public List <Component> read_components_from_xlsx(InputFile file, IEnumerable <Correction> correctionFactors)
{
raw_components_in_file.Clear();
string absolute_path = file.directory + "\\" + file.filename + file.extension;
using (SpreadsheetDocument spreadsheetDocument = SpreadsheetDocument.Open(absolute_path, false))
{
// Get Data in Sheet1 of Excel file
IEnumerable <Sheet> sheetcollection = spreadsheetDocument.WorkbookPart.Workbook.GetFirstChild <Sheets>().Elements <Sheet>(); // Get all sheets in spread sheet document
WorksheetPart worksheet_1 = (WorksheetPart)spreadsheetDocument.WorkbookPart.GetPartById(sheetcollection.First().Id.Value); // Get sheet1 Part of Spread Sheet Document
SheetData sheet_1 = worksheet_1.Worksheet.Elements <SheetData>().First();
List <Row> rowcollection = worksheet_1.Worksheet.Descendants <Row>().ToList();
Component new_component = new Component();
int charge_row_index = 0;
string scan_range = "";
for (int i = 0; i < rowcollection.Count(); i++)
{
if (i == 0)
{
continue; //skip component header
}
IEnumerable <Cell> cells = rowcollection[i].Descendants <Cell>();
List <string> cellStrings = new List <string>();
for (int k = 0; k < rowcollection[i].Descendants <Cell>().Count(); k++)
{
cellStrings.Add(GetCellValue(spreadsheetDocument, rowcollection[i].Descendants <Cell>().ElementAt(k)));
}
if (cellStrings.Count > 4) //component row
{
if (i > 1)
{
add_component(new_component); // here we're adding the previously read component
}
new_component = new Component(cellStrings, file); // starting fresh here with a newly created componet.
charge_row_index = 0;
scan_range = cellStrings[8];
}
else if (cellStrings.Count == 4) //charge-state row
{
if (charge_row_index == 0)
{
charge_row_index += 1;
continue; //skip charge state headers
}
else
{
new_component.add_charge_state(cellStrings, Correction.GetCorrectionFactor(file.filename, scan_range, correctionFactors));
}
}
}
add_component(new_component); //add the final component
}
final_components = remove_monoisotopic_duplicates_harmonics_from_same_scan(raw_components_in_file);
scan_ranges = new HashSet <string>(final_components.Select(c => c.scan_range).ToList()).ToList();
return(final_components);
}
public static List <Correction> CorrectionFactorInterpolation(IEnumerable <Correction> cFactors)
{
List <Correction> correction_factors = cFactors.OrderBy(p => p.scan_number).ToList();
bool found_first_defined = false;
double recent_correction = 0;
List <Correction> undefined_corrections = new List <Correction>();
for (int i = 0; i < correction_factors.Count; i++)
{
Correction this_correction = correction_factors[i];
if (Double.IsNaN(this_correction.correction))
{
undefined_corrections.Add(this_correction); // Add all undefined corrections to a list for interpolating later
}
else if (!found_first_defined) //Found the first defined correction factor.
{
//Copy the first defined correction factor to all undefined correction factors at the head of the list.
found_first_defined = true;
foreach (Correction c in undefined_corrections)
{
c.correction = this_correction.correction;
}
recent_correction = this_correction.correction;
undefined_corrections.Clear();
}
else
{
//Average this defined correction value and the last one observed, and copy this to each recently seen undefined correction.
double correction_value = (recent_correction + this_correction.correction) / 2;
foreach (Correction c in undefined_corrections)
{
c.correction = correction_value;
}
recent_correction = this_correction.correction;
undefined_corrections.Clear();
}
}
//We ran out of real estate. Let's do something with any remaining undefined corrections.
foreach (Correction c in undefined_corrections)
{
c.correction = recent_correction;
}
return(correction_factors);
}
