public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
SequencerDecisionTree decTree = new SequencerDecisionTree(inputs.FastqFile);
inputs.FastqFile.Tests();
return(inputs);
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
List <FqSequence> foundSequences = inputs.FastqFile.findSequence(inputs.NucleotideSequence);
FastqController.getInstance().GetFqFileMap().AddSequenceQueryResults(foundSequences);
return(inputs);
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.cleanStarts(inputs.NucleotidesToClean);
inputs.FastqFile.cleanEnds(inputs.NucleotidesToClean);
inputs.FastqFile.Tests();
return(inputs);
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
SequencerDecisionTree decTree = new SequencerDecisionTree(inputs.FastqFile);
inputs.FastqFile.Tests();
return inputs;
}
/// <summary>
/// Updates the GUI. Calls the richText_Display and FastqGUI_Charts classes to update the information contained within them.
/// </summary>
/// <param name="newFqFile"></param>
public void UpdateGUI(GenericFastqInputs input)
{
Console.WriteLine("Total Memory Allocated: {0}", HelperMethods.ConvertBytesToMegabytes(GC.GetTotalMemory(false)));
ResetChartsSelectors();
drawChart(FastqController.getInstance().GetFqFileMap().GlobalDetails, FastqGUI_Charts.FastqChartTypes.Distribution.ToString());
display.Update(input, richText_Display);
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.cleanStarts(inputs.NucleotidesToClean);
inputs.FastqFile.cleanEnds(inputs.NucleotidesToClean);
inputs.FastqFile.Tests();
return inputs;
}
/// <summary>
/// Method responds to button clicks on the "remove sequences > with failed reads" menu item. It hands the task to the controller for
/// processing
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void withFailedReadsToolStripMenuItem_Click(object sender, EventArgs e)
{
if (FastqController.getInstance().fqFileMap != null && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
GenericFastqInputs inputs = new GenericFastqInputs();
inputs.TaskAction = Task_RemoveMisSeqeuence.statement;
FastqController.getInstance().InitializeAction(inputs);
}
}
/// <summary>
/// Method updates the GUI when on this thread or calls an invoke upon it for instances when called from non
/// COM thread. Ensures that alterations that occur within the GUI occur within its on thread model.
/// </summary>
/// <param name="newFqFile"></param>
public void UpdateGUIThread(GenericFastqInputs input)
{
if (this.InvokeRequired)
{
this.BeginInvoke(new UpdateFastqGUI(UpdateGUIThread), new object[] { input });
return;
}
UpdateGUI(input);
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
if (Preferences.getInstance().getSeqDecisionMethod())
{
SequencerDetermination seqDetermine = new SequencerDetermination(inputs.FastqFile);
}
else if (!Preferences.getInstance().getSeqDecisionMethod())
{
SequencerDecisionTree decTree = new SequencerDecisionTree(inputs.FastqFile);
}
return inputs;
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
writer = inputs.SaveStreamWriter;
FqFile_Component component = (FqFile_Component) inputs.FastqFile;
for (int i = 0; i < component.getFastqArraySize(); i++)
{
writer.Write(component.getFastqSequenceByPosition(i).createFastqBlock(component.getMap()));
}
return inputs;
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
if (Preferences.getInstance().getSeqDecisionMethod())
{
SequencerDetermination seqDetermine = new SequencerDetermination(inputs.FastqFile);
}
else if (!Preferences.getInstance().getSeqDecisionMethod())
{
SequencerDecisionTree decTree = new SequencerDecisionTree(inputs.FastqFile);
}
return(inputs);
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
writer = inputs.SaveStreamWriter;
FqFile_Component component = (FqFile_Component)inputs.FastqFile;
for (int i = 0; i < component.getFastqArraySize(); i++)
{
writer.Write(component.getFastqSequenceByPosition(i).createFastqBlock(component.getMap()));
}
return(inputs);
}
/// <summary>
/// Entry point for the thread, allows controller to create unified method signature for the PerformAction method.
/// Method checks threads state and hands of to PerformAction.
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
public void RunTask(object sender, DoWorkEventArgs e)
{
BackgroundWorker worker = sender as BackgroundWorker;
GenericFastqInputs input = (GenericFastqInputs)e.Argument;
if ((worker.CancellationPending == true))
{
e.Cancel = true;
}
else
{
PerformAction(worker, input);
}
}
/// <summary>
/// Method responds to button clicks on the find sequences tool strip menu iteam and then hands details to controller for processing
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void findSequenceToolStripMenuItem_Click(object sender, EventArgs e)
{
if (FastqController.getInstance().fqFileMap != null && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
InputBoxResult result = InputBox.Show("Enter a sequence you wish to find:", "Find Sequence", "", new InputBoxValidatingHandler(inputBox_SequenceValidating));
if (result.OK)
{
GenericFastqInputs inputs = new GenericFastqInputs();
inputs.NucleotideSequence = result.Text.Trim();
inputs.TaskAction = Task_FindSequences.statement;
FastqController.getInstance().GetFqFileMap().InitializeNewSequenceSearchList();
FastqController.getInstance().InitializeAction(inputs);
}
}
}
/// <summary>
/// Method responds to button clicks on the tail clean tool strip menu item. It obtains int for nucleotides to clean
/// from sequences and hands to controller for processing
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void cleanTailsToolStripMenuItem_Click(object sender, EventArgs e)
{
if (FastqController.getInstance().fqFileMap != null && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
InputBoxResult result = InputBox.Show("Enter a number of nucleotides to clean from tails:", "Clean Sequence Tails", "", new InputBoxValidatingHandler(inputBox_Validating));
if (result.OK)
{
if (HelperMethods.safeParseInt(result.Text.Trim()) == true)
{
GenericFastqInputs inputs = new GenericFastqInputs();
inputs.NucleotidesToClean = Int32.Parse(result.Text.Trim());
inputs.TaskAction = Task_TailCleanTask.statement;
FastqController.getInstance().InitializeAction(inputs);
}
}
}
}
private void belowLengthToolStripMenuItem_Click(object sender, EventArgs e)
{
if (FastqController.getInstance().fqFileMap != null && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
InputBoxResult result = InputBox.Show("Remove Sequences Below Threshold: ", "Remove Sequences", "", new InputBoxValidatingHandler(inputBox_SequenceLengthThresholdValidating));
if (result.OK)
{
if (HelperMethods.safeParseInt(result.Text.Trim()) == true)
{
GenericFastqInputs inputs = new GenericFastqInputs();
inputs.LengthThreshold = Int32.Parse(result.Text.Trim());
inputs.TaskAction = Task_RemoveSequencesBelowLength.statement;
FastqController.getInstance().InitializeAction(inputs);
}
}
}
}
/// <summary>
/// Key method in the display class, makes a decision on what to output based on the previous active task from the generic
/// inputs transport class. Also accepts instance of the richtextbox which will display the output.
/// </summary>
/// <param name="input">Instance of the transport class. Used in this instance to inform the display class of previous activity</param>
/// <param name="textBox">The rich text box that will display the outputs</param>
public void Update(GenericFastqInputs input, RichTextBox textBox)
{
this.fqMap = FastqController.getInstance().GetFqFileMap();
this.textBox = textBox;
if (input.TaskAction == Task_FindSequences.statement)
{
AddFoundSequenceData();
}
else
{
ClearText();
DisplayFileDetails();
DisplayFastqFileDetails();
DisplayComponentDetais();
}
}
/// <summary>
/// Responds to button click on the Save CSV Menu Item, opens dialogue to select filename and then passes details to the
/// controller class for processing.
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void saveCSVDataToolStripMenuItem_Click(object sender, EventArgs e)
{
if (FastqController.getInstance().fqFileMap != null && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
SaveFileDialog save = new SaveFileDialog();
save.Filter = "CSV File|*.csv|Text File|*.txt";
save.Title = "Save CSV File";
if (save.ShowDialog() == DialogResult.OK)
{
String fileName = save.FileName;
GenericFastqInputs inputs = new GenericFastqInputs();
inputs.SaveFileName = fileName;
inputs.TaskAction = Task_SaveCSV.statement;
FastqController.getInstance().InitializeAction(inputs);
}
}
}
/// <summary>
/// First point of call for the creation of a task within this class. Checks controller state is ready, then builds
/// a background worker thread for tasks and launches thread.
/// </summary>
/// <param name="genericInputs">Input details that are necessary within the task, including potential file components</param>
public void InitializeAction(GenericFastqInputs genericInputs)
{
if (fqFileMap != null && CONTROLLER_STATE == FastqControllerState.STATE_READY)
{
BackgroundWorker taskWorker = new BackgroundWorker();
taskWorker.WorkerReportsProgress = true;
taskWorker.WorkerSupportsCancellation = true;
taskWorker.DoWork += new DoWorkEventHandler(RunTask);
taskWorker.ProgressChanged += new ProgressChangedEventHandler(observer.loadWorker_ProgressChanged);
taskWorker.RunWorkerCompleted += new RunWorkerCompletedEventHandler(observer.loadWorker_Completed);
if (taskWorker.IsBusy != true)
{
taskWorker.RunWorkerAsync(genericInputs);
}
}
}
/// <summary>
/// Responds to button click on the Save Fastq Menu Item, opens dialogue to select filename and then passes details to the
/// controller class for processing.
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void saveFastqToolStripMenuItem_Click(object sender, EventArgs e)
{
if (FastqController.getInstance().fqFileMap != null && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
SaveFileDialog save = new SaveFileDialog();
save.Filter = FILE_DIALOGUE_FILTER;
save.Title = "Save Fastq File";
if (save.ShowDialog() == DialogResult.OK)
{
String fileName = save.FileName;
GenericFastqInputs inputs = new GenericFastqInputs();
inputs.SaveFileName = fileName;
inputs.InitializeStreamWriter(fileName);
inputs.TaskAction = Task_SaveFastq.statement;
FastqController.getInstance().InitializeAction(inputs);
}
}
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
StreamWriter writer;
String extension = Path.GetExtension(inputs.SaveFileName);
String fileName = Path.GetFileNameWithoutExtension(inputs.SaveFileName);
String[] part = Path.GetFileNameWithoutExtension(inputs.FastqFile.getFileName()).Split('_');
String directory = Path.GetDirectoryName(inputs.SaveFileName);
String number = part[part.Length - 1];
String FullName = String.Format(@"{0}{1}{2}_{3}{4}", directory, Path.DirectorySeparatorChar, fileName, number, extension);
string COMMA_DELIMITER = ",";
string[] output;
IFqFile fqFile = inputs.FastqFile;
writer = new StreamWriter(FullName);
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));
}
Console.WriteLine("Saving CSV TO: {0}", FullName);
writer.Flush();
writer.Close();
return(inputs);
}
public GenericFastqInputs cleanAdapters(List <Adapters.Adapter> adapters, Dictionary <int, FqNucleotideRead> map)
{
String sequence = createSequenceString(map);
GenericFastqInputs removedAdapter = null;
foreach (Adapters.Adapter adapter in adapters)
{
Match match = Regex.Match(adapter.AdapterSequence, sequence.ToUpper(), RegexOptions.IgnoreCase);
{
if (match.Success)
{
int key = match.Groups[1].Index;
cleanEnds(index - key);
removedAdapter = new GenericFastqInputs();
removedAdapter.AdapterName = adapter.AdapterName;
removedAdapter.SequenceIndex = SequenceIndex;
InfoLine = InfoLine + "||Removed Adapter:" + adapter.AdapterName;
}
}
}
return(removedAdapter);
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
StreamWriter writer;
String extension = Path.GetExtension(inputs.SaveFileName);
String fileName = Path.GetFileNameWithoutExtension(inputs.SaveFileName);
String[] part = Path.GetFileNameWithoutExtension(inputs.FastqFile.getFileName()).Split('_');
String directory = Path.GetDirectoryName(inputs.SaveFileName);
String number = part[part.Length - 1];
String FullName = String.Format(@"{0}{1}{2}_{3}{4}", directory, Path.DirectorySeparatorChar, fileName, number, extension);
string COMMA_DELIMITER = ",";
string[] output;
IFqFile fqFile = inputs.FastqFile;
writer = new StreamWriter(FullName);
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));
}
Console.WriteLine("Saving CSV TO: {0}", FullName);
writer.Flush();
writer.Close();
return inputs;
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.Tests();
return inputs;
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.removeBelowSequenceLength(inputs.LengthThreshold);
inputs.FastqFile.Tests();
return(inputs);
}
/// <summary>
/// Key method in the display class, makes a decision on what to output based on the previous active task from the generic
/// inputs transport class. Also accepts instance of the richtextbox which will display the output.
/// </summary>
/// <param name="input">Instance of the transport class. Used in this instance to inform the display class of previous activity</param>
/// <param name="textBox">The rich text box that will display the outputs</param>
public void Update(GenericFastqInputs input, RichTextBox textBox)
{
this.fqMap = FastqController.getInstance().GetFqFileMap();
this.textBox = textBox;
if (input.TaskAction == Task_FindSequences.statement)
AddFoundSequenceData();
else
{
ClearText();
DisplayFileDetails();
DisplayFastqFileDetails();
DisplayComponentDetais();
}
}
/// <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();
}
}
/// <summary>
/// First point of call for the creation of a task within this class. Checks controller state is ready, then builds
/// a background worker thread for tasks and launches thread.
/// </summary>
/// <param name="genericInputs">Input details that are necessary within the task, including potential file components</param>
public void InitializeAction(GenericFastqInputs genericInputs)
{
if (fqFileMap != null && CONTROLLER_STATE == FastqControllerState.STATE_READY)
{
BackgroundWorker taskWorker = new BackgroundWorker();
taskWorker.WorkerReportsProgress = true;
taskWorker.WorkerSupportsCancellation = true;
taskWorker.DoWork += new DoWorkEventHandler(RunTask);
taskWorker.ProgressChanged += new ProgressChangedEventHandler(observer.loadWorker_ProgressChanged);
taskWorker.RunWorkerCompleted += new RunWorkerCompletedEventHandler(observer.loadWorker_Completed);
if (taskWorker.IsBusy != true)
{
taskWorker.RunWorkerAsync(genericInputs);
}
}
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
//Show error message
return inputs;
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
//Show error message
return(inputs);
}
abstract public GenericFastqInputs perform(GenericFastqInputs inputs);
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.performSequenceStatistics();
return(inputs);
}
public GenericFastqInputs cleanAdapters(List<Adapters.Adapter> adapters, Dictionary<int, FqNucleotideRead> map)
{
String sequence = createSequenceString(map);
GenericFastqInputs removedAdapter = null;
foreach (Adapters.Adapter adapter in adapters)
{
Match match = Regex.Match(adapter.AdapterSequence, sequence.ToUpper(), RegexOptions.IgnoreCase);
{
if (match.Success)
{
int key = match.Groups[1].Index;
cleanEnds(index - key);
removedAdapter = new GenericFastqInputs();
removedAdapter.AdapterName = adapter.AdapterName;
removedAdapter.SequenceIndex = SequenceIndex;
InfoLine = InfoLine + "||Removed Adapter:" + adapter.AdapterName;
}
}
}
return removedAdapter;
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.removeBelowSequenceLength(inputs.LengthThreshold);
inputs.FastqFile.Tests();
return inputs;
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.removeSequencesAboveGCThreshold(inputs.GCThreshold);
inputs.FastqFile.Tests();
return inputs;
}
/// <summary>
/// Responds to button click on the Save Fastq Menu Item, opens dialogue to select filename and then passes details to the
/// controller class for processing.
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void saveFastqToolStripMenuItem_Click(object sender, EventArgs e)
{
if (FastqController.getInstance().fqFileMap != null && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
SaveFileDialog save = new SaveFileDialog();
save.Filter = FILE_DIALOGUE_FILTER;
save.Title = "Save Fastq File";
if (save.ShowDialog() == DialogResult.OK)
{
String fileName = save.FileName;
GenericFastqInputs inputs = new GenericFastqInputs();
inputs.SaveFileName = fileName;
inputs.InitializeStreamWriter(fileName);
inputs.TaskAction = Task_SaveFastq.statement;
FastqController.getInstance().InitializeAction(inputs);
}
}
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.removeBelowMeanThreshold(inputs.MeanThreshold);
inputs.FastqFile.Tests();
return inputs;
}
/// <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>
/// Method updates the GUI when on this thread or calls an invoke upon it for instances when called from non
/// COM thread. Ensures that alterations that occur within the GUI occur within its on thread model.
/// </summary>
/// <param name="newFqFile"></param>
public void UpdateGUIThread(GenericFastqInputs input)
{
if (this.InvokeRequired)
{
this.BeginInvoke(new UpdateFastqGUI(UpdateGUIThread), new object[] { input });
return;
}
UpdateGUI(input);
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.removeBelowMeanThreshold(inputs.MeanThreshold);
inputs.FastqFile.Tests();
return(inputs);
}
/// <summary>
/// Method responds to button clicks on the tail clean tool strip menu item. It obtains int for nucleotides to clean
/// from sequences and hands to controller for processing
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void cleanTailsToolStripMenuItem_Click(object sender, EventArgs e)
{
if (FastqController.getInstance().fqFileMap != null && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
InputBoxResult result = InputBox.Show("Enter a number of nucleotides to clean from tails:", "Clean Sequence Tails", "", new InputBoxValidatingHandler(inputBox_Validating));
if (result.OK)
{
if (HelperMethods.safeParseInt(result.Text.Trim()) == true)
{
GenericFastqInputs inputs = new GenericFastqInputs();
inputs.NucleotidesToClean = Int32.Parse(result.Text.Trim());
inputs.TaskAction = Task_TailCleanTask.statement;
FastqController.getInstance().InitializeAction(inputs);
}
}
}
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.removeSequencesWithMisreads();
inputs.FastqFile.Tests();
return inputs;
}
/// <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();
}
}
public abstract GenericFastqInputs perform(GenericFastqInputs inputs);
/// <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>
/// Updates the GUI. Calls the richText_Display and FastqGUI_Charts classes to update the information contained within them.
/// </summary>
/// <param name="newFqFile"></param>
public void UpdateGUI(GenericFastqInputs input)
{
Console.WriteLine("Total Memory Allocated: {0}", HelperMethods.ConvertBytesToMegabytes(GC.GetTotalMemory(false)));
ResetChartsSelectors();
drawChart(FastqController.getInstance().GetFqFileMap().GlobalDetails, FastqGUI_Charts.FastqChartTypes.Distribution.ToString());
display.Update(input, richText_Display);
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.removeSequencesAboveGCThreshold(inputs.GCThreshold);
inputs.FastqFile.Tests();
return(inputs);
}
/// <summary>
/// Method corresponds to the "remove sequences > below mean threshold" button click. It accepts a value for the mean threshold and then
/// passes to the controller for processing
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void belowMeanThresholdToolStripMenuItem_Click(object sender, EventArgs e)
{
if (FastqController.getInstance().fqFileMap != null && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
InputBoxResult result = InputBox.Show("Enter the Phred Mean Threshold For Sequences:", "Remove Sequences", "", new InputBoxValidatingHandler(inputBox_MeanThresholdValidating));
if (result.OK)
{
if (HelperMethods.safeParseInt(result.Text.Trim()) == true)
{
GenericFastqInputs inputs = new GenericFastqInputs();
inputs.MeanThreshold = Int32.Parse(result.Text.Trim());
inputs.TaskAction = Task_RemoveBelowMeanThreshold.statement;
FastqController.getInstance().InitializeAction(inputs);
}
}
}
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.performSequenceStatistics();
return inputs;
}
/// <summary>
/// Method responds to button clicks on the find sequences tool strip menu iteam and then hands details to controller for processing
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void findSequenceToolStripMenuItem_Click(object sender, EventArgs e)
{
if (FastqController.getInstance().fqFileMap != null && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
InputBoxResult result = InputBox.Show("Enter a sequence you wish to find:", "Find Sequence", "", new InputBoxValidatingHandler(inputBox_SequenceValidating));
if (result.OK)
{
GenericFastqInputs inputs = new GenericFastqInputs();
inputs.NucleotideSequence = result.Text.Trim();
inputs.TaskAction = Task_FindSequences.statement;
FastqController.getInstance().GetFqFileMap().InitializeNewSequenceSearchList();
FastqController.getInstance().InitializeAction(inputs);
}
}
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.cleanAdapters();
inputs.FastqFile.Tests();
return(inputs);
}
/// <summary>
/// Responds to button click on the Save CSV Menu Item, opens dialogue to select filename and then passes details to the
/// controller class for processing.
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void saveCSVDataToolStripMenuItem_Click(object sender, EventArgs e)
{
if (FastqController.getInstance().fqFileMap != null && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
SaveFileDialog save = new SaveFileDialog();
save.Filter = "CSV File|*.csv|Text File|*.txt";
save.Title = "Save CSV File";
if (save.ShowDialog() == DialogResult.OK)
{
String fileName = save.FileName;
GenericFastqInputs inputs = new GenericFastqInputs();
inputs.SaveFileName = fileName;
inputs.TaskAction = Task_SaveCSV.statement;
FastqController.getInstance().InitializeAction(inputs);
}
}
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
inputs.FastqFile.removeSequencesWithMisreads();
inputs.FastqFile.Tests();
return(inputs);
}
/// <summary>
/// Method responds to button clicks on the "remove sequences > with failed reads" menu item. It hands the task to the controller for
/// processing
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void withFailedReadsToolStripMenuItem_Click(object sender, EventArgs e)
{
if (FastqController.getInstance().fqFileMap != null && FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
GenericFastqInputs inputs = new GenericFastqInputs();
inputs.TaskAction = Task_RemoveMisSeqeuence.statement;
FastqController.getInstance().InitializeAction(inputs);
}
}
public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
List<FqSequence> foundSequences = inputs.FastqFile.findSequence(inputs.NucleotideSequence);
FastqController.getInstance().GetFqFileMap().AddSequenceQueryResults(foundSequences);
return inputs;
}
