public static bool SaveToFile(string filename, PeptideArray PA)
{
try
{
PA.Version = typeof(Analyzer).Assembly.GetName().Version.ToString();
string json = JsonConvert.SerializeObject(PA);
File.WriteAllText(filename, json);
return(true);
}
catch { return(false); }
}
public static PeptideArray ReadFromFile(string filename)
{
try
{
PeptideArray PA = null;
if (File.Exists(filename))
{
PA = JsonConvert.DeserializeObject <PeptideArray>(File.ReadAllText(filename));
if (PA.Version == "")
{
PA.Version = "Old version";
PA.Upgrade("PositiveThreshold");
}
}
return(PA);
}
catch { return(null); }
}
public static bool ReadQuantificationData(string fileName, PeptideArray PA, bool headersExist)
{
try
{
FileInfo existingFile = new FileInfo(fileName);
string[,] data = null;
if (existingFile.Extension.StartsWith(".xls"))
{
data = ReadArrayFromExcel(existingFile);
}
else if (existingFile.Extension.StartsWith(".csv"))
{
data = ReadArrayFromCSV(existingFile);
}
PA.SetQuantificationMatrix(data, headersExist);
return(true);
}
catch
{
return(false);
}
}
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);
}
}
