/// <summary>
/// This method would create combo field.
/// </summary>
/// <param name="alignmentAttribute">Alignment parameter</param>
/// <param name="parentPanel">Stack panel, the field will be added to this stackpanel</param>
/// <param name="tag">Tag of the control object</param>
private void CreateComboField(
AlignmentInfo alignmentAttribute,
StackPanel parentPanel,
string tag)
{
TextBlock block = new TextBlock();
block.Margin = new Thickness(0, 5, 0, 0);
block.TextWrapping = TextWrapping.Wrap;
block.Text = alignmentAttribute.Name;
block.Height = 20;
ComboBox combo = new ComboBox();
combo.HorizontalAlignment = HorizontalAlignment.Left;
combo.IsSynchronizedWithCurrentItem = true;
combo.Margin = new Thickness(0, 0, 0, 0);
combo.Tag = tag;
combo.Width = 180;
combo.Height = 22;
combo.ToolTip = alignmentAttribute.Description;
StringListValidator validator = alignmentAttribute.Validator as StringListValidator;
combo.ItemsSource = validator.ValidValues;
combo.SelectedIndex = validator.ValidValues.ToList().IndexOf(alignmentAttribute.DefaultValue);
if (alignmentAttribute.Name == "Similarity Matrix")
{
combo.SelectedIndex = validator.ValidValues.ToList().IndexOf(this.defaultSM);
}
parentPanel.Children.Add(block);
parentPanel.Children.Add(combo);
}
public void ValidatePairwiseAlignmentAttributes()
{
var pwAlignAttrib = new PairwiseAlignmentAttributes();
Dictionary<string, AlignmentInfo> attributes = pwAlignAttrib.Attributes;
AlignmentInfo similarityMatrixObj = attributes["SIMILARITYMATRIX"];
AlignmentInfo gapOpenCostObj = attributes["GAPOPENCOST"];
AlignmentInfo gapExtensionCostObj = attributes["GAPEXTENSIONCOST"];
Assert.AreEqual("Similarity Matrix", similarityMatrixObj.Name);
var validator = new StringListValidator(
"Diagonal (Match x Mismatch)",
SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.AmbiguousRna.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum45.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum50.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum62.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum80.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum90.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.DiagonalScoreMatrix.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Pam250.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Pam30.ToString());
Assert.IsTrue(validator.IsValid(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna.ToString()));
validator.AddValidValues(SimilarityMatrix.StandardSimilarityMatrix.Pam70.ToString());
Assert.AreEqual("Diagonal (Match x Mismatch)", validator.ValidValues[0]);
Assert.AreEqual("Gap Cost", gapOpenCostObj.Name);
Assert.AreEqual("Gap Extension Cost", gapExtensionCostObj.Name);
ApplicationLog.WriteLine(
"PairwiseAlignmentAttributes BVT: Successfully validated all the attributes.");
}
public void ValidatePairwiseAlignmentAttributes()
{
var pwAlignAttrib = new PairwiseAlignmentAttributes();
Dictionary <string, AlignmentInfo> attributes = pwAlignAttrib.Attributes;
AlignmentInfo similarityMatrixObj = attributes["SIMILARITYMATRIX"];
AlignmentInfo gapOpenCostObj = attributes["GAPOPENCOST"];
AlignmentInfo gapExtensionCostObj = attributes["GAPEXTENSIONCOST"];
Assert.AreEqual("Similarity Matrix", similarityMatrixObj.Name);
var validator = new StringListValidator(
"Diagonal (Match x Mismatch)",
SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.AmbiguousRna.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum45.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum50.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum62.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum80.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Blosum90.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.DiagonalScoreMatrix.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Pam250.ToString(),
SimilarityMatrix.StandardSimilarityMatrix.Pam30.ToString());
Assert.IsTrue(validator.IsValid(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna.ToString()));
validator.AddValidValues(SimilarityMatrix.StandardSimilarityMatrix.Pam70.ToString());
Assert.AreEqual("Diagonal (Match x Mismatch)", validator.ValidValues[0]);
Assert.AreEqual("Gap Cost", gapOpenCostObj.Name);
Assert.AreEqual("Gap Extension Cost", gapExtensionCostObj.Name);
ApplicationLog.WriteLine(
"PairwiseAlignmentAttributes BVT: Successfully validated all the attributes.");
}
/// <summary>
/// This method would create combo field.
/// </summary>
/// <param name="alignmentAttribute">Alignment parameter</param>
/// <param name="parentPanel">Stack panel, the field will be added to this stackpanel</param>
/// <param name="tag">Tag of the control object</param>
private void CreateComboField(
AlignmentInfo alignmentAttribute,
StackPanel parentPanel,
string tag)
{
TextBlock block = new TextBlock {
Margin = new Thickness(0, 10, 0, 0),
TextWrapping = TextWrapping.Wrap,
Text = alignmentAttribute.Name,
Height = 20
};
ComboBox combo = new ComboBox {
HorizontalAlignment = HorizontalAlignment.Left,
IsSynchronizedWithCurrentItem = true,
Margin = new Thickness(0, 0, 0, 0),
Tag = tag,
Width = 180,
Height = 22,
ToolTip = alignmentAttribute.Description
};
StringListValidator validator = alignmentAttribute.Validator as StringListValidator;
combo.ItemsSource = validator.ValidValues;
combo.SelectedIndex = validator.ValidValues.ToList().IndexOf(alignmentAttribute.DefaultValue);
if (alignmentAttribute.Name == "Similarity Matrix")
{
combo.SelectedIndex = validator.ValidValues.ToList().IndexOf(GetDefaultSM(this.sequenceAlphabet));
}
parentPanel.Children.Add(block);
parentPanel.Children.Add(combo);
}
/// <summary>
/// Initializes a new instance of the PairwiseAlignmentAttributes class.
/// </summary>
public PairwiseAlignmentAttributes()
{
attributes = new Dictionary <string, AlignmentInfo>();
StringListValidator similarityMatrixList = new StringListValidator(
Properties.Resource.SimilarityMatrix_AutoDetectString, // Autodetect
Properties.Resource.SimilarityMatrix_DiagonalSM,
SM.StandardSimilarityMatrix.AmbiguousDna.ToString(),
SM.StandardSimilarityMatrix.AmbiguousRna.ToString(),
SM.StandardSimilarityMatrix.Blosum45.ToString(),
SM.StandardSimilarityMatrix.Blosum50.ToString(),
SM.StandardSimilarityMatrix.Blosum62.ToString(),
SM.StandardSimilarityMatrix.Blosum80.ToString(),
SM.StandardSimilarityMatrix.Blosum90.ToString(),
SM.StandardSimilarityMatrix.DiagonalScoreMatrix.ToString(),
SM.StandardSimilarityMatrix.Pam250.ToString(),
SM.StandardSimilarityMatrix.Pam30.ToString(),
SM.StandardSimilarityMatrix.Pam70.ToString());
AlignmentInfo alignmentAttribute = new AlignmentInfo(
Properties.Resource.SIMILARITY_MATRIX_NAME,
Properties.Resource.SIMILARITY_MATRIX_DESCRIPTION,
true,
Properties.Resource.SimilarityMatrix_AutoDetectString,
AlignmentInfo.StringListType,
similarityMatrixList);
attributes.Add(SimilarityMatrix, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
Properties.Resource.GAP_COST_NAME,
Properties.Resource.GAP_COST_DESCRIPTION,
true,
"-8",
AlignmentInfo.IntType,
null);
attributes.Add(GapOpenCost, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
Properties.Resource.GAP_EXTENSION_COST_NAME,
Properties.Resource.GAP_EXTENSION_COST_DESCRIPTION,
true,
"-8",
AlignmentInfo.IntType,
null);
attributes.Add(GapExtensionCost, alignmentAttribute);
}
/// <summary>
/// Initializes a new instance of the PairwiseAlignmentAttributes class.
/// </summary>
public PairwiseAlignmentAttributes()
{
attributes = new Dictionary<string, AlignmentInfo>();
StringListValidator similarityMatrixList = new StringListValidator(
Properties.Resource.SimilarityMatrix_DiagonalSM,
SM.StandardSimilarityMatrix.AmbiguousDna.ToString(),
SM.StandardSimilarityMatrix.AmbiguousRna.ToString(),
SM.StandardSimilarityMatrix.Blosum45.ToString(),
SM.StandardSimilarityMatrix.Blosum50.ToString(),
SM.StandardSimilarityMatrix.Blosum62.ToString(),
SM.StandardSimilarityMatrix.Blosum80.ToString(),
SM.StandardSimilarityMatrix.Blosum90.ToString(),
SM.StandardSimilarityMatrix.DiagonalScoreMatrix.ToString(),
SM.StandardSimilarityMatrix.Pam250.ToString(),
SM.StandardSimilarityMatrix.Pam30.ToString(),
SM.StandardSimilarityMatrix.Pam70.ToString());
AlignmentInfo alignmentAttribute = new AlignmentInfo(
Properties.Resource.SIMILARITY_MATRIX_NAME,
Properties.Resource.SIMILARITY_MATRIX_DESCRIPTION,
true,
SM.StandardSimilarityMatrix.AmbiguousDna.ToString(),
AlignmentInfo.StringListType,
similarityMatrixList);
attributes.Add(SimilarityMatrix, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
Properties.Resource.GAP_COST_NAME,
Properties.Resource.GAP_COST_DESCRIPTION,
true,
"-10",
AlignmentInfo.IntType,
null);
attributes.Add(GapOpenCost, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
Properties.Resource.GAP_EXTENSION_COST_NAME,
Properties.Resource.GAP_EXTENSION_COST_DESCRIPTION,
true,
"-8",
AlignmentInfo.IntType,
null);
attributes.Add(GapExtensionCost, alignmentAttribute);
}
/// <summary>
/// This method would create combo field for the Blast parameter dialog,
/// It will use the fieldname (which is the parameter name)
/// and stackpanel to be added.
/// </summary>
/// <param name="fieldName">field name</param>
/// <param name="parentPanel">Stack panel, the field will be added to this stackpanel</param>
private static void CreateComboField(string fieldName, StackPanel parentPanel)
{
TextBlock block = new TextBlock();
block.Margin = new Thickness(0, 5, 5, 0);
block.TextWrapping = TextWrapping.Wrap;
block.Text = fieldName;
parentPanel.Children.Add(block);
ComboBox combo = new ComboBox();
combo.HorizontalAlignment = HorizontalAlignment.Left;
combo.IsSynchronizedWithCurrentItem = true;
combo.Margin = new Thickness(0, 5, 5, 0);
combo.Tag = fieldName;
combo.Width = 100;
StringListValidator validator = BlastParameters.Parameters[fieldName].Validator as StringListValidator;
combo.ItemsSource = validator.ValidValues;
combo.SelectedIndex = validator.ValidValues.IndexOf(BlastParameters.Parameters[fieldName].DefaultValue);
parentPanel.Children.Add(combo);
}
/// <summary>
/// Initializes a new instance of the PairwiseAlignmentAttributes class.
/// </summary>
public PamsamAlignmentAttributes()
{
AlignmentInfo alignmentAttribute;
attributes = new Dictionary <string, AlignmentInfo>();
alignmentAttribute = new AlignmentInfo(
KmerLength,
"Kmer Length",
true,
"3",
AlignmentInfo.IntType,
null);
attributes.Add(KmerLength, alignmentAttribute);
StringListValidator listValidator = new StringListValidator(
Enum.GetNames(typeof(DistanceFunctionTypes))
);
alignmentAttribute = new AlignmentInfo(
DistanceFunctionType,
"Distance Function Type",
true,
DistanceFunctionTypes.EuclideanDistance.ToString(),
AlignmentInfo.StringListType,
listValidator);
attributes.Add(DistanceFunctionType, alignmentAttribute);
listValidator = new StringListValidator(
Enum.GetNames(typeof(UpdateDistanceMethodsTypes))
);
alignmentAttribute = new AlignmentInfo(
UpdateDistanceMethodsType,
"Update Distance Methods Type",
true,
UpdateDistanceMethodsTypes.Average.ToString(),
AlignmentInfo.StringListType,
listValidator);
attributes.Add(UpdateDistanceMethodsType, alignmentAttribute);
listValidator = new StringListValidator(
Enum.GetNames(typeof(ProfileAlignerNames))
);
alignmentAttribute = new AlignmentInfo(
ProfileAlignerName,
"Profile Aligner Name",
true,
ProfileAlignerNames.NeedlemanWunschProfileAligner.ToString(),
AlignmentInfo.StringListType,
listValidator);
attributes.Add(ProfileAlignerName, alignmentAttribute);
listValidator = new StringListValidator(
Enum.GetNames(typeof(ProfileScoreFunctionNames))
);
alignmentAttribute = new AlignmentInfo(
ProfileScoreFunctionName,
"Profile Score Function Name",
true,
ProfileScoreFunctionNames.WeightedInnerProduct.ToString(),
AlignmentInfo.StringListType,
listValidator);
attributes.Add(ProfileScoreFunctionName, alignmentAttribute);
listValidator = new StringListValidator(
SM.StandardSimilarityMatrix.AmbiguousDna.ToString(),
SM.StandardSimilarityMatrix.AmbiguousRna.ToString(),
SM.StandardSimilarityMatrix.Blosum45.ToString(),
SM.StandardSimilarityMatrix.Blosum50.ToString(),
SM.StandardSimilarityMatrix.Blosum62.ToString(),
SM.StandardSimilarityMatrix.Blosum80.ToString(),
SM.StandardSimilarityMatrix.Blosum90.ToString(),
SM.StandardSimilarityMatrix.Pam250.ToString(),
SM.StandardSimilarityMatrix.Pam30.ToString(),
SM.StandardSimilarityMatrix.Pam70.ToString()
);
alignmentAttribute = new AlignmentInfo(
SimilarityMatrix,
"Similarity Matrix",
true,
SM.StandardSimilarityMatrix.AmbiguousDna.ToString(),
AlignmentInfo.StringListType,
listValidator);
attributes.Add(SimilarityMatrix, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
GapOpenPenalty,
"Gap Open Penalty",
true,
"-4",
AlignmentInfo.IntType,
null);
attributes.Add(GapOpenPenalty, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
GapExtendPenalty,
"Gap Extention Penalty",
true,
"-1",
AlignmentInfo.IntType,
null);
attributes.Add(GapExtendPenalty, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
NumberOfPartitions,
"Number Of Partitions",
true,
(Environment.ProcessorCount * 2).ToString(),
AlignmentInfo.IntType,
null);
attributes.Add(NumberOfPartitions, alignmentAttribute);
alignmentAttribute = new AlignmentInfo(
DegreeOfParallelism,
"Degree Of Parallelism",
true,
Environment.ProcessorCount.ToString(),
AlignmentInfo.IntType,
null);
attributes.Add(DegreeOfParallelism, alignmentAttribute);
}
