Exemple #1
0
 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); }
 }
Exemple #2
0
        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);
        }
Exemple #3
0
 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); }
 }
Exemple #4
0
 public Motif(OPALArray OA)
     : this(OA.NormalizedPeptideWeights, null, OA.WildTypePeptide, OA.PositiveThreshold, OA.NegativeThreshold)
 {
 }
Exemple #5
0
        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);
            }
        }