//################################### MAIN PROGRAM #########################################
static void Main(string[] args)
{
Console.Clear();
string[] input = args;
bool check;
//Check if all input variables are valid. If valid check = true.
check = Validation.ValidationInput(input);
if (check)
{
// Variables to hold the arguments passed by the user
string searchType = input[0];
string fileName = input[1];
string fullpath = fileName;
string searchParameter1 = input[2];
string searchParameter2;
if (input.Length <= 3)
{
searchParameter2 = "";
}
else
{
searchParameter2 = input[3];
}
// Variables used to print and save sequence in the search type: level2 and level3
bool printControl = false;
int numLines = 0;
bool searchFound = false; //Used to print message for sequences not found
List <string> query = new List <string>();
if (searchType == "-level3")
{
numLines = Function.CounLine(searchParameter1); // Count the number of line in a file
query = Function.CreateListFromFile(searchParameter1); // Save sequences found in a list to be saved in a file (-level3)
}
int[] queryFound = new int[numLines]; //Used to print message for sequences not found (-level3)
string[] sequencesFound = new string[numLines * 2]; //Hold the sequences found in a list (-level3)
// Open file (input[1]) and execute the search program.
FileStream newFile = new FileStream(fullpath, FileMode.Open, FileAccess.Read);
StreamReader readFile = new StreamReader(newFile);
string recordIn = readFile.ReadLine();
double countDna = 0;
int indexNumber = 0;
// Search 4 using direct access
if (searchType == "-level4")
{
Search.SearchLevel_4(fileName, searchParameter1, searchParameter2, input[4]);
}
else
{
while (recordIn != null)
{
string line = recordIn;
countDna = countDna + 1;
if (searchType == "-level1")
{
Search.SearchLevel_1(line, countDna, searchParameter1, searchParameter2);
}
else if (searchType == "-level2")
{
if (printControl)
{
Console.WriteLine(line);
printControl = false;
}
printControl = Search.SearchLevel_2(line, countDna, searchParameter1);
if (printControl)
{
searchFound = true;
}
}
else if (searchType == "-level3")
{
// Lines which will be included in the file
if (printControl)
{
sequencesFound[indexNumber] = line;
indexNumber++;
printControl = false;
}
bool controlLine = false; // Controle the line that will be save in the array.
for (int i = 0; i < query.Count; i++)
{
string lineFound = Search.SearchLevel_3(line, countDna, query[i]);
// Lines which will be included in the file
if (lineFound != null && controlLine == false)
{
sequencesFound[indexNumber] = line;
indexNumber++;
printControl = true;
controlLine = true;
}
// Control the sequences that were not found to return an alert to the user
if (lineFound != null)
{
queryFound[i] = 1;
}
}
}
else if (searchType == "-level5")
{
int count = 0;
int sequenceFound = Search.SearchLevel_5(fileName, searchParameter1, countDna, line);
count = count + sequenceFound;
if (count > 0)
{
searchFound = true;
}
}
else if (searchType == "-level6")
{
int count = 0;
int sequenceFound = Search.SearchLevel_6(searchParameter1, countDna, line);
count = count + sequenceFound;
if (count > 0)
{
searchFound = true;
}
}
else if (searchType == "-level7")
{
string pattern = searchParameter1.Replace("*", "[A-Z]*"); // Create a regex pattern
pattern = "^" + pattern + "$"; // Create a regex pattern
Match patterFound = Regex.Match(line, pattern); // Compare the pattern to each line of the file
if (patterFound.Success)
{
Search.SearchLevel_7(fileName, countDna);
searchFound = true;
}
}
recordIn = readFile.ReadLine();
}
readFile.Close();
newFile.Close();
}
// Print error messages for sequences lines that exceed the number of the lines in the file
if (searchType == "-level1")
{
Validation.ValidationOutput(fileName, searchParameter1, searchParameter2, countDna);
}
// Write to file seqeunces found and print message for sequences not found
if (searchType == "-level3")
{
Validation.ValidationOutput(searchParameter2, query, queryFound, sequencesFound);
}
// Print message for sequences not found in search -level2, 5, 6 and 7.
if (
(searchType == "-level2" && searchFound != true) ||
(searchType == "-level5" && searchFound != true) ||
(searchType == "-level6" && searchFound != true) ||
(searchType == "-level7" && searchFound != true)
)
{
Alerts.Alert_7(searchParameter1);
}
}
}