//search level 4 code
static public void SearchLevel_4(string fileName, string parameter1, string parameter2, string resultFile)
{
List <string> indexList = Function.CreateListFromFile(parameter1); // List whith the sequeces plus offset
List <string> queryList = Function.CreateListFromFile(parameter2); // List with the sequeces to be searched
List <string> sequenceFound = new List <string>();
List <int> sequenceOffSet = new List <int>(); // Hold the list of offset to be used in the direct access
List <int> sequenceSize = new List <int>(); // Hold the sequence size to be used in the direct access
List <string> sequenceDnaList = new List <string>(); // Hold the sequence found to be used in writed file and erro alerts
// Split the data from the file index and put in lists
for (int q = 0; q < queryList.Count; q++)
{
for (int i = 0; i < indexList.Count; i++)
{
string[] sequenceId = indexList[i].Split(' ');
if (queryList[q] == sequenceId[0])
{
int offSet = Int32.Parse(sequenceId[1]);
int size = Int32.Parse(sequenceId[2]);
sequenceFound.Add(sequenceId[0]);
sequenceOffSet.Add(offSet);
sequenceSize.Add(size);
}
}
}
// Search the file using direct access
using (FileStream fs = new FileStream(fileName, FileMode.Open, FileAccess.Read))
{
for (int i = 0; i < sequenceFound.Count; i++)
{
byte[] bytes = new byte[sequenceSize[i] - 1];
fs.Seek(sequenceOffSet[i], SeekOrigin.Begin);
fs.Read(bytes, 0, sequenceSize[i] - 1); // Get data from the file
string sequenceDna = Encoding.Default.GetString(bytes);
if (!sequenceDnaList.Contains(sequenceDna)) // Avoid duplicate data in the file
{
sequenceDnaList.Add(sequenceDna);
}
}
}
// Write sequences found in a file
try
{
Function.WriteToFile(resultFile, sequenceDnaList.ToArray());
// Send alerts to the user informing the sequeces not found
for (int i = 0; i < queryList.Count; i++)
{
if (!sequenceFound.Contains(queryList[i]))
{
Alerts.Alert_9(queryList[i]);
}
}
}
catch // If 'resulFile' name is invalid
{
Alerts.Alert_8(resultFile);
}
}
// Write to file sequences found and print message for sequences not found (Search level 3)
static public void ValidationOutput(string searchParameter2, List <string> query, int[] queryFound, string[] sequencesFound)
{
try
{
Function.WriteToFile(searchParameter2, sequencesFound);
for (int i = 0; i < queryFound.Length; i++)
{
if (queryFound[i] == 0)
{
Alerts.Alert_9(query[i]);
}
}
}
catch
{
Alerts.Alert_8(searchParameter2);
}
}