(trait, line); // Set the trait name
							}
							else
								return false; // Oops!
						}
						else if (strcmp(line, "<DOMINANT_ALLELE>") == 0)
						{
							if (getNextLine(line, 127))
							{
								strcpy(domDesc, line); // Set the dominant allele name
							}
							else
								return false; // Oops!
						}
						else if (strcmp(line, "<DOMINANT_SYMBOL>") == 0)
						{
							if (getNextLine(line, 127))
							{
								*domSymbol = line[0]; // Set the dominant allele symbol
							}
							else
								return false; // Oops!
						}
						else if (strcmp(line, "<RECESSIVE_ALLELE>") == 0)
						{
							if (getNextLine(line, 127))
							{
								strcpy(recDesc, line); // Set the recessive allele name
							}
							else
								return false; // Oops!
						}
						else if (strcmp(line, "<RECESSIVE_SYMBOL>") == 0)
						{
							if (getNextLine(line, 127))
							{
								*recSymbol = line[0]; // Set the dominant allele symbol
							}
							else
								return false; // Oops!
						}
						else if (strcmp(line, "</GENE>") == 0)
						{
							m_iNextGeneNumber++; // Increment for next call to this function
							inFile->close();
							delete inFile; // Delete the istream object not the file
							return true; // Got it
						}
					} // end while
				} // end if(gNum == nextGene)
				else
				{
					gNum++; // Check the next one
				}
			}
		}
		inFile->close();
		delete inFile; // Delete the istream object not the file
	} // end if file open
	return false; // If we get here we have got all the genes
}

//--------------------------------------------------------------------------
// Get data on the next parent
// Args:	*genotype - pointer to a character array to hold the genotype
//						description as a string, e.g. "Tt Ss Ww Cc".  This
//                      is a pea plant with the phenotype of tall with
//						wrinkled, green seeds and purple flowers.  Its
//						genotype if heterozygous tall, heterozygous wrinkled
//						seeds, heterozygous green seeds, and heterozygous
//						purple flowers.
//--------------------------------------------------------------------------
bool GeneticsSimDataParser::getParentGenotype(char *genotype)
{
	int pNum = 0;
	char line[128];
	// Limit to only two parents in any one test
	if (m_iNextParentNumber >= 2) return false;

	// Reopen the file
	inFile = new ifstream();
	inFile->open(m_sFileName, fstream::in);
	if (inFile->is_open())
	{
		// Read to the the current sensor count
		while (getNextLine(line, 127))
		{
			if (strcmp(line, "<PARENT>") == 0) // Got one
			{
				if (pNum == m_iNextParentNumber)
				{
					// Get data on this one
					while (getNextLine(line, 127))
					{
						// Get the sensor type
						if (strcmp(line, "<GENOTYPE>") == 0)
						{
							if (getNextLine(line, 127)) // Read the genotype string
							{
								strcpy(genotype, line);
							}
							else
								return false; // Oops!
						}
						else if (strcmp(line, "</PARENT>") == 0)
						{
							m_iNextParentNumber++; // Increment for next call to this function
							inFile->close();
							delete inFile; // Delete the istream object not the file
							return true; // Got one
						}
					} // end while
				} // end if(pNum == nextParentNum)
				else
				{
					pNum++; // Check the next one
				}
			}
		}
		inFile->close();
		delete inFile; // Delete the istream object not the file
	} // end if file open
	return false; // If we get here we have got all the parents or failed to open file
}

//------------------------------------------------
// Function: getNextLine()
// Purpose: Reads lines from a file and places
//   them in buffer, removing any leading white
//   space.  Skips blank lines. Ignors comment
//   lines starting with <!-- and ending with -->
//
// Args:  buffer -- char array to read line into.
//        n -- length of buffer.
// Returns: True if a line was successfully read,
//    false if the end of file was encountered.
// Notes: Function provided by instructor.
//------------------------------------------------
bool GeneticsSimDataParser::getNextLine(char *buffer, int n)
{
	bool    done = false;
	char    tempBuf[128];
	char	*temp;
	while (!done)
	{
		inFile->getline(tempBuf, n); // Read a line from the file

		if (inFile->good())          // If a line was successfully read check it
		{
			if (strlen(tempBuf) == 0)     // Skip any blank lines
				continue;
			else if (strncmp(tempBuf, "<!--", 4) == 0) // Skip comment lines
				continue;
			else done = true;    // Got a valid data line so return with this line
		}
		else
		{
			strcpy(buffer, "");  // Clear the buffer array
			return false;        // Flag end of file
		}
	} // end while
	// Remove white space from end of string
	temp = &tempBuf[strlen(tempBuf)]; // point to closing \0
	temp--; // back up 1 space
	while (isspace(*temp))
	{
		*temp = '\0'; // Make it another NULL terminator
		temp--;  // Back up 1 char
	}
	// Remove white space from front of string
	temp = tempBuf;
	while (isspace(*temp)) temp++; // Skip leading white space
	// Copy remainder of string into the buffer
	strcpy(buffer, temp);
	return true;  // Flag a successful read
}


GeneticsSimDataParser::GeneticsSimDataParser()
{

}