/// <summary>
/// Constructor
/// </summary>
public ControlOptions()
{
InitializeComponent();
this.cmbSettings.DisplayMember = nameof(NeedlemanWunschOptions.Name);
this.cmbSettings.Items.AddRange(NeedlemanWunschOptions.LoadOptions().ToArray());
}
public void NeedlemanWunschDirectionTest(string seqDirA, string seqDirB, string optionSet, string resultDir)
{
List <Sequence> seqA = Controller.GetSequences(seqDirA);
ConvertSequences(seqA);
List <Sequence> seqB = Controller.GetSequences(seqDirB);
ConvertSequences(seqB);
decimal[,] resultArr = ReadResultMatrix(resultDir);
int[,] expectedDirs = new int[resultArr.GetLength(0), resultArr.GetLength(1)];
for (int i = 0; i < resultArr.GetLength(0); i++)
{
for (int j = 0; j < resultArr.GetLength(1); j++)
{
expectedDirs[i, j] = (int)resultArr[i, j];
}
}
NeedlemanWunschOptions options = ReadOptionsFromFile(optionSet);
NeedlemanWunsch matrix = new NeedlemanWunsch(seqA.ToList(), seqB.ToList(), options);
int[,] actualDirs = GetAlignDirections(matrix);
CollectionAssert.AreEqual(expectedDirs, actualDirs);
}
private void cmbSettings_SelectedIndexChanged(object sender, EventArgs e)
{
if (this.cmbSettings.SelectedItem is NeedlemanWunschOptions options)
{
this.varOptions = options;
}
}
private void SetDataToGui(NeedlemanWunschOptions _options)
{
this.txtName.Text = _options.Name;
this.cbxUberLogic.Checked = _options.UberLogic;
this.nudGapPenalty.Value = _options.GapPenalty;
this.cbxAffineGap.Checked = _options.UseAffineGaps;
this.nudAffineGapPenalty.Value = _options.GapExtensionPenalty;
this.nudDamagePenalty.Value = _options.DamagePenalty;
this.cbxAffineDamage.Checked = _options.UseAffineDamages;
this.nudAffineDamagePenalty.Value = _options.DamageExtensionPenalty;
this.nudConversionPenalty.Value = _options.ConversionPenalty;
// Weights - Rest
this.nudRestDuration.Value = _options.WeightRestDuration;
this.nudRestBreveduration.Value = _options.WeightRestBreveDuration;
// Weights - Note
this.nudNoteBreveduration.Value = _options.WeightNoteBreveduration;
this.nudNoteColoration.Value = _options.WeightNoteColoration;
this.nudNoteDuration.Value = _options.WeightNoteDuration;
this.nudNoteFermata.Value = _options.WeightNoteFermata;
this.nudNoteLigatureForm.Value = _options.WeightNoteLigatureForm;
this.nudNoteLigaturePosition.Value = _options.WeightNoteLigaturePosition;
this.nudNotePitchWithAccid.Value = _options.WeightNotePitchWithAccid;
this.nudNoteStem.Value = _options.WeightNoteStem;
this.nudNoteWrittenPitch.Value = _options.WeightNoteWrittenPitch;
// Weights - Mensur
this.nudMensurLogic.Value = _options.WeightMensurMaximodus;
this.nudMensurRatio.Value = _options.WeightMensurRatio;
this.nudMensurSign.Value = _options.WeightMensurSign;
// Weights - Proportion
this.nudProportionAffected.Value = _options.WeightProportionAffected;
this.nudProportionRatio.Value = _options.WeightProportionRatio;
this.nudProportioSign.Value = _options.WeightProportionSign;
}
private void btnSaveSettings_Click(object sender, EventArgs e)
{
// Check if settings with the Name already exists
NeedlemanWunschOptions optionsFound = this.lstOptions.FirstOrDefault(option => option.Name == this.txtName.Text);
// If yes ask the user if he wants to replace them
if (optionsFound != null)
{
if (MessageBox.Show(this.FindForm(), "Settings with this name already exist. Replace them?", "Question", MessageBoxButtons.YesNo, MessageBoxIcon.Question) != DialogResult.Yes)
{
return;
}
// We're still here, read the data from the gui into the object
this.GetDataFromGui(optionsFound);
}
else
{
this.GetDataFromGui(this.options2Edit);
// And append them to the list
this.lstOptions.Add(this.options2Edit);
}
NeedlemanWunschOptions.SaveOptions();
MessageBox.Show(this.FindForm(), "Options saved!");
/*
* // Refresh the ComboBox
* this.cmbSettings.Items.Clear();
* this.cmbSettings.Items.AddRange(this.lstOptions.ToArray());
*/
}
private void btnNewOptions_Click(object sender, EventArgs e)
{
this.varOptions = new NeedlemanWunschOptions();
using (DialogNeedlemanWunschOptions dialogOptions = new DialogNeedlemanWunschOptions())
{
dialogOptions.Options = this.varOptions;
if (dialogOptions.ShowDialog(this.FindForm()) == DialogResult.OK)
{
this.varOptions = dialogOptions.Options;
this.RefillCombobox();
}
}
}
//[DataSource("Microsoft.VisualStudio.TestTools.DataSource.CSV", "..\\..\\files\\tests.csv", "..\\..\\files\\tests#csv", DataAccessMethod.Sequential)]
public void NeedlemanWunschMatrixTest(string seqDirA, string seqDirB, string optionSet, string resultDir)
{
//List<Sequence> seqA = Controller.GetSequences(TestContext.DataRow["seqA"].ToString());
List <Sequence> seqA = Controller.GetSequences(seqDirA);
ConvertSequences(seqA);
//List<Sequence> seqB = Controller.GetSequences(TestContext.DataRow["seqB"].ToString());
List <Sequence> seqB = Controller.GetSequences(seqDirB);
ConvertSequences(seqB);
decimal[,] expectedResult = ReadResultMatrix(resultDir);
NeedlemanWunschOptions options = ReadOptionsFromFile(optionSet);
NeedlemanWunsch matrix = new NeedlemanWunsch(seqA.ToList(), seqB.ToList(), options);
decimal[,] alignmatrix = GetAlignmatrix(matrix);
CollectionAssert.AreEqual(expectedResult, alignmatrix);
}
private void GetDataFromGui(NeedlemanWunschOptions _options)
{
_options.Name = this.txtName.Text;
_options.UberLogic = this.cbxUberLogic.Checked;
_options.GapPenalty = this.nudGapPenalty.Value;
_options.UseAffineGaps = this.cbxAffineGap.Checked;
_options.GapExtensionPenalty = this.nudAffineGapPenalty.Value;
_options.DamagePenalty = this.nudDamagePenalty.Value;
_options.UseAffineDamages = this.cbxAffineDamage.Checked;
_options.DamageExtensionPenalty = this.nudAffineDamagePenalty.Value;
_options.ConversionPenalty = this.nudConversionPenalty.Value;
// Weights - Rest
_options.WeightRestDuration = this.nudRestDuration.Value;
_options.WeightRestBreveDuration = this.nudRestBreveduration.Value;
// Weights - Note
_options.WeightNoteBreveduration = this.nudNoteBreveduration.Value;
_options.WeightNoteColoration = this.nudNoteColoration.Value;
_options.WeightNoteDuration = this.nudNoteDuration.Value;
_options.WeightNoteFermata = this.nudNoteFermata.Value;
_options.WeightNoteLigatureForm = this.nudNoteLigatureForm.Value;
_options.WeightNoteLigaturePosition = this.nudNoteLigaturePosition.Value;
_options.WeightNotePitchWithAccid = this.nudNotePitchWithAccid.Value;
_options.WeightNoteStem = this.nudNoteStem.Value;
_options.WeightNoteWrittenPitch = this.nudNoteWrittenPitch.Value;
// Weights - Mensur
_options.WeightMensurMaximodus = this.nudMensurLogic.Value;
_options.WeightMensurModus = this.nudMensurLogic.Value;
_options.WeightMensurProlatio = this.nudMensurLogic.Value;
_options.WeightMensurTempus = this.nudMensurLogic.Value;
_options.WeightMensurRatio = this.nudMensurRatio.Value;
_options.WeightMensurSign = this.nudMensurSign.Value;
// Weights - Proportion
_options.WeightProportionAffected = this.nudProportionAffected.Value;
_options.WeightProportionRatio = this.nudProportionRatio.Value;
_options.WeightProportionSign = this.nudProportioSign.Value;
}
private void RefillCombobox()
{
this.cmbSettings.Items.Clear();
this.cmbSettings.Items.AddRange(NeedlemanWunschOptions.LoadOptions().ToArray());
this.cmbSettings.SelectedItem = this.varOptions;
}
/// <summary>
/// Konstruktor - Mostly harmless
/// </summary>
public DialogNeedlemanWunschOptions()
{
InitializeComponent();
this.lstOptions = NeedlemanWunschOptions.LoadOptions();
}
private void btnRandomSequenceModel_Click(object sender, EventArgs e)
{
// Check if we either have an saved Sequence or the user has chosen a sequence to use
if (this.listBoxChosenCompares.Items.Count == 0 && this.lstRandomizedObjectsA == null && this.lstRandomizedObjectsB == null)
{
MessageBox.Show("Please select at least one compare or load a randomized set of data", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
// Extract the options
NeedlemanWunschOptions options = this.controlOptions.Options;
List <ObjectInSequence> lstSequenceA = new List <ObjectInSequence>(), lstSequenceB = new List <ObjectInSequence>();
// Make 2 List for the ObjectsInSequences
List <List <ObjectInSequence> > lstSequencesA = new List <List <ObjectInSequence> >(), lstSequencesB = new List <List <ObjectInSequence> >();
// Differ if we have loaded sequences or use the chosen compares
if (this.lstRandomizedObjectsA != null && this.lstRandomizedObjectsB != null)
{
lstSequenceA = this.lstRandomizedObjectsA[0];
lstSequencesA = this.lstRandomizedObjectsA.GetRange(1, this.lstRandomizedObjectsA.Count - 1);
lstSequenceB = this.lstRandomizedObjectsB[0];
lstSequencesB = this.lstRandomizedObjectsB.GetRange(1, this.lstRandomizedObjectsB.Count - 1);
// GO!
ConcurrentBag <Tuple <decimal, int, int, int, int> > lstDistances = new ConcurrentBag <Tuple <decimal, int, int, int, int> >();
// Create the Alignment
NeedlemanWunsch nw = new NeedlemanWunsch(lstSequenceA, lstSequenceB, options, true);
// DebugCode if we need to see the Original Alignment
//DialogNeedlemanWunschShowAlign dialogShow = new DialogNeedlemanWunschShowAlign();
//dialogShow.SetData(nw);
//dialogShow.ShowDialog(this.FindForm());
// Now loop over the created sequences and compare all of them
Parallel.ForEach(lstSequencesA, seqA =>
{
Parallel.ForEach(lstSequencesB, seqB =>
{
// Build the alignment
NeedlemanWunsch nwRandom = new NeedlemanWunsch(seqA, seqB, options, true);
// Now we need the distance
lstDistances.Add(Tuple.Create(nwRandom.Distance, nwRandom.NumberOfChanges, nwRandom.Backtraces.Min(bt => bt.WayBack.Count), nwRandom.SequenceA.Count, nwRandom.SequenceB.Count));
});
});
MessageBox.Show(this.FindForm(), $"Distance: {nw.Distance}{Environment.NewLine}" +
$"Average Random Distance: {lstDistances.Sum(dis => dis.Item1) / lstDistances.Count}{Environment.NewLine}" +
$"Minimum Random Distance: {lstDistances.Min(dis => dis.Item1)}{Environment.NewLine}" +
$"Maximum Random Distance: {lstDistances.Max(dis => dis.Item1)}{Environment.NewLine}");
// Export all distances if wanted
if (this.saveFileDialogCSV.ShowDialog(this.FindForm()) == DialogResult.OK)
{
SaveCSV(this.saveFileDialogCSV.FileName, nw, lstDistances, lstSequenceA, lstSequenceB);
}
}
else
{
// Here we loop over the chosen Compares
foreach (object objAktuell in this.listBoxChosenCompares.Items)
{
if (objAktuell is CompareObject compObj)
{
// Create the original sequences - Copy the choosen ones from the List if possible as default
lstSequenceA = new List <ObjectInSequence>();
lstSequenceB = new List <ObjectInSequence>();
compObj.SequenceA.ForEach(item => lstSequenceA.AddRange(item.ObjectsInSequence));
compObj.SequenceB.ForEach(item => lstSequenceB.AddRange(item.ObjectsInSequence));
// Check if we have locked sequences or create new ones
if (compObj.RandomizedSequencesA != null && compObj.RandomizedSequencesB != null)
{
lstSequencesA = new List <List <ObjectInSequence> >(compObj.RandomizedSequencesA);
lstSequencesB = new List <List <ObjectInSequence> >(compObj.RandomizedSequencesB);
}
else
{
RandomizeSequence(compObj.SequenceA, lstSequencesA);
RandomizeSequence(compObj.SequenceB, lstSequencesB);
}
// Now we have everything, runrunrun
ConcurrentBag <Tuple <decimal, int, int, int, int> > lstDistances = new ConcurrentBag <Tuple <decimal, int, int, int, int> >();
// Create the Alignment
NeedlemanWunsch nw = new NeedlemanWunsch(lstSequenceA, lstSequenceB, options, true);
// DebugCode if we need to see the Original Alignment
//DialogNeedlemanWunschShowAlign dialogShow = new DialogNeedlemanWunschShowAlign();
//dialogShow.SetData(nw);
//dialogShow.ShowDialog(this.FindForm());
// Now loop over the created sequences and compare all of them
Parallel.ForEach(lstSequencesA, seqA =>
{
Parallel.ForEach(lstSequencesB, seqB =>
{
// Build the alignment
NeedlemanWunsch nwRandom = new NeedlemanWunsch(seqA, seqB, options, true);
// Now we need the distance
lstDistances.Add(Tuple.Create(nwRandom.Distance, nwRandom.NumberOfChanges, nwRandom.Backtraces.Min(bt => bt.WayBack.Count), nwRandom.SequenceA.Count, nwRandom.SequenceB.Count));
//if (nwRandom.Distance < 35m)
//{
// lstSusp.Add(nwRandom);
//}
});
});
// We get the filename from the CompareObject
string strSavePath = Path.Combine(Path.GetDirectoryName(compObj.SavePath), Path.GetFileNameWithoutExtension(compObj.SavePath) + $"_{options.Name}" + Path.GetExtension(compObj.SavePath));
SaveCSV(strSavePath, nw, lstDistances, lstSequenceA, lstSequenceB);
// Also save the Sequences
string strSavePathSequencesA, strSavePathSequencesB;
strSavePathSequencesA = Path.Combine(Path.GetDirectoryName(compObj.SavePath), Path.GetFileNameWithoutExtension(compObj.SavePath) + "_sequencesA.xml");
strSavePathSequencesB = Path.Combine(Path.GetDirectoryName(compObj.SavePath), Path.GetFileNameWithoutExtension(compObj.SavePath) + "_sequencesB.xml");
// Insert the original Sequence in A and save them
lstSequencesA.Insert(0, lstSequenceA);
DataContractSerializer serializer = new DataContractSerializer(typeof(List <List <ObjectInSequence> >));
using (XmlWriter writer = XmlWriter.Create(strSavePathSequencesA))
{
serializer.WriteObject(writer, lstSequencesA);
writer.Close();
}
// Same for B
lstSequencesB.Insert(0, lstSequenceB);
using (XmlWriter writer = XmlWriter.Create(strSavePathSequencesB))
{
serializer.WriteObject(writer, lstSequencesB);
writer.Close();
}
// Save the options?
}
}
// Show something so the user knows were done
MessageBox.Show(this.FindForm(), "Done!");
}
}
