/// <summary>
/// worker_RunWorkerCompleted
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void worker_RunWorkerCompleted(object sender, RunWorkerCompletedEventArgs e)
{
// new score calculation
double newScore = ORF.CPBcalculator(optimizedORF);
//new orf to display
textBox.Text = newScore.ToString();
optimizedORF.Insert(0, textBox.Text);
Data.Rows.Add(optimizedORF.ToArray());
OptimizationDataGrid.ItemsSource = Data.DefaultView;
SaveToFASTAButton.IsEnabled = true;
//max score Textbox update
if (MaximalizeRadioButton.IsChecked == true)
{
maxScores.Add(newScore);
BestMaxCPBscoreTextBox.Text = maxScores.Max().ToString();
}
//min score Textbox update
if (MinimalizeRadioButton.IsChecked == true)
{
minScores.Add(newScore);
BestMinCPBscoreTextBox.Text = minScores.Min().ToString();
}
NcScoreOptimizedTextBox.Text = ORF.NcCalculator(optimizedORF, ORF.aminoAcidCounts).ToString();
}
/// <summary>
/// Method for calculating and displaying
/// </summary>
/// <param name="orf"></param>
/// <param name="amino"></param>
private void CalculateAndDisplayORF(List <string> orf, List <string> amino)
{
Data = new DataTable();
int columnIdx = 0;
Data.Columns.Add(new DataColumn("CPB"));
foreach (var k in ORF.aminoORFseq)
{
Data.Columns.Add(new DataColumn(columnIdx.ToString()));
columnIdx++;
}
// CPBcalculator method initialization
try
{
OriginalCPBscoreTextBox.Text = ORF.CPBcalculator(ORF.orfSeq).ToString();
// datagrid filling
ORF.aminoORFseq.Insert(0, "");
ORF.orfSeq.Insert(0, OriginalCPBscoreTextBox.Text);
Data.Rows.Add(ORF.aminoORFseq.ToArray());
Data.Rows.Add(ORF.orfSeq.ToArray());
ORF.aminoORFseq.RemoveAt(0);
ORF.orfSeq.RemoveAt(0);
OptimizationDataGrid.ItemsSource = Data.DefaultView;
GeneticCode.UploadGeneticCode();
ORF.aminoAcidCounts = ORF.aminoORFseq.GroupBy(i => i)
.ToDictionary(i => i.Key, i => i.Count());
NcScoreTextBox.Text = ORF.NcCalculator(ORF.orfSeq, ORF.aminoAcidCounts).ToString();
}
catch
{
string message = "Something went wrong. Please verify your FASTA file for incorrect codons or check your ranking.";
ModernDialog.ShowMessage(message.ToString(), "Error", MessageBoxButton.OK);
}
}
public string RunPrefMRF(double regularization, double learnRate, int maxEpoch, List <double> quantizer,
int topN = 10)
{
// Load OMFDistribution from file
Dictionary <Tuple <int, int>, List <double> > OMFDistributionByUserItem;
if (File.Exists(GetDataFileName("PrefOMF_")))
{
OMFDistributionByUserItem = Utils.IO <Dictionary <Tuple <int, int>, List <double> > > .LoadObject(GetDataFileName("PrefOMF_"));
}
else
{
return("Abort, Run OMF first.");
}
if (!ReadyForOrdinal)
{
GetReadyForOrdinal();
}
StringBuilder log = new StringBuilder();
log.AppendLine(Utils.PrintHeading("PrefMRF: PrefNMF based ORF"));
// Prediction
Utils.StartTimer();
DataMatrix R_predicted_expectations;
DataMatrix R_predicted_mostlikely;
// Convert PR_train into user-wise preferences
DataMatrix R_train_positions = new DataMatrix(PR_train.GetPositionMatrix());
R_train_positions.Quantization(quantizer[0], quantizer[quantizer.Count - 1] - quantizer[0], quantizer);
ORF orf = new ORF();
orf.PredictRatings(R_train_positions, R_unknown, StrongSimilarityIndicatorsByItemPref,
OMFDistributionByUserItem, regularization, learnRate, maxEpoch,
quantizer.Count, out R_predicted_expectations, out R_predicted_mostlikely);
log.AppendLine(Utils.StopTimer());
// Evaluation
var topNItemsByUser_expectations = ItemRecommendationCore.GetTopNItemsByUser(R_predicted_expectations, topN);
for (int n = 1; n <= topN; n++)
{
log.AppendLine(Utils.PrintValue("NCDG@" + n, NCDG.Evaluate(RelevantItemsByUser,
topNItemsByUser_expectations, n).ToString("0.0000")));
}
for (int n = 1; n <= topN; n++)
{
log.AppendLine(Utils.PrintValue("MAP@" + n, MAP.Evaluate(RelevantItemsByUser, topNItemsByUser_expectations, n).ToString("0.0000")));
}
return(log.ToString());
}
public string RunNMFbasedORF(double regularization, double learnRate,
int maxEpoch, List <double> quantizer, int topN = 0)
{
// Load OMFDistribution from file
Dictionary <Tuple <int, int>, List <double> > OMFDistributionByUserItem;
if (File.Exists(GetDataFileName("RatingOMF_")))
{
OMFDistributionByUserItem = Utils.IO <Dictionary <Tuple <int, int>, List <double> > > .LoadObject(GetDataFileName("RatingOMF_"));
}
else
{
return("Abort, Run OMF first.");
}
if (!ReadyForNumerical)
{
GetReadyForNumerical();
}
StringBuilder log = new StringBuilder();
log.AppendLine(Utils.PrintHeading("NMF based ORF"));
// Prediction
Utils.StartTimer();
DataMatrix R_predicted_expectations;
DataMatrix R_predicted_mostlikely;
ORF orf = new ORF();
orf.PredictRatings(R_train, R_unknown, StrongSimilarityIndicatorsByItemRating,
OMFDistributionByUserItem, regularization, learnRate, maxEpoch,
quantizer.Count, out R_predicted_expectations, out R_predicted_mostlikely);
log.AppendLine(Utils.StopTimer());
// Numerical Evaluation
log.AppendLine(Utils.PrintValue("RMSE", RMSE.Evaluate(R_test, R_predicted_expectations).ToString("0.0000")));
log.AppendLine(Utils.PrintValue("MAE", RMSE.Evaluate(R_test, R_predicted_mostlikely).ToString("0.0000")));
// Top-N Evaluation
if (topN != 0)
{
var topNItemsByUser_expectations = ItemRecommendationCore.GetTopNItemsByUser(R_predicted_expectations, topN);
for (int n = 1; n <= topN; n++)
{
log.AppendLine(Utils.PrintValue("NCDG@" + n, NCDG.Evaluate(RelevantItemsByUser, topNItemsByUser_expectations, n).ToString("0.0000")));
}
for (int n = 1; n <= topN; n++)
{
log.AppendLine(Utils.PrintValue("MAP@" + n, MAP.Evaluate(RelevantItemsByUser, topNItemsByUser_expectations, n).ToString("0.0000")));
}
}
return(log.ToString());
}
/// <summary>
/// LoadORFButton Click event handler
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void LoadORFButton_Click(object sender, RoutedEventArgs e)
{
// extensions setting
extensions = "Fasta files|*.fa;*.fas;*.fasta";
// openFileDialog method initialization
initializeOpenFileDialog(extensions);
// show openFileDialog file dialog
Nullable <bool> openResult = openFileDialog.ShowDialog();
if (openResult == true)
{
//new ORF object
ORF = new ORF();
file_seq = openFileDialog.FileName; // file handler
// sequenceParser method initialization
var tupleTemp = SeqParser.sequenceParser(file_seq);
if (tupleTemp.Item2 != 1)
{
string message = "Something went wrong. Probably you tried to use an improper file. Try again. \nFor more information about using Codon Context Ranking check the \"How to use\" page.";
ModernDialog.ShowMessage(message.ToString(), "Warning", MessageBoxButton.OK);
}
else
{
ORF.orfSeq = tupleTemp.Item1;
ORF.aminoORFseq = SeqParser.codonToAminoParser(ORF.orfSeq);
CalculateAndDisplayORF(ORF.orfSeq, ORF.aminoORFseq);
// Enabling checkboxes and button
MaximalizeRadioButton.IsEnabled = true;
MinimalizeRadioButton.IsEnabled = true;
OptimizeORFButton.IsEnabled = true;
}
}
else
{
// modern dialog initialization
string message = "Something went wrong. Probably you tried to use an improper file. Try again. \nFor more information about using Optimalizator check the \"How to use\" page.";
ModernDialog.ShowMessage(message.ToString(), "Warning", MessageBoxButton.OK);
}
}
