private List<QuantFile> CombineQuantFiles(List<QuantFile> quantFiles)
{
List<QuantFile> retList = new List<QuantFile>();
if (quantFiles.Count > 1)
{
UpdateLog("Combining Quant Files...");
}
QuantFile combinedQuantFile = new QuantFile(quantFiles, FileNameAndHeadertoUniqueGroupName);
retList.Add(combinedQuantFile);
return retList;
}
private List<QuantFile> ImportQuantFiles()
{
UpdateLog("Importing Quant Files...");
//This will be the list of Quant Files
List<QuantFile> retList = new List<QuantFile>();
//Load the headers that you will want to print in the final document.
String[] headersToPrintArray = new string[headersToPrintListBox.CheckedItems.Count];
headersToPrintListBox.CheckedItems.CopyTo(headersToPrintArray, 0);
List<String> headersToPrintList = headersToPrintArray.ToList();
if (!headersToPrintList.Contains(UniprotHeader))
{
headersToPrintList.Add(UniprotHeader);
}
//Load the two strings that you will use to determine a unique group when combining files
string uniqueIDString = headerComboBox.SelectedItem.ToString();
string uniqueIDString2 = headerComboBox2.SelectedItem.ToString();
//Create Quant Files for each loaded CSV - Files will not be combined at this time
foreach (KeyValuePair<string, List<string>> kvp in FileNametoHeadersToQuantify)
{
//Open the CSV file
using (CsvReader reader = new CsvReader(new StreamReader(kvp.Key), true))
{
//Create the Quant File that you will populate
QuantFile quantFile = new QuantFile(kvp.Key, kvp.Value);
//Set the UniprotHeader
quantFile.UniprotHeader = UniprotHeader;
//Read in each line and make a Quant Entry
while (reader.ReadNextRecord())
{
//Make sure that there is quantitative data for all measurements in the file
bool addQuantData = true;
//Do this check if you are mean normalizing
if (ValueForComparison == ValueType.MeanNormalizedFoldChange || ValueForComparison == ValueType.MeanNormalizedLog2Change || medianNorm.Checked || sumNorm.Checked)
{
//Check all of the headers in the file regardless of if they are in a comparison
foreach (string header in kvp.Value)
{
string parseThis = reader[header];
double outDouble = 0;
if (!double.TryParse(parseThis, out outDouble) || outDouble == 0)
{
addQuantData = false;
}
}
}
else
{
//Only check the headers that are involved in a comparison HeadersToIncludeByFile
foreach (string header in HeadersToIncludeByFile[kvp.Key])
{
string parseThis = reader[header];
double outDouble = 0;
if (!double.TryParse(parseThis, out outDouble) || outDouble == 0)
{
addQuantData = false;
}
}
}
//If there are not "0" or "-" values then add this Quant Entry
if (addQuantData)
{
//Make a new Quant Entry
QuantEntry quantEntry = new QuantEntry(quantFile.FileLoaction, reader[uniqueIDString], reader[uniqueIDString2], UniqueGroupNametoGroupString);
//Load up the data in the columns that you will want to print at the end.
foreach (string header in headersToPrintList)
{
string outString = null;
if (!quantFile.HeadersToPrint.TryGetValue(header, out outString))
{
quantFile.HeadersToPrint.Add(header, header);
}
quantEntry.HeadersToPrintDict.Add(header, reader[header]);
}
//Load up the data from each of the columns that you want to quantify.
foreach (string header in kvp.Value)
{
//Get the Quant Value to Parse
string testit = reader[header];
double a = double.Parse(reader[header]);
quantFile.HeadertoValueDict[header].Add(double.Parse(reader[header]));
quantEntry.SampleValues.Add(header, double.Parse(reader[header]));
//Get the file name + header and create a unique hash code that you will map the unique header name
string fileAndHeader = quantFile.FileLoaction + header;
long fileAndHeaderHash = fileAndHeader.GetHashCode();
//Only add these once - this will map the File Location + Header code to the unique name given by the user
string outString = null;
if (!quantFile.UniqueGroupNamesToPrint.TryGetValue(fileAndHeader, out outString))
{
quantFile.UniqueGroupNamesToPrint.Add(fileAndHeader, FileNameAndHeadertoUniqueGroupName[fileAndHeader]);
}
}
//Add that Quant Entry to the List within the Quant File
quantFile.QuantEntries.Add(quantEntry);
}
}
retList.Add(quantFile);
}
}
return retList;
}
