/// <summary>
/// Gets the list of alignment argument based on the algorithm selected
/// </summary>
/// <returns>Alignment arguments</returns>
private IAlignmentAttributes GetAlignmentAttribute(string algo)
{
IAlignmentAttributes alignmentAttributes = null;
ISequenceAligner sequenceAligner = ChooseAlgorithm(algo);
if (sequenceAligner is NucmerPairwiseAligner)
{
alignmentAttributes = new NUCmerAttributes();
}
else if (sequenceAligner is MUMmerAligner)
{
alignmentAttributes = new MUMmerAttributes();
}
else if ((sequenceAligner is SmithWatermanAligner) ||
(sequenceAligner is NeedlemanWunschAligner) ||
(sequenceAligner is PairwiseOverlapAligner))
{
alignmentAttributes = new PairwiseAlignmentAttributes();
}
else if (sequenceAligner is PAMSAMMultipleSequenceAligner)
{
alignmentAttributes = new PamsamAlignmentAttributes();
}
return(alignmentAttributes);
}
/// <summary>
/// Initializes a new instance of the AssemblerDialog class.
/// </summary>
/// <param name="defaultSM">default similarity matrix name</param>
public AlignerDialog(string defaultSM)
{
InitializeComponent();
this.defaultSM = defaultSM;
// Add aligners to the drop down
foreach (ISequenceAligner aligner in SequenceAligners.All)
{
cmbAlgorithms.Items.Add(aligner.Name);
}
this.cmbAlgorithms.SelectedIndex = 0;
if (this.cmbAlgorithms.Items.Count > 0)
{
IAlignmentAttributes alignmentAttributes = this.GetAlignmentAttribute(this.cmbAlgorithms.SelectedItem.ToString());
this.LoadAlignmentArguments(alignmentAttributes);
}
this.cmbAlgorithms.SelectionChanged += new SelectionChangedEventHandler(cmbAlgorithms_SelectionChanged);
this.Owner = Application.Current.MainWindow;
this.btnSubmit.Click += new RoutedEventHandler(this.OnSubmitButtonClicked);
this.btnCancel.Click += new RoutedEventHandler(this.OnCancelClicked);
this.btnSubmit.Focus();
}
/// <summary>
/// Load the list of arguments as appropriate control on the UI.
/// </summary>
/// <param name="alignmentAttributes">List of Alignment parameters</param>
private void LoadAlignmentArguments(IAlignmentAttributes alignmentAttributes)
{
stkAlingerParam.Children.Clear();
if (null != alignmentAttributes)
{
foreach (KeyValuePair <string, AlignmentInfo> attribute in alignmentAttributes.Attributes)
{
if (attribute.Value.DataType.Equals(AlignmentInfo.StringListType))
{
this.CreateComboField(
attribute.Value,
stkAlingerParam,
attribute.Key);
}
else
{
this.CreateTextField(
attribute.Value,
stkAlingerParam,
attribute.Key);
}
}
}
this.UpdateLayout();
}
/// <summary>
/// Initializes a new instance of the AssemblerDialog class.
/// </summary>
/// <param name="algorithms">Algorithms</param>
/// <param name="defaultSM">Default similarity matrix</param>
/// <param name="sequences">Sequences to assemble</param>
public AssemblerDialog(IEnumerable <string> algorithms, string defaultSM, IList <ISequence> sequences)
{
InitializeComponent();
this.defaultSM = defaultSM;
this.InitializeAlignmentAlgorithms(algorithms);
if (this.cmbAlgorithms.Items.Count > 0)
{
IAlignmentAttributes alignmentAttributes = this.GetAlignmentAttribute(this.cmbAlgorithms.SelectedItem.ToString());
this.LoadAlignmentArguments(alignmentAttributes);
}
this.cmbAlgorithms.SelectionChanged += new SelectionChangedEventHandler(cmbAlgorithms_SelectionChanged);
this.Owner = Application.Current.MainWindow;
this.simpleSequenceAssemblerOptionButton.Checked += new RoutedEventHandler(OnAssemblerSelectionChanged);
this.padenaOptionButton.Checked += new RoutedEventHandler(OnAssemblerSelectionChanged);
this.btnSubmit.Click += new RoutedEventHandler(this.OnSubmitButtonClicked);
this.btnCancel.Click += new RoutedEventHandler(this.OnCancelClicked);
// Get default values for padena
int estimatedKmerLength = ParallelDeNovoAssembler.EstimateKmerLength(sequences);
txtKmerLength.Text = estimatedKmerLength.ToString();
txtDangleThreshold.Text = (estimatedKmerLength + 1).ToString();
txtRedundantThreshold.Text = (3 * (estimatedKmerLength + 1)).ToString();
this.cmbLibraryNames.SelectionChanged += new SelectionChangedEventHandler(OnLibraryNames_SelectionChanged);
this.InitializeLibraryNames();
this.btnSubmit.Focus();
}
/// <summary>
/// Load the list of arguments as appropriate control on the UI.
/// </summary>
/// <param name="alignmentAttributes">List of Alignment parameters</param>
private void LoadAlignmentArguments(string algoName)
{
IAlignmentAttributes alignmentAttributes = this.GetAlignmentAttribute(algoName);
stkAlingerParam.Children.Clear();
if (null != alignmentAttributes)
{
foreach (KeyValuePair <string, AlignmentInfo> attribute in alignmentAttributes.Attributes)
{
if (attribute.Value.DataType.Equals(AlignmentInfo.StringListType))
{
this.CreateComboField(
attribute.Value,
stkAlingerParam,
attribute.Key);
}
else
{
this.CreateTextField(
attribute.Value,
stkAlingerParam,
attribute.Key);
}
}
this.InvalidateVisual();
}
}
/// <summary>
/// Gets the list of alignment argument based on the algorithm selected
/// </summary>
/// <param name="algoName">Name of the algorithm used</param>
/// <returns>Alignment arguments</returns>
private IAlignmentAttributes GetAlignmentAttribute(string algoName)
{
IAlignmentAttributes alignmentAttributes = null;
ISequenceAligner sequenceAligner = ChooseAlgorithm(algoName);
this.Aligner = sequenceAligner;
if (sequenceAligner is NUCmer3)
{
alignmentAttributes = new NUCmerAttributes();
}
else if (sequenceAligner is MUMmer3)
{
alignmentAttributes = new MUMmerAttributes();
}
else if ((sequenceAligner is SmithWatermanAligner) ||
(sequenceAligner is NeedlemanWunschAligner) ||
(sequenceAligner is PairwiseOverlapAligner))
{
alignmentAttributes = new PairwiseAlignmentAttributes();
}
return(alignmentAttributes);
}
/// <summary>
/// Selection change event of Aligner combo.
/// </summary>
/// <param name="sender">Sender object.</param>
/// <param name="e">Selection Changed EventArgs.</param>
private void cmbAlgorithms_SelectionChanged(object sender, SelectionChangedEventArgs e)
{
string algo = string.Empty;
if (e.AddedItems.Count > 0)
{
algo = e.AddedItems[0].ToString();
}
IAlignmentAttributes alignmentAttributes = this.GetAlignmentAttribute(algo);
this.LoadAlignmentArguments(alignmentAttributes);
}
