/// <summary>
/// Populate input parameters for PaDeNA
/// </summary>
/// <param name="input">AssemblyInputEventArgs object to which the parameters should be populated</param>
public void GetPaDeNAInput(AssemblyInputEventArgs input)
{
input.AssemblerUsed = AssemblerType.PaDeNA;
input.KmerLength = this.kmerLength;
input.DanglingLinksThreshold = this.dangleThreshold;
input.RedundantPathLengthThreshold = this.redundantThreshold;
input.ErosionEnabled = this.IsErosionEnabled;
if (this.IsErosionEnabled)
{
input.ErosionThreshold = this.erosionThreshold;
}
input.LowCoverageContigRemovalEnabled = this.IsLowCoverageContigRemovalEnabled;
if (this.IsLowCoverageContigRemovalEnabled)
{
input.LowCoverageContigRemovalThreshold = this.lowCoverageContigRemovalThreshold;
}
if (scaffoldGenerationParameters.IsChecked == true)
{
input.GenerateScaffolds = true;
input.ScaffoldRedundancy = this.scaffoldRedundancy;
input.Depth = this.depth;
}
else
{
input.GenerateScaffolds = false;
}
}
/// <summary>
/// Gets called when submit button is clicked.
/// </summary>
/// <param name="sender">Submit button.</param>
/// <param name="e">Event data.</param>
private void OnSubmitButtonClicked(object sender, RoutedEventArgs e)
{
bool valid = this.ParseValues();
// Validation required. Try to read the arguments and validate the input
AssemblyInputEventArgs assemblerInput = new AssemblyInputEventArgs(null, null);
if (valid && simpleSequenceAssemblerOptionButton.IsChecked == true)
{
assemblerInput.AlignerInput = new AlignerInputEventArgs();
valid = GetAlignmentInput(stkAlingerParam, assemblerInput, null);
}
if (valid)
{
this.submit = true;
this.Close();
}
}
/// <summary>
/// Populate input parameters for PaDeNA
/// </summary>
/// <param name="input">AssemblyInputEventArgs object to which the parameters should be populated</param>
public void GetPaDeNAInput(AssemblyInputEventArgs input)
{
input.AssemblerUsed = AssemblerType.PaDeNA;
input.KmerLength = this.kmerLength;
input.DanglingLinksThreshold = this.dangleThreshold;
input.RedundantPathLengthThreshold = this.redundantThreshold;
if (scaffoldGenerationParameters.IsChecked == true)
{
input.ScaffoldRedundancy = this.scaffoldRedundancy;
input.Depth = this.depth;
}
else
{
input.ScaffoldRedundancy = null;
input.Depth = null;
}
}
/// <summary>
/// Get the aligner input paramater from the controls in stack panel
/// </summary>
/// <param name="stkPanel">Stack panel object</param>
/// <param name="assemblyInput">aligner input object</param>
/// <param name="alphabet"> Alphabet of the Selected sequences.</param>
/// <returns>Are parameters valid</returns>
public bool GetAlignmentInput(
StackPanel stkPanel,
AssemblyInputEventArgs assemblyInput, IAlphabet alphabet)
{
AlignerInputEventArgs alignerInput;
TextBox textBox;
int intValue;
float floatValue;
alignerInput = assemblyInput.AlignerInput;
foreach (UIElement uiElement in stkPanel.Children)
{
if (uiElement is TextBox)
{
textBox = uiElement as TextBox;
switch (textBox.Tag.ToString())
{
case PairwiseAlignmentAttributes.GapOpenCost:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.GapCost = intValue;
}
else
{
MessageDialogBox.Show(
Resource.INVALID_TEXT
+ PairwiseAlignmentAttributes.GapOpenCost
+ Resource.VALUE_TEXT,
Properties.Resource.CAPTION,
MessageDialogButton.OK);
return(false);
}
break;
case PairwiseAlignmentAttributes.GapExtensionCost:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.GapExtensionCost = intValue;
}
else
{
MessageDialogBox.Show(
Resource.INVALID_TEXT
+ PairwiseAlignmentAttributes.GapExtensionCost
+ Resource.VALUE_TEXT,
Properties.Resource.CAPTION,
MessageDialogButton.OK);
return(false);
}
break;
case MUMmerAttributes.LengthOfMUM:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.LengthOfMUM = intValue;
}
else
{
MessageDialogBox.Show(
Resource.INVALID_TEXT
+ NUCmerAttributes.LengthOfMUM
+ Resource.VALUE_TEXT,
Properties.Resource.CAPTION,
MessageDialogButton.OK);
return(false);
}
break;
case NUCmerAttributes.FixedSeparation:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.FixedSeparation = intValue;
}
else
{
MessageDialogBox.Show(
Resource.INVALID_TEXT
+ NUCmerAttributes.FixedSeparation
+ Resource.VALUE_TEXT,
Properties.Resource.CAPTION,
MessageDialogButton.OK);
return(false);
}
break;
case NUCmerAttributes.MaximumSeparation:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.MaximumSeparation = intValue;
}
else
{
MessageDialogBox.Show(
Resource.INVALID_TEXT
+ NUCmerAttributes.MaximumSeparation
+ Resource.VALUE_TEXT,
Properties.Resource.CAPTION,
MessageDialogButton.OK);
return(false);
}
break;
case NUCmerAttributes.MinimumScore:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.MinimumScore = intValue;
}
else
{
MessageDialogBox.Show(
Resource.INVALID_TEXT
+ NUCmerAttributes.MinimumScore
+ Resource.VALUE_TEXT,
Properties.Resource.CAPTION,
MessageDialogButton.OK);
return(false);
}
break;
case NUCmerAttributes.SeparationFactor:
if (float.TryParse(textBox.Text.Trim(), out floatValue))
{
alignerInput.SeparationFactor = floatValue;
}
else
{
MessageDialogBox.Show(
Resource.INVALID_TEXT
+ NUCmerAttributes.SeparationFactor
+ Resource.VALUE_TEXT,
Properties.Resource.CAPTION,
MessageDialogButton.OK);
return(false);
}
break;
case NUCmerAttributes.BreakLength:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.BreakLength = intValue;
}
else
{
MessageDialogBox.Show(
Resource.INVALID_TEXT
+ NUCmerAttributes.BreakLength
+ Resource.VALUE_TEXT,
Properties.Resource.CAPTION,
MessageDialogButton.OK);
return(false);
}
break;
default:
break;
}
}
else if (uiElement is ComboBox)
{
ComboBox comboBox = uiElement as ComboBox;
switch (comboBox.Tag.ToString())
{
case PairwiseAlignmentAttributes.SimilarityMatrix:
if (comboBox.SelectedValue != null && comboBox.SelectedIndex == 0) // DSM
{
int matchScore = 0;
int missmatchScore = 0;
int.TryParse(txtMatchScore.Text, out matchScore);
int.TryParse(txtMisMatchScore.Text, out missmatchScore);
alignerInput.SimilarityMatrix = new DiagonalSimilarityMatrix(matchScore, missmatchScore);
}
if (null != comboBox.SelectedValue && comboBox.SelectedIndex > 0)
{
string similarityMatrixOption = comboBox.SelectedValue.ToString();
if (Enum.IsDefined(
typeof(SimilarityMatrix.StandardSimilarityMatrix),
similarityMatrixOption))
{
SimilarityMatrix.StandardSimilarityMatrix matrix =
(SimilarityMatrix.StandardSimilarityMatrix)Enum.Parse(
typeof(SimilarityMatrix.StandardSimilarityMatrix),
similarityMatrixOption,
true);
alignerInput.SimilarityMatrix = new SimilarityMatrix(matrix);
}
else
{
MessageDialogBox.Show(
Resource.INVALID_TEXT
+ PairwiseAlignmentAttributes.SimilarityMatrix
+ Resource.VALUE_TEXT,
Properties.Resource.CAPTION,
MessageDialogButton.OK);
return(false);
}
}
break;
default:
break;
}
}
}
return(true);
}