public static UserResponse getInstance()
{
if (uniqueInstance == null)
{
lock (syncLock)
{
uniqueInstance = new UserResponse();
}
}
return uniqueInstance;
}
private void SaveFastqAction(IFqFile fq, String fileName)
{
StreamWriter writer;
try
{
writer = new StreamWriter(@fileName);
saveWorker.ReportProgress(40, "[CREATING FASTQ FORMAT]");
for (int i = 0; i < fqFile.getFastqArraySize(); i++)
{
writer.Write(fqFile.getFastqSequenceByPosition(i).createFastqBlock(fqFile.getMap()));
}
saveWorker.ReportProgress(100, "[FASTQ FORMAT CREATED]");
writer.Flush();
writer.Close();
}
catch (IOException exception)
{
Console.WriteLine(exception.ToString());
UserResponse.ErrorResponse(exception.ToString());
}
}
private void SaveCSVAction(IFqFile fq, String fileName)
{
StreamWriter writer;
string COMMA_DELIMITER = ",";
string[] output;
try
{
writer = new StreamWriter(@fileName);
saveWorker.ReportProgress(30, "[CREATING CSV FORMAT]");
output = new string[] { "Sequence Index", "Header", "Total Nucleotides", "G Count", "C Count", "Misread Count", "Lower Threshold", "First Quartile",
"Median", "Mean", "Third Quartile", "Upper Threshold" };
writer.WriteLine(string.Join(COMMA_DELIMITER, output));
for (int i = 0; i < fqFile.getFastqArraySize(); i++)
{
FqSequence fqSeq = fqFile.getFastqSequenceByPosition(i);
output = new string[] { fqSeq.getSeqIndex().ToString(), fqSeq.getSequenceHeader(), fqSeq.getFastqSeqSize().ToString(), fqSeq.getGCount().ToString(),
fqSeq.getCCount().ToString(), fqSeq.getNCount().ToString(), fqSeq.getLowerThreshold().ToString(),
fqSeq.getFirstQuartile().ToString(), fqSeq.getMedian().ToString(), fqSeq.getMean().ToString(),
fqSeq.getThirdQuartile().ToString(), fqSeq.getUpperThreshold().ToString(),
fqSeq.createSequenceString(fqFile.getMap()) };
writer.WriteLine(string.Join(COMMA_DELIMITER, output));
}
saveWorker.ReportProgress(100, "[FASTQ FORMAT CREATED]");
writer.Flush();
writer.Close();
}
catch (IOException exception)
{
Console.WriteLine(exception.ToString());
UserResponse.ErrorResponse(exception.ToString());
}
}
private void SaveFastaAction(IFqFile fq, String fileName)
{
saveWorker.ReportProgress(40, "[CREATING FASTA FORMAT]");
String output = fqFile.createFastaFormat("");
saveWorker.ReportProgress(100, "[FASTA FORMAT CREATED]");
StreamWriter writer;
try
{
writer = new StreamWriter(@fileName);
writer.Write(output);
writer.Flush();
writer.Close();
}
catch (IOException exception)
{
Console.WriteLine(exception.ToString());
UserResponse.ErrorResponse(exception.ToString());
}
}
/// <summary>
/// Parses file into component chunks through the parseFastq class before handing component details to FastqController
/// for processing.
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void loadWorker_DoWork(object sender, DoWorkEventArgs e)
{
BackgroundWorker worker = sender as BackgroundWorker;
InputFq input = (InputFq)e.Argument;
FileStream fileStream = input.fileStream;
String fileName = input.fileName;
ParseFastq parseFq;
if ((worker.CancellationPending == true))
{
e.Cancel = true;
}
else
{
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
try
{
worker.ReportProgress(3, "[PARSING FILE]");
parseFq = new ParseFastq(fileStream, fileName);
if (parseFq.getFastqFileCheck() == true && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
//Create new fqFileMap in controller and prime state for load
FastqController.CONTROLLER_STATE = FastqController.FastqControllerState.PARSING;
FastqController.getInstance().CreateNewFastqFile(fileName, parseFq.GetFastqFileLength());
FastqController.getInstance().GetFqFileMap().InitializeReadMap();
int fqFileComponentNumber = 1;
ProtocolBuffersSerialization protoBuf = new ProtocolBuffersSerialization();
GenericFastqInputs processInputs = new GenericFastqInputs();
processInputs.TaskAction = Task_LoadTask.statement;
ITaskStrategy task = TaskDiscrimination.getTask(processInputs.TaskAction);
// Uses IEnummerable yield return to parse components back to this class via this foreach loop
foreach (FqFile_Component fqFileComponent in parseFq.ParseComponents())
{
Double progressPercent = (Double)(((fqFileComponentNumber - 1) * FqFileMap.FQ_BLOCK_LIMIT) / (Double)(parseFq.GetLineCount() / 4));
worker.ReportProgress((int)(progressPercent * 100), ParseFastq.REPORT_STATEMENT);
if (fqFileComponent.getFastqArraySize() >= 1)
{
int threadId;
String componentFileName = FastqController.getInstance().GetFqFileMap().FileGUID + "_" + Path.GetFileNameWithoutExtension(fileName) + "_" + fqFileComponentNumber + ProtocolBuffersSerialization.PROTOBUF_FILE_EXTENSION;
fqFileComponent.setFastqFileName(componentFileName);
fqFileComponent.setComponentNumber(fqFileComponentNumber);
fqFileComponent.setFqHashMap(FastqController.getInstance().GetFqFileMap().FqReadMap);
processInputs.FastqFile = fqFileComponent;
processInputs = task.perform(processInputs);
FastqController.getInstance().BuildFqFileMap(processInputs.FastqFile);
ProtocolBuffersSerialization.ProbufSerializeFqFile_AsyncMethodCaller caller
= new ProtocolBuffersSerialization.ProbufSerializeFqFile_AsyncMethodCaller(protoBuf.ProtobufSerializeFqFile);
IAsyncResult result = caller.BeginInvoke((processInputs.FastqFile as FqFile_Component), componentFileName, out threadId, null, null);
Boolean returnValue = caller.EndInvoke(out threadId, result);
if (returnValue == false)
{
UserResponse.ErrorResponse("File serialization methods failed, please check you have hard disk space and restart the application", "File Error");
Console.WriteLine("Serialization failed");
loadWorker.CancelAsync();
}
else
{
FastqController.getInstance().addFqFileComponentDirectory(componentFileName);
}
fqFileComponentNumber++;
}
}
parseFq.CloseReader();
task.confirmTaskEnd();
Console.WriteLine("\n*********\n");
FastqController.getInstance().GetFqFileMap().CalculateGlobalFileScores();
FastqController.getInstance().GetFqFileMap().GlobalDetails.OutputToConsole();
loadWorker.ReportProgress(100, task.getReportStatement());
stopwatch.Stop();
Console.WriteLine("Task: {0} Completed in Time: {1}", task.getStatement(), stopwatch.Elapsed);
FastqController.getInstance().GetFqFileMap().LastTask = processInputs.TaskAction;
FastqController.getInstance().GetFqFileMap().TimeTaken = stopwatch.Elapsed.ToString();
this.UpdateGUIThread(processInputs);
}
else
{
worker.ReportProgress(0, "");
UserResponse.InformationResponse("File does not conform to standard format.", "File Error");
parseFq.CloseReader();
}
}
catch (IOException exception)
{
Console.Write(exception.StackTrace);
UserResponse.ErrorResponse(exception.ToString());
}
catch (InsufficientMemoryException exception)
{
Console.Write(exception.StackTrace);
UserResponse.ErrorResponse(exception.ToString());
}
catch (OutOfMemoryException exception)
{
Console.Write(exception.StackTrace);
UserResponse.ErrorResponse(exception.ToString());
}
catch (ArithmeticException exception)
{
Console.Write(exception.StackTrace);
UserResponse.ErrorResponse(exception.ToString());
}
FastqController.CONTROLLER_STATE = FastqController.FastqControllerState.STATE_READY;
stopwatch.Stop();
}
}
