/// <summary>
/// This event is fired when user wants to assemble the sequences.
/// This event will be raised by IAssembler. The controller class
/// instantiates algorithm implementation to perform assembly.
/// </summary>
/// <param name="e">Assembly input arguments.</param>
private void OnRunAssemblerAlgorithm(AssemblyInputEventArgs e)
{
if (e.Sequences != null && e.Aligner != null)
{
this.btnCancelAssemble.Enabled = this.cancelAssemblyButtonState = true;
this.ChangeStatusBar(string.Format(Resources.ASSEMBLER_STATUS_BAR, Resources.ASSEMBLING));
this.assemblerThread = new BackgroundWorker();
this.assemblerThread.WorkerSupportsCancellation = true;
this.assemblerThread.DoWork += this.OnAssembleStarted;
this.assemblerThread.RunWorkerCompleted += this.OnAssemblerCompleted;
this.assemblerThread.RunWorkerAsync(e);
}
}
/// <summary>
/// This method runs assembly on the list of sequences passed.
/// Additionally the user is allowed to select the
/// alignment algorithm.
/// </summary>
/// <param name="input">Input for the assembly process.</param>
/// <param name="worker">The Assembly parser thread</param>
/// <returns>IDeNovoAssembly instance.</returns>
private static IDeNovoAssembly RunAssembly(AssemblyInputEventArgs input, BackgroundWorker worker)
{
double mergeThreshold = input.MergeThreshold;
List<ISequence> sequence = input.Sequences.ToList();
var assemble = new OverlapDeNovoAssembler();
assemble.OverlapAlgorithm = input.Aligner;
// Special casing for SW alignment.
if (assemble.OverlapAlgorithm is SmithWatermanAligner)
{
// If we set the Threshold value lesser than the Max score, then the result will be “JUNK”.
// So setting the threshold value to 25 approximately supports sequence length of 15,0000.
mergeThreshold = 25;
}
assemble.MergeThreshold = mergeThreshold;
assemble.OverlapAlgorithm.SimilarityMatrix = input.AlignerInput.SimilarityMatrix;
assemble.OverlapAlgorithm.GapOpenCost = input.AlignerInput.GapCost;
assemble.OverlapAlgorithm.GapExtensionCost = input.AlignerInput.GapExtensionCost;
assemble.ConsensusResolver = new SimpleConsensusResolver(input.ConsensusThreshold);
assemble.AssumeStandardOrientation = false;
AssignAlignerParameter(assemble.OverlapAlgorithm, input.AlignerInput);
IDeNovoAssembly assemblyOutput = assemble.Assemble(sequence);
if (worker != null && worker.CancellationPending)
{
return null;
}
return assemblyOutput;
}
/// <summary>
/// Callback method from input selection model which will actually do the selected operation
/// </summary>
/// <param name="selectedSequences">List of sequences depending on the user selections made</param>
/// <param name="args">Any arguments passed when calling the selection model</param>
private void DoAssembly(List<ISequence> selectedSequences, params object[] args)
{
// Verify none of the sequences are protein - we cannot assembly these because we
// cannot align them (no complements).
if (selectedSequences.Any(s => s.Alphabet is ProteinAlphabet))
{
MessageBox.Show(
Resources.PROTEIN_NOT_SUPPORTED,
Resources.CAPTION,
MessageBoxButtons.OK,
MessageBoxIcon.Error);
return;
}
Globals.ThisAddIn.Application.Cursor = XlMousePointer.xlWait;
var assemblerDialog = new AssemblyInputDialog(false, selectedSequences[0].Alphabet);
var assemblyInputHelper = new WindowInteropHelper(assemblerDialog);
assemblyInputHelper.Owner = (IntPtr)Globals.ThisAddIn.Application.Hwnd;
assemblerDialog.Activated += this.OnWPFWindowActivated;
if (assemblerDialog.Show())
{
var eventArgs = new AssemblyInputEventArgs(selectedSequences, assemblerDialog.Aligner);
eventArgs.ConsensusThreshold = assemblerDialog.ConsensusThreshold;
eventArgs.MatchScore = assemblerDialog.MatchScore;
eventArgs.MergeThreshold = assemblerDialog.MergeThreshold;
eventArgs.MismatchScore = assemblerDialog.MisMatchScore;
eventArgs.AlignerInput = assemblerDialog.GetAlignmentInput();
if (eventArgs.AlignerInput != null) // If fetching parameters were successful
{
this.OnRunAssemblerAlgorithm(eventArgs);
}
}
}
