public static bool SaveToFile(string filename, PermutationArray 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 PermutationArray ReadPermutationArrayQuantificationData(string fileName)
{
string[,] data = ReadArrayFromFile(fileName);
bool permX = false, permY = false;
PermutationArray.CheckPermutationAxis(data, ref permX, ref permY);
if (!permX && !permY)
{
return(null);
}
Settings settings = Settings.Load("default.settings");
PermutationArray PA = new PermutationArray(data, permX, settings.WildTypeYAxisTopToBottom, out List <string> warnings, out string error);
return(PA);
}
public static PermutationArray ReadFromFile(string filename)
{
try
{
PermutationArray PA = null;
if (File.Exists(filename))
{
PA = JsonConvert.DeserializeObject <PermutationArray>(File.ReadAllText(filename));
if (PA.Version == "")
{
PA.Version = "Old version";
PA.Upgrade("NormalizedPeptideWeights");
PA.Upgrade("PositiveThreshold");
}
if (PA.NormalizedMatrixMin == PA.NormalizedMatrixMax)
{
PA.Upgrade("NormalizedMatrixRange");
}
}
return(PA);
}
catch { return(null); }
}
public Motif(PermutationArray PA)
: this(PA.NormalizedPeptideWeights, PA.NormalizedWildtypeWeights, PA.WildTypePeptide, PA.GetPositiveThreshold(), PA.GetNegativeThreshold())
{
}
public static bool ExportPermutationArrayToExcel(string fileName, PermutationArray 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");
List <string> headerrow = new List <string>();
List <string> headercolumn = new List <string>();
if (PA.PermutationXAxis)
{
headercolumn = PA.WildTypePeptide.ToCharArray().ToList().ConvertAll(c => c.ToString());
if (!PA.WildTypeYAxisTopToBottom)
{
headercolumn.Reverse();
}
headerrow = PA.Permutation.ToList().ConvertAll(c => c.ToString());
}
else
{
headerrow = PA.WildTypePeptide.ToCharArray().ToList().ConvertAll(c => c.ToString());
headercolumn = PA.Permutation.ToList().ConvertAll(c => c.ToString());
}
int startrow = 2;
int lastrow = MatrixToExcel(worksheet, 1, "Peptide Matrix", PA.PeptideMatrix);
if (lastrow < 0)
{
return(false);
}
ListToExcelRow(worksheet, startrow, 1, "", headerrow);
ListToExcelColumn(worksheet, startrow, 1, "", headercolumn);
startrow = lastrow + 3;
lastrow = MatrixToExcel(worksheet, lastrow + 3, "Quantification Matrix", PA.QuantificationMatrix);
if (lastrow < 0)
{
return(false);
}
ListToExcelRow(worksheet, startrow + 1, 1, "", headerrow);
ListToExcelColumn(worksheet, startrow + 1, 1, "", headercolumn);
//put the normalization values
if (PA.NormMode == NormalizationMode.Mean)
{
worksheet.Cells[++lastrow, 1].Value = "Norm By:";
worksheet.Cells[lastrow, 2].Value = PA.NormalizationValue;
}
else if (PA.PermutationXAxis)
{
ListToExcelColumn(worksheet, startrow + 1, PA.QuantificationMatrix.GetLength(1) + 2, "Norm By", PA.NormBy.ToList());
}
else
{
ListToExcelRow(worksheet, lastrow + 1, 1, "Norm By", PA.NormBy.ToList());
}
startrow = lastrow + 3;
lastrow = MatrixToExcel(worksheet, lastrow + 3, "Normalized Matrix", PA.NormalizedMatrix);
ListToExcelRow(worksheet, startrow + 1, 1, "", headerrow);
ListToExcelColumn(worksheet, startrow + 1, 1, "", headercolumn);
worksheet.Cells[lastrow + 2, 1].Value = "Positive Threshold: ";
worksheet.Cells[lastrow + 2, 2].Value = PA.GetPositiveThreshold();
worksheet.Cells[lastrow + 3, 1].Value = "Negative Threshold: ";
worksheet.Cells[lastrow + 3, 2].Value = PA.GetNegativeThreshold();
WriteToSheetWeighedPeptideList(package, PA.NormalizedPeptideWeights, PA.GetPositiveThreshold(), PA.GetNegativeThreshold(), PA.WildTypePeptide);
WriteToSheetMotif(package, new Motif(PA));
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);
}
}