/// <summary>
/// The key method in the controller class, where fastqFile_components are serialized and deserialized in and out of
/// the classes queues for processing. The tasks are constructed through an interface - ITaskStrategy - which
/// is designated through the task abstract factory class (TaskDiscriminator.cs). After processing, files are deserialized and a details class
/// for each component is populated, as are the global scores. The use of Abstract/interface classes here allows multiple components
/// to be processed with multiple task types within this basic code structure.
/// </summary>
/// <param name="worker">The backgroundworker thread</param>
/// <param name="input">Generic inputs, including taskname and any further details necessary to complete a task such as nucleotide scores etc.</param>
public void PerformAction(BackgroundWorker worker, GenericFastqInputs input)
{
BackgroundWorker loadWorker = worker;
if (fqFileMap != null && (CONTROLLER_STATE == FastqControllerState.STATE_READY || CONTROLLER_STATE == FastqControllerState.PARSING))
{
sw = new Stopwatch();
sw.Start();
try
{
toDeserialize = new Queue <String>(fqFileMap.getFileComponentDirectories());
PrimeFqFileComponentQueue();
protobufSerialization = new ProtocolBuffersSerialization();
ITaskStrategy task = TaskDiscrimination.getTask(input.TaskAction);
Console.WriteLine("Performing {0}", task.getStatement());
int count = 0;
while (toPerform.Count != 0)
{
Double progressPercent = (Double)(count / (Double)fqFileMap.getFileComponentDirectories().Count);
loadWorker.ReportProgress((int)(progressPercent * 100), task.getReportStatement());
FqFile_Component activeComponent = toPerform.Dequeue();
activeComponent.setFqHashMap(fqFileMap.FqReadMap);
if (toDeserialize.Count != 0)
{
int threadId;
ProtocolBuffersSerialization.ProbufDeserializeFqFile_AsyncMethodCaller caller
= new ProtocolBuffersSerialization.ProbufDeserializeFqFile_AsyncMethodCaller(protobufSerialization.ProtobufDerializeFqFile);
String componentFileName = toDeserialize.Dequeue();
IAsyncResult result = caller.BeginInvoke(componentFileName, out threadId, null, null);
Console.WriteLine("\n*** Processing: {0} ***\n", activeComponent.getFileName());
input.FastqFile = activeComponent;
input = task.perform(input);
activeComponent = (FqFile_Component)input.FastqFile;
BuildFqFileMap(activeComponent);
FqFile_Component returnValue = caller.EndInvoke(out threadId, result);
toPerform.Enqueue(returnValue);
}
else if (toDeserialize.Count == 0)
{
Console.WriteLine("\n*** Processing: {0} ***\n", activeComponent.getFileName());
input.FastqFile = activeComponent;
input = task.perform(input);
activeComponent = (FqFile_Component)input.FastqFile;
BuildFqFileMap(activeComponent);
}
toSerialize.Enqueue(activeComponent);
SerializeFqComponentToMemory();
count++;
}
SerializeRemainingFqComponents();
task.confirmTaskEnd();
Console.WriteLine("\n*********\n");
fqFileMap.CalculateGlobalFileScores();
fqFileMap.GlobalDetails.OutputToConsole();
loadWorker.ReportProgress(100, task.getReportStatement());
sw.Stop();
Console.WriteLine("Task: {0} Completed in Time: {1}", task.getStatement(), sw.Elapsed);
fqFileMap.LastTask = input.TaskAction;
fqFileMap.TimeTaken = sw.Elapsed.ToString();
observer.UpdateGUIThread(input);
}
catch (IOException exception)
{
ControllerStateFailureResponse(exception.ToString(), "Error");
}
catch (InsufficientMemoryException exception)
{
ControllerStateFailureResponse(exception.ToString(), "Error");
}
catch (OutOfMemoryException exception)
{
ControllerStateFailureResponse(exception.ToString(), "Error");
}
catch (ArithmeticException exception)
{
ControllerStateFailureResponse(exception.ToString(), "Error");
}
sw.Stop();
}
}
/// <summary>
/// The key method in the controller class, where fastqFile_components are serialized and deserialized in and out of
/// the classes queues for processing. The tasks are constructed through an interface - ITaskStrategy - which
/// is designated through the task abstract factory class (TaskDiscriminator.cs). After processing, files are deserialized and a details class
/// for each component is populated, as are the global scores. The use of Abstract/interface classes here allows multiple components
/// to be processed with multiple task types within this basic code structure.
/// </summary>
/// <param name="worker">The backgroundworker thread</param>
/// <param name="input">Generic inputs, including taskname and any further details necessary to complete a task such as nucleotide scores etc.</param>
public void PerformAction(BackgroundWorker worker, GenericFastqInputs input)
{
BackgroundWorker loadWorker = worker;
if (fqFileMap != null && (CONTROLLER_STATE == FastqControllerState.STATE_READY || CONTROLLER_STATE == FastqControllerState.PARSING))
{
sw = new Stopwatch();
sw.Start();
try
{
toDeserialize = new Queue<String>(fqFileMap.getFileComponentDirectories());
PrimeFqFileComponentQueue();
protobufSerialization = new ProtocolBuffersSerialization();
ITaskStrategy task = TaskDiscrimination.getTask(input.TaskAction);
Console.WriteLine("Performing {0}", task.getStatement());
int count = 0;
while (toPerform.Count != 0)
{
Double progressPercent = (Double)(count / (Double)fqFileMap.getFileComponentDirectories().Count);
loadWorker.ReportProgress((int)(progressPercent * 100), task.getReportStatement());
FqFile_Component activeComponent = toPerform.Dequeue();
activeComponent.setFqHashMap(fqFileMap.FqReadMap);
if (toDeserialize.Count != 0)
{
int threadId;
ProtocolBuffersSerialization.ProbufDeserializeFqFile_AsyncMethodCaller caller
= new ProtocolBuffersSerialization.ProbufDeserializeFqFile_AsyncMethodCaller(protobufSerialization.ProtobufDerializeFqFile);
String componentFileName = toDeserialize.Dequeue();
IAsyncResult result = caller.BeginInvoke(componentFileName, out threadId, null, null);
Console.WriteLine("\n*** Processing: {0} ***\n", activeComponent.getFileName());
input.FastqFile = activeComponent;
input = task.perform(input);
activeComponent = (FqFile_Component)input.FastqFile;
BuildFqFileMap(activeComponent);
FqFile_Component returnValue = caller.EndInvoke(out threadId, result);
toPerform.Enqueue(returnValue);
}
else if (toDeserialize.Count == 0)
{
Console.WriteLine("\n*** Processing: {0} ***\n", activeComponent.getFileName());
input.FastqFile = activeComponent;
input = task.perform(input);
activeComponent = (FqFile_Component)input.FastqFile;
BuildFqFileMap(activeComponent);
}
toSerialize.Enqueue(activeComponent);
SerializeFqComponentToMemory();
count++;
}
SerializeRemainingFqComponents();
task.confirmTaskEnd();
Console.WriteLine("\n*********\n");
fqFileMap.CalculateGlobalFileScores();
fqFileMap.GlobalDetails.OutputToConsole();
loadWorker.ReportProgress(100, task.getReportStatement());
sw.Stop();
Console.WriteLine("Task: {0} Completed in Time: {1}", task.getStatement(), sw.Elapsed);
fqFileMap.LastTask = input.TaskAction;
fqFileMap.TimeTaken = sw.Elapsed.ToString();
observer.UpdateGUIThread(input);
}
catch (IOException exception)
{
ControllerStateFailureResponse(exception.ToString(), "Error");
}
catch (InsufficientMemoryException exception)
{
ControllerStateFailureResponse(exception.ToString(), "Error");
}
catch (OutOfMemoryException exception)
{
ControllerStateFailureResponse(exception.ToString(), "Error");
}
catch (ArithmeticException exception)
{
ControllerStateFailureResponse(exception.ToString(), "Error");
}
sw.Stop();
}
}
