public static bool SaveToFile(string filename, OPALArray OA)
{
try
{
OA.Version = typeof(Analyzer).Assembly.GetName().Version.ToString();
string json = JsonConvert.SerializeObject(OA);
File.WriteAllText(filename, json);
return(true);
}
catch { return(false); }
}
public static OPALArray ReadOPALArrayQuantificationData(string fileName)
{
string[,] data = ReadArrayFromFile(fileName);
bool permX = false, permY = false;
OPALArray.CheckPermutationAxis(data, ref permX, ref permY);
if (!permX && !permY)
{
return(null);
}
Settings settings = Settings.Load("default.settings");
OPALArray OA = new OPALArray(data, permX, settings.WildTypeYAxisTopToBottom, out string error);
return(OA);
}
public static OPALArray ReadFromFile(string filename)
{
try
{
OPALArray OA = null;
if (File.Exists(filename))
{
OA = JsonConvert.DeserializeObject <OPALArray>(File.ReadAllText(filename));
if (OA.Version == "")
{
OA.Version = "Old version";
OA.Upgrade("PositiveThreshold");
OA.Upgrade("NormalizedMatrixRange");
}
}
return(OA);
}
catch { return(null); }
}
public Motif(OPALArray OA)
: this(OA.NormalizedPeptideWeights, null, OA.WildTypePeptide, OA.PositiveThreshold, OA.NegativeThreshold)
{
}
public static bool ExportOPALArrayToExcel(string fileName, OPALArray OA, 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");
List <string> headerrow = new List <string>();
List <string> headercolumn = new List <string>();
if (OA.PermutationXAxis)
{
headercolumn = OA.PositionCaptions.ToList().ConvertAll(c => c.ToString());
headerrow = OA.Permutation.ToList().ConvertAll(c => c.ToString());
}
else
{
headerrow = OA.PositionCaptions.ToList().ConvertAll(c => c.ToString());
headercolumn = OA.Permutation.ToList().ConvertAll(c => c.ToString());
}
int startrow = 1;
int lastrow = MatrixToExcel(worksheet, startrow, "Quantification Matrix", OA.QuantificationMatrix);
if (lastrow < 0)
{
return(false);
}
ListToExcelRow(worksheet, startrow + 1, 1, "", headerrow);
ListToExcelColumn(worksheet, startrow + 1, 1, "", headercolumn);
//put the normalization values
if (OA.NormMode == NormalizationMode.Max)
{
worksheet.Cells[++lastrow, 1].Value = "Norm By:";
worksheet.Cells[lastrow, 2].Value = OA.NormalizationValue;
}
else if (OA.PermutationXAxis)
{
ListToExcelColumn(worksheet, startrow + 1, OA.QuantificationMatrix.GetLength(1) + 2, "Norm By", OA.NormBy.ToList());
}
else
{
ListToExcelRow(worksheet, lastrow + 1, 1, "Norm By", OA.NormBy.ToList());
}
startrow = lastrow + 3;
lastrow = MatrixToExcel(worksheet, startrow, "Normalized Matrix", OA.NormalizedMatrix);
ListToExcelRow(worksheet, startrow + 1, 1, "", headerrow);
ListToExcelColumn(worksheet, startrow + 1, 1, "", headercolumn);
WriteToSheetMotif(package, new Motif(OA));
WriteToSheetReferenceInfo(package, OA);
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);
}
}
