/// <summary>
/// Get the aligner input paramater from the controls in stack panel
/// </summary>
/// <param name="assemblyInput">aligner input object</param>
/// <returns>Are parameters valid</returns>
public AlignerInputEventArgs GetAlignmentInput()
{
StackPanel stkPanel = this.stkAlingerParam;
AlignerInputEventArgs alignerInput = new AlignerInputEventArgs();
TextBox textBox;
int intValue;
float floatValue;
alignerInput.Aligner = this.Aligner;
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
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ PairwiseAlignmentAttributes.GapOpenCost
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return(null);
}
break;
case PairwiseAlignmentAttributes.GapExtensionCost:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.GapExtensionCost = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ PairwiseAlignmentAttributes.GapExtensionCost
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return(null);
}
break;
case MUMmerAttributes.LengthOfMUM:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.LengthOfMUM = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ NUCmerAttributes.LengthOfMUM
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return(null);
}
break;
case NUCmerAttributes.FixedSeparation:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.FixedSeparation = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ NUCmerAttributes.FixedSeparation
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return(null);
}
break;
case NUCmerAttributes.MaximumSeparation:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.MaximumSeparation = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ NUCmerAttributes.MaximumSeparation
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return(null);
}
break;
case NUCmerAttributes.MinimumScore:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.MinimumScore = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ NUCmerAttributes.MinimumScore
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return(null);
}
break;
case NUCmerAttributes.SeparationFactor:
if (float.TryParse(textBox.Text.Trim(), out floatValue))
{
alignerInput.SeparationFactor = floatValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ NUCmerAttributes.SeparationFactor
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return(null);
}
break;
case NUCmerAttributes.BreakLength:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.BreakLength = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ NUCmerAttributes.BreakLength
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return(null);
}
break;
default:
break;
}
}
else if (uiElement is ComboBox)
{
ComboBox comboBox = uiElement as ComboBox;
switch (comboBox.Tag.ToString())
{
case PairwiseAlignmentAttributes.SimilarityMatrix:
if (comboBox.SelectedIndex > 0) // user selected a SM other than 'DiagonalSM'
{
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
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT + PairwiseAlignmentAttributes.SimilarityMatrix + Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK,
MessageBoxImage.Error);
return(null);
}
}
else
{
// If DSM is selected
alignerInput.SimilarityMatrix = new DiagonalSimilarityMatrix(this.MatchScore, this.MisMatchScore);
}
break;
default:
break;
}
}
}
return(alignerInput);
}
/// <summary>
/// Assign the aligner specific parameters
/// </summary>
/// <param name="sequenceAligner">Sequence Aligner object</param>
/// <param name="alignerInput">Aligner Input object</param>
private static void AssignAlignerParameter(ISequenceAligner sequenceAligner, AlignerInputEventArgs alignerInput)
{
if (sequenceAligner is NucmerPairwiseAligner)
{
var nucmer = sequenceAligner as NucmerPairwiseAligner;
nucmer.LengthOfMUM = alignerInput.LengthOfMUM;
nucmer.FixedSeparation = alignerInput.FixedSeparation;
nucmer.MaximumSeparation = alignerInput.MaximumSeparation;
nucmer.MinimumScore = alignerInput.MinimumScore;
nucmer.SeparationFactor = alignerInput.SeparationFactor;
nucmer.BreakLength = alignerInput.BreakLength;
}
else if (sequenceAligner is MUMmerAligner)
{
var mummer = sequenceAligner as MUMmerAligner;
mummer.LengthOfMUM = alignerInput.LengthOfMUM;
}
}
/// <summary>
/// Get the aligner input parameter from the controls in stack panel
/// </summary>
/// <returns>Are parameters valid</returns>
public AlignerInputEventArgs GetAlignmentInput()
{
StackPanel stkPanel = this.stkAlingerParam;
AlignerInputEventArgs alignerInput = new AlignerInputEventArgs { Aligner = this.Aligner };
foreach (UIElement uiElement in stkPanel.Children)
{
if (uiElement is TextBox)
{
TextBox textBox = uiElement as TextBox;
int intValue;
switch (textBox.Tag.ToString())
{
case PairwiseAlignmentAttributes.GapOpenCost:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.GapCost = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ PairwiseAlignmentAttributes.GapOpenCost
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return null;
}
break;
case PairwiseAlignmentAttributes.GapExtensionCost:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.GapExtensionCost = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ PairwiseAlignmentAttributes.GapExtensionCost
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return null;
}
break;
case MUMmerAttributes.LengthOfMUM:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.LengthOfMUM = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ NUCmerAttributes.LengthOfMUM
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return null;
}
break;
case NUCmerAttributes.FixedSeparation:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.FixedSeparation = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ NUCmerAttributes.FixedSeparation
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return null;
}
break;
case NUCmerAttributes.MaximumSeparation:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.MaximumSeparation = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ NUCmerAttributes.MaximumSeparation
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return null;
}
break;
case NUCmerAttributes.MinimumScore:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.MinimumScore = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ NUCmerAttributes.MinimumScore
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return null;
}
break;
case NUCmerAttributes.SeparationFactor:
float floatValue;
if (float.TryParse(textBox.Text.Trim(), out floatValue))
{
alignerInput.SeparationFactor = floatValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ NUCmerAttributes.SeparationFactor
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return null;
}
break;
case NUCmerAttributes.BreakLength:
if (int.TryParse(textBox.Text.Trim(), out intValue))
{
alignerInput.BreakLength = intValue;
}
else
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT
+ NUCmerAttributes.BreakLength
+ Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK, MessageBoxImage.Error);
return null;
}
break;
default:
break;
}
}
else if (uiElement is ComboBox)
{
ComboBox comboBox = uiElement as ComboBox;
switch (comboBox.Tag.ToString())
{
case PairwiseAlignmentAttributes.SimilarityMatrix:
if (comboBox.SelectedIndex > 0) // user selected a SM other than 'DiagonalSM'
{
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
{
MessageBox.Show(
Properties.Resources.INVALID_TEXT + PairwiseAlignmentAttributes.SimilarityMatrix + Properties.Resources.VALUE_TEXT,
Properties.Resources.CAPTION,
MessageBoxButton.OK,
MessageBoxImage.Error);
return null;
}
}
else
{
// If DSM is selected
alignerInput.SimilarityMatrix = new DiagonalSimilarityMatrix(this.MatchScore, this.MisMatchScore);
}
break;
default:
break;
}
}
}
return alignerInput;
}
