private void linkLoadFromFile_LinkClicked(object sender, LinkLabelLinkClickedEventArgs e)
{
try
{
DialogResult dlg = dlgOpenQuantification.ShowDialog();
if (dlg != DialogResult.OK)
{
return;
}
SetText(dlgOpenProject);
string filename = dlgOpenQuantification.FileName;
if (System.IO.File.Exists(filename))
{
OA = FileUtil.ReadOPALArrayQuantificationData(filename);
thresholdEntry.SetInitialValues(OA.GetPositiveThreshold(), OA.GetNegativeThreshold());
cbPermutationXAxis.Checked = PermutationXAxis;
cbYAxisTopToBottom.Checked = OA.PositionYAxisTopToBottom;
if (OA.QuantificationMatrix != null)
{
LoadQuantificationFromOPALArrayToGrid();
}
GridUtil.LoadNumericMatrixToGrid(dgNormalized, OA.NormalizedMatrix, 1, 1);
FillGridHeaders(dgNormalized);
Run();
ColorGridsandDrawMotifs();
}
}
catch
{
MessageBox.Show("There is a problem with loading the quantification file.\r\nPlease make sure the quantification data is the only data in the loaded file.\r\n", Application.ProductName);
}
}
private void frmOPALArray_Load(object sender, EventArgs e)
{
thresholdEntry.SetInitialValues(0.5, 0.5);
ResetSettings();
GridUtil.FormatGrid(dgQuantification);
GridUtil.FormatGrid(dgNormalized);
}
private void LoadQuantificationFromPermutationArrayToGrid()
{
GridUtil.LoadNumericMatrixToGrid(dgQuantification, PA.QuantificationMatrix, 1, 1);
cbWildTypeXAxis.Checked = !PA.PermutationXAxis;
FillGridHeaders(dgQuantification);
quantificationLoaded = true;
}
private void LoadQuantificationFromOPALArrayToGrid()
{
GridUtil.LoadNumericMatrixToGrid(dgQuantification, OA.QuantificationMatrix, 1, 1);
PermutationXAxis = cbPermutationXAxis.Checked = OA.PermutationXAxis;
FillGridHeaders(dgQuantification);
quantificationLoaded = true;
}
private void cmiPaste_Click(object sender, EventArgs e)
{
GridUtil.PasteClipboard(dgQuantification);
quantificationLoaded = true;
ResetSettings();
Run();
}
private void cmiPastePeptide_Click(object sender, EventArgs e)
{
try
{
string[,] matrix = MatrixUtil.ClipboardToMatrix();
matrix = MatrixUtil.StripHeaderRowColumns(matrix, false);
rowCount = matrix.GetLength(0);
colCount = matrix.GetLength(1);
PA = new PeptideArray(rowCount, colCount, rowsFirst);
PA.SetPeptideMatrix(matrix);
peptidelength = PA.PeptideLength;
ePeptideLength.Text = peptidelength.ToString();
dgQuantification.RowCount = dgQuantification.ColumnCount = 0;
dgNormalized.RowCount = dgNormalized.ColumnCount = 0;
SetRowColumnCount();
GridUtil.LoadStringMatrixToGrid(dgPeptides, matrix);
peptidesLoaded = true;
quantificationLoaded = false;
FillPAValues();
ClearMotifs();
}
catch
{
}
}
private void cmiPasteQuantification_Click(object sender, EventArgs e)
{
try
{
if (PA == null)
{
MessageBox.Show("The peptide array needs to be loaded before the quantification array.", Analyzer.ProgramName);
return;
}
string[,] matrix = MatrixUtil.ClipboardToMatrix();
matrix = MatrixUtil.StripHeaderRowColumns(matrix, true);
if (matrix == null || rowCount != matrix.GetLength(0) || colCount != matrix.GetLength(1))
{
MessageBox.Show("The dimensions of the quantification data does not match the peptide matrix.", Analyzer.ProgramName);
return;
}
double[,] dMatrix = MatrixUtil.ConvertToNumericMatrix(matrix);
PA.SetQuantificationMatrix(matrix, false);
GridUtil.LoadNumericMatrixToGrid(dgQuantification, dMatrix);
PA.NormalizationValue = MatrixUtil.GetMaxValue(dMatrix);
eNormalizeBy.Text = PA.NormalizationValue.ToString();
quantificationLoaded = true;
Renormalize();
}
catch
{
}
}
private void frmPeptideArray_Load(object sender, EventArgs e)
{
ResetSettings();
UpdateArrayInfo();
GridUtil.FormatGrid(dgPeptides);
GridUtil.FormatGrid(dgQuantification);
GridUtil.FormatGrid(dgNormalized);
}
private void cmiPaste_Click(object sender, EventArgs e)
{
GridUtil.PasteClipboard(dgQuantification);
quantificationLoaded = true;
dgPeptides.RowCount = dgPeptides.ColumnCount = 0;
dgNormalized.RowCount = dgNormalized.ColumnCount = 0;
ResetSettings();
Run();
}
private void LoadProject()
{
try
{
DialogResult dlg = dlgOpenProject.ShowDialog();
if (dlg != DialogResult.OK)
{
return;
}
SetText(dlgOpenProject);
string filename = dlgOpenProject.FileName;
try
{
OA = OPALArray.ReadFromFile(filename);
}
catch
{
MessageBox.Show("The file may be corrupted or not a valid PeSA project file.", Analyzer.ProgramName);
}
thresholdEntry.SetInitialValues(OA.GetPositiveThreshold(), OA.GetNegativeThreshold());
rbMaxValue.Checked = OA.NormMode == NormalizationMode.Max;
rbPerRowColumn.Checked = OA.NormMode != NormalizationMode.Max;
cbPermutationXAxis.Checked = PermutationXAxis;
cbYAxisTopToBottom.Checked = OA.PositionYAxisTopToBottom;
if (OA.QuantificationMatrix != null)
{
LoadQuantificationFromOPALArrayToGrid();
}
GridUtil.LoadNumericMatrixToGrid(dgNormalized, OA.NormalizedMatrix, 1, 1);
FillGridHeaders(dgNormalized);
bool gridOK = ColorGridsandDrawMotifs();//also creates/draws the motif
eNotes.Text = OA.Notes;
imageReference.Image = null;
try
{
Image img = FileUtil.Base64ToImage(OA.ImageStr);
imageReference.Image = img;
}
catch { }
DrawColorMatrix();
if (!gridOK)
{
MessageBox.Show("There is a problem in loading the file. It is highly recommended to re-run the analysis.", Analyzer.ProgramName);
}
}
catch
{
MessageBox.Show("There is a problem in loading the file. It is highly recommended to re-run the analysis.", Analyzer.ProgramName);
}
linkRun.Visible = true;
}
private void rbPerRowColumn_CheckedChanged(object sender, EventArgs e)
{
if (!rbMaxValue.Focused && !rbPerRowColumn.Focused)
{
return;
}
if (rbPerRowColumn.Checked && OA != null)
{
OA.NormMode = NormalizationMode.PerRowColumn;
OA.Renormalize();
GridUtil.LoadNumericMatrixToGrid(dgNormalized, OA.NormalizedMatrix, 1, 1);
ColorGridsandDrawMotifs();
DrawColorMatrix();
}
}
private void Run()
{
string[,] values = new string[dgQuantification.RowCount, dgQuantification.ColumnCount];
for (int iRow = 0; iRow < dgQuantification.RowCount; iRow++)
{
for (int iCol = 0; iCol < dgQuantification.ColumnCount; iCol++)
{
values[iRow, iCol] = dgQuantification[iCol, iRow].Value?.ToString() ?? "";
}
}
string error = "";
bool xPossible = true, yPossible = true;
OPALArray.CheckPermutationAxis(values, ref xPossible, ref yPossible);
if (xPossible && yPossible)
{
PermutationXAxis = cbPermutationXAxis.Checked;
}
else if (xPossible)
{
PermutationXAxis = true;
cbPermutationXAxis.Checked = true;
}
else if (yPossible)
{
PermutationXAxis = false;
cbPermutationXAxis.Checked = false;
}
if (!xPossible && !yPossible)
{
MessageBox.Show("Please make sure one the axes have OPAL array (each amino acid has to exist at most once)", Analyzer.ProgramName);
return;
}
;
OA = new OPALArray(values, PermutationXAxis, cbYAxisTopToBottom.Checked, out error);
OA.SetPositiveThreshold(thresholdEntry.PositiveThreshold, out bool negChanged);
OA.SetNegativeThreshold(thresholdEntry.NegativeThreshold, out bool posChanged2);
if (error != "")
{
MessageBox.Show(error, Analyzer.ProgramName);
return;
}
GridUtil.LoadNumericMatrixToGrid(dgNormalized, OA.NormalizedMatrix, 1, 1);
FillGridHeaders(dgNormalized);
ColorGridsandDrawMotifs();
DrawColorMatrix();
}
private void LoadPeptidesFromPermutationArrayToGrid()
{
GridUtil.LoadStringMatrixToGrid(dgPeptides, PA.PeptideMatrix, 1, 1);
FillGridHeaders(dgPeptides);
}
private void LoadNormalizedMatrixFromPeptideArrayToGrid()
{
GridUtil.LoadNumericMatrixToGrid(dgNormalized, PA.NormalizedMatrix, 1, 1);
FillGridHeaders(dgNormalized);
}
public frmAnalyzePeptideArray()
{
InitializeComponent();
dgPeptideHelper = new GridUtil(dgPeptides);
}
private void LoadPeptidesFromPeptideArrayToGrid()
{
GridUtil.LoadStringMatrixToGrid(dgPeptides, PA.PeptideMatrix);
peptidesLoaded = true;
}
private void LoadQuantificationFromPeptideArrayToGrid()
{
GridUtil.LoadNumericMatrixToGrid(dgQuantification, PA.QuantificationMatrix);
quantificationLoaded = true;
}
