/// <summary>
/// If all input parameters are satisfactory, this method is called to
/// prepare the parameters for analysis/post-QC filtering
/// </summary>
/// <param name="sender">Run button element</param>
/// <param name="e">Routed event args</param>
protected override void PrepareRun(object sender, RoutedEventArgs e)
{
#region Prepare event arguments for trimming
// Build event arguments
bool trimFromStart = this.comboItemFromLeft.IsSelected;
// Verify input parser
bool canAutoParse = base.VerifyInputParser(this.ioControl.Input, this.ioControl.SelectedInputParserType);
if (!canAutoParse)
{
MessageBox.Show(Resource.AUTOPARSE_FAIL);
}
else
{
// Verify output sequence formatters
ISequenceFormatter filtered = DetermineSequenceFormatter(this.ioControl.SelectedOutputParserType, this.ioControl.OutputFilename);
ISequenceFormatter discarded = DetermineSequenceFormatter(this.ioControl.SelectedOutputParserType, this.ioControl.DiscardedFilename);
if (filtered == null)
{
// The program shouldn't reach here
throw new ApplicationException(Resource.NonsenseError);
}
FilterToolArgs args;
if (this.IsInByLengthMode)
{
args = new TrimByLengthArgs(Convert.ToDouble(this.trimLengthValue.Text), trimFromStart, this.ioControl.Input, filtered, discarded, this.ioControl.OutputFilename);
}
else if (this.IsInByQualityMode)
{
int minLength = this.trimQualityMinLengthValue.Text.Equals("") ? TrimByQuality.MIN_LENGTH_DEFAULT : Convert.ToInt32(this.trimQualityMinLengthValue.Text);
args = new TrimByQualityArgs(Convert.ToByte(this.trimQualityValue.Text), trimFromStart, minLength, this.ioControl.Input, filtered, discarded, this.ioControl.OutputFilename);
}
else if (this.IsInByRegexMode)
{
args = new TrimByRegexArgs(this.ioControl.Input, filtered, discarded, this.trimRegexPattern.Text, this.ioControl.OutputFilename);
}
else
{
// The program shouldn't reach here either.
throw new ApplicationException(Resource.NonsenseError);
}
this.PrepareToTrim(sender, args);
// release files from memory
filtered.Dispose();
if (discarded != null)
{
discarded.Dispose();
}
}
#endregion
}
/// <summary>
/// If all input parameters are satisfactory, this method is called to
/// prepare the parameters for analysis/post-QC filtering
/// </summary>
/// <param name="sender">Run button element</param>
/// <param name="e">Routed event args</param>
protected override void PrepareRun(object sender, RoutedEventArgs e)
{
#region Prepare event arguments for discarding
// Verify input parser
bool canAutoParse = base.VerifyInputParser(this.ioControl.Input, this.ioControl.SelectedInputParserType);
if (!canAutoParse)
{
MessageBox.Show(Resource.AUTOPARSE_FAIL);
}
else
{
// Verify output sequence formatters
ISequenceFormatter filtered = DetermineSequenceFormatter(this.ioControl.SelectedOutputParserType, this.ioControl.OutputFilename);
ISequenceFormatter discarded = DetermineSequenceFormatter(this.ioControl.SelectedOutputParserType, this.ioControl.DiscardedFilename);
if (filtered == null)
{
// The program shouldn't reach here
throw new ApplicationException(Resource.NonsenseError);
}
FilterToolArgs args;
if (this.IsInByLengthMode)
{
args = new DiscardByLengthArgs(this.ioControl.Input, filtered, discarded, Convert.ToInt64(this.discardLengthValue.Text), this.ioControl.OutputFilename);
}
else if (this.IsInByQualityMode)
{
args = new DiscardByMeanQualityArgs(this.ioControl.Input, filtered, discarded, Convert.ToByte(this.discardQualityValue), this.ioControl.OutputFilename);
}
else if (this.IsInByRegexMode)
{
args = new DiscardByRegexArgs(this.ioControl.Input, filtered, discarded, this.discardRegexPattern.Text, this.ioControl.OutputFilename);
}
else
{
// The program shouldn't reach here either.
throw new ApplicationException(Resource.NonsenseError);
}
this.PrepareToDiscard(sender, args);
filtered.Dispose();
if (discarded != null)
{
discarded.Dispose();
}
}
#endregion
}
public static void ConvertFromOneFormatToAnother(string inputFileName, string outputFileName, ISequenceFormatter targetFormatter)
{
var parser = SequenceParsers.FindParserByFileName(inputFileName);
var sequenceList = parser.Parse();
var sequences = Helper.ConvertIenumerableToList(sequenceList);
targetFormatter.Open(outputFileName);
foreach (var sequence in sequences)
{
targetFormatter.Write(sequence);
}
targetFormatter.Close();
targetFormatter.Dispose();
}
public static void ConvertFromOneFormatToAnother(string inputFileName, string outputFileName, ISequenceFormatter targetFormatter)
{
var parser = SequenceParsers.FindParserByFileName(inputFileName);
var sequenceList = parser.Parse();
var sequences = Helper.ConvertIenumerableToList(sequenceList);
targetFormatter.Open(outputFileName);
foreach (var sequence in sequences)
{
targetFormatter.Write(sequence);
}
targetFormatter.Close();
targetFormatter.Dispose();
}
