private static void WriteToSheetFrequencyMotif(ExcelPackage package, Motif motif, string title, ref int rowind, bool clear = true)
{
ExcelWorksheet worksheet =
clear ? GetWorksheetBlank(package, "Motif") : GetWorksheetKeepData(package, "Motif");
if (clear)
{
worksheet.Drawings.Clear();
}
worksheet.Cells[rowind, 1].Value = "Frequency Threshold:";
worksheet.Cells[rowind++, 2].Value = motif.PositiveThreshold;
Settings settings = Settings.Load("default.settings");
int heightImage = 200;
int widthImage = 800;
if (settings != null)
{
heightImage = settings.MotifHeight;
widthImage = settings.MotifWidth;
}
Bitmap bmp = motif.GetFrequencyMotif(widthImage, heightImage);
if (bmp != null)
{
var picture = worksheet.Drawings.AddPicture(title, bmp);
picture.SetPosition(rowind, 0, 1, 0);
}
int occupiedRows = (int)Math.Round(heightImage / worksheet.Row(rowind).Height);
rowind += occupiedRows + 1;
DumpMotifData(worksheet, ref rowind, null, motif.Frequencies);
}
public static bool SaveToFile(string filename, Motif motif)
{
try
{
motif.Version = typeof(Analyzer).Assembly.GetName().Version.ToString();
string json = JsonConvert.SerializeObject(motif);
File.WriteAllText(filename, json);
return(true);
}
catch { return(false); }
}
public static Motif ReadFromFile(string filename)
{
try
{
Motif motif = null;
if (File.Exists(filename))
{
motif = JsonConvert.DeserializeObject <Motif>(File.ReadAllText(filename));
if (motif.Version == "")
{
motif.Version = "Old version";
}
}
return(motif);
}
catch (Exception exc) { return(null); }
}
public bool Run(Motif motif, int posSpec, int negSpec)
{
if (motif == null)
{
return(false);
}
Motif = motif;
PositiveSpecificity = posSpec;
NegativeSpecificity = negSpec;
if (!GenerateTemplate())
{
return(false);
}
FullSequenceList = SequenceGenerator.Combinations(FullTemplate);
PositiveSequenceList = SequenceGenerator.Combinations(PositiveTemplate);
NegativeSequenceList = FullSequenceList.Except(PositiveSequenceList).ToList();
return(true);
}
public static bool ExportPeptideArrayToExcel(string fileName, PeptideArray PA, bool overwrite, out string errormsg)
{
try
{
errormsg = "";
FileInfo existingFile = new FileInfo(fileName);
if (existingFile.Exists && !overwrite)
{
return(false);
}
using (ExcelPackage package = new ExcelPackage(existingFile))
{
if (existingFile.Exists)
{
while (package.Workbook.Worksheets.Count > 0)
{
package.Workbook.Worksheets.Delete(1);
}
}
ExcelWorksheet worksheet = GetWorksheetBlank(package, "Arrays");
int lastrow = MatrixToExcel(worksheet, 1, "Peptide Matrix", PA.PeptideMatrix);
if (lastrow < 0)
{
return(false);
}
lastrow = MatrixToExcel(worksheet, lastrow + 3, "Binary Matrix", PA.BinaryMatrix);
if (lastrow < 0)
{
return(false);
}
lastrow = MatrixToExcel(worksheet, lastrow + 3, "Quantification Matrix", PA.QuantificationMatrix);
if (lastrow < 0)
{
return(false);
}
worksheet.Cells[++lastrow, 1].Value = "Norm By:";
worksheet.Cells[lastrow, 2].Value = PA.NormalizationValue;
lastrow = MatrixToExcel(worksheet, lastrow + 3, "Normalized Matrix", PA.NormalizedMatrix);
WriteToSheetWeighedPeptideList(package, PA.NormalizedPeptideWeights, PA.PositiveThreshold, PA.NegativeThreshold);
if (PA.KeyPosition != null && PA.KeyAA != ' ')
{
int rowind = 1;
List <string> mainList = PA.ModifiedPeptides.Where(s => s[(int)PA.KeyPosition - 1] == PA.KeyAA).ToList();
List <string> shiftedList = Analyzer.ShiftPeptides(PA.ModifiedPeptides.Where(s => s[(int)PA.KeyPosition - 1] != PA.KeyAA).ToList(), PA.KeyAA, PA.PeptideLength, (int)PA.KeyPosition - 1,
out List <string> replacements);
Motif motif = new Motif(mainList, PA.PeptideLength);
motif.FreqThreshold = PA.FrequencyThreshold;
WriteToSheetFrequencyMotif(package, motif, "Motif", ref rowind);
rowind++;
motif = new Motif(shiftedList, PA.PeptideLength);
motif.FreqThreshold = PA.FrequencyThreshold;
WriteToSheetFrequencyMotif(package, motif, "Shifted Motif", ref rowind, false);
}
else
{
Motif motif = new Motif(PA.ModifiedPeptides, PA.PeptideLength);
motif.FreqThreshold = PA.FrequencyThreshold;
int rowind = 1;
WriteToSheetFrequencyMotif(package, motif, "Motif", ref rowind);
}
WriteToSheetReferenceInfo(package, PA);
try
{
package.Save();
}
catch
{
errormsg = "There is a problem with saving the export file. Please make sure the file is not open and you have writing rights to the specific folder.";
return(false);
}
}
return(true);
}
catch
{
errormsg = "There is a problem with creating the export file. Please try again.";
return(false);
}
}
private static void WriteToSheetMotif(ExcelPackage package, Motif motif)
{
ExcelWorksheet worksheet = GetWorksheetBlank(package, "Motif");
worksheet.Drawings.Clear();
Settings settings = Settings.Load("default.settings");
int heightImage = 200;
int widthImage = 800;
if (settings != null)
{
heightImage = settings.MotifHeight;
widthImage = settings.MotifWidth;
}
int rowind = 1;
worksheet.Cells[rowind, 1].Value = "Positive Threshold:";
worksheet.Cells[rowind++, 2].Value = motif.PositiveThreshold;
if (motif.WildTypePeptide != "")
{
worksheet.Cells[rowind, 1].Value = "Wildtype Sequence:";
worksheet.Cells[rowind++, 2].Value = motif.WildTypePeptide;
}
Bitmap bmp = motif.GetPositiveMotif(widthImage, heightImage);
if (bmp != null)
{
var picture = worksheet.Drawings.AddPicture("Positive Motif", bmp);
picture.SetPosition(rowind, 0, 1, 0);
}
int occupiedRows = (int)Math.Round(heightImage / worksheet.Row(rowind).Height);
rowind += occupiedRows + 1;
Dictionary <int, Dictionary <char, double> > scaledcolumns = motif.GetScaledColumns(motif.PositiveColumns);
DumpMotifData(worksheet, ref rowind, motif.PositiveColumns, scaledcolumns);
rowind += 2;
worksheet.Cells[rowind, 1].Value = "Negative Threshold:";
worksheet.Cells[rowind++, 2].Value = motif.NegativeThreshold;
bmp = motif.GetNegativeMotif(widthImage, heightImage);
if (bmp != null)
{
var picture = worksheet.Drawings.AddPicture("Negative Motif", bmp);
picture.SetPosition(rowind, 0, 1, 0);
}
occupiedRows = (int)Math.Round(heightImage / worksheet.Row(rowind).Height);
rowind += occupiedRows + 1;
scaledcolumns = motif.GetScaledColumns(motif.NegativeColumns);
DumpMotifData(worksheet, ref rowind, motif.NegativeColumns, scaledcolumns);
rowind += 2;
worksheet.Cells[rowind++, 1].Value = "Bar Chart:";
bmp = motif.GetBarChart(widthImage / 2);
if (bmp != null)
{
var picture = worksheet.Drawings.AddPicture("Bar Chart", bmp);
picture.SetPosition(rowind, 0, 1, 0);
}
occupiedRows = (int)Math.Round(heightImage / worksheet.Row(rowind).Height);
rowind += occupiedRows + 1;
}