/// <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
AlignerInputEventArgs alignerInput = new AlignerInputEventArgs();
valid = valid && GetAlignmentInput(stkAlingerParam, alignerInput, null);
if (valid)
{
this.submit = true;
this.Close();
}
}
/// <summary>
/// Get the aligner input parameter 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,
AlignerInputEventArgs alignerInput, IAlphabet alphabet)
{
TextBox textBox;
int intValue;
float floatValue;
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);
}
public bool GetPamsamInput(
StackPanel stkPanel,
AlignerInputEventArgs alignerInput, IAlphabet alphabet)
{
TextBox textBox;
int intValue;
try
{
foreach (UIElement uiElement in stkPanel.Children)
{
if (uiElement is TextBox)
{
textBox = uiElement as TextBox;
switch (textBox.Tag.ToString())
{
case PamsamAlignmentAttributes.KmerLength:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.KmerLength = intValue;
}
else
{
throw new ArgumentException(PamsamAlignmentAttributes.KmerLength);
}
break;
case PamsamAlignmentAttributes.GapOpenPenalty:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.GapOpenPenalty = intValue;
}
else
{
throw new ArgumentException(PamsamAlignmentAttributes.GapOpenPenalty);
}
break;
case PamsamAlignmentAttributes.GapExtendPenalty:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.GapExtendPenalty = intValue;
}
else
{
throw new ArgumentException(PamsamAlignmentAttributes.GapExtendPenalty);
}
break;
case PamsamAlignmentAttributes.NumberOfPartitions:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.NumberOfPartitions = intValue;
}
else
{
throw new ArgumentException(PamsamAlignmentAttributes.NumberOfPartitions);
}
break;
case PamsamAlignmentAttributes.DegreeOfParallelism:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.DegreeOfParallelism = intValue;
}
else
{
throw new ArgumentException(PamsamAlignmentAttributes.DegreeOfParallelism);
}
break;
}
}
else if (uiElement is ComboBox)
{
ComboBox comboBox = uiElement as ComboBox;
switch (comboBox.Tag.ToString())
{
case PamsamAlignmentAttributes.SimilarityMatrix:
if (null != comboBox.SelectedValue)
{
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;
case PamsamAlignmentAttributes.DistanceFunctionType:
if (!Enum.TryParse <DistanceFunctionTypes>(comboBox.Text, out alignerInput.DistanceFunctionName))
{
throw new ArgumentException(PamsamAlignmentAttributes.DistanceFunctionType);
}
break;
case PamsamAlignmentAttributes.UpdateDistanceMethodsType:
if (!Enum.TryParse <UpdateDistanceMethodsTypes>(comboBox.Text, out alignerInput.UpdateDistanceMethodsType))
{
throw new ArgumentException(PamsamAlignmentAttributes.UpdateDistanceMethodsType);
}
break;
case PamsamAlignmentAttributes.ProfileAlignerName:
if (!Enum.TryParse <ProfileAlignerNames>(comboBox.Text, out alignerInput.ProfileAlignerName))
{
throw new ArgumentException(PamsamAlignmentAttributes.ProfileAlignerName);
}
break;
case PamsamAlignmentAttributes.ProfileScoreFunctionName:
if (!Enum.TryParse <ProfileScoreFunctionNames>(comboBox.Text, out alignerInput.ProfileScoreFunctionName))
{
throw new ArgumentException(PamsamAlignmentAttributes.ProfileScoreFunctionName);
}
break;
}
}
}
}
catch (ArgumentException ae)
{
MessageDialogBox.Show(Resource.INVALID_TEXT
+ ae.Message
+ Resource.VALUE_TEXT,
Properties.Resource.CAPTION,
MessageDialogButton.OK);
return(false);
}
return(true);
}