public QuantFile(List <QuantFile> quantFiles, Dictionary <string, string> fileNameAndHeadertoUniqueGroupName)
{
CombinedQuantEntryDict = new Dictionary <string, QuantEntry>();
CombinedHeadersToPrint = new Dictionary <string, string>();
CombinedGroupNamesToPrint = new Dictionary <string, string>();
FileLocations = new List <string>();
Comparisons = new Dictionary <string, Comparison>();
foreach (QuantFile quantFile in quantFiles)
{
//Add the file locations for all files
FileLocations.Add(quantFile.FileLoaction);
UniprotHeader = quantFile.UniprotHeader;
//Add all of the headers to print to one dictionary - should all be the same headers
foreach (KeyValuePair <string, string> kvp in quantFile.HeadersToPrint)
{
string outString = null;
if (!CombinedHeadersToPrint.TryGetValue(kvp.Key, out outString))
{
CombinedHeadersToPrint.Add(kvp.Key, kvp.Value);
}
}
//Combine all of the unique group names to print out
foreach (KeyValuePair <string, string> kvp in quantFile.UniqueGroupNamesToPrint)
{
string outString = null;
if (!CombinedGroupNamesToPrint.TryGetValue(kvp.Key, out outString))
{
CombinedGroupNamesToPrint.Add(kvp.Key, kvp.Value);
}
}
//Combine the quantitation entries from each file
foreach (QuantEntry quantEntry in quantFile.QuantEntries)
{
QuantEntry outQuantEntry = null;
if (CombinedQuantEntryDict.TryGetValue(quantEntry.UniqueID, out outQuantEntry))
{
//If this entry already exsits simply add to the quant entry that exists
outQuantEntry.AddQuantEntry(quantEntry, fileNameAndHeadertoUniqueGroupName);
}
else
{
//Simply add the quant entry of it is the first time it is added
quantEntry.FillCombinedDictionary(fileNameAndHeadertoUniqueGroupName);
CombinedQuantEntryDict.Add(quantEntry.UniqueID, quantEntry);
}
}
}
}
public void AddQuantEntry(QuantEntry addQuantEntry, Dictionary <string, string> fileNameAndHeadertoUniqueGroupName)
{
//Make a combined dictionary for Log2Normalized Values
foreach (KeyValuePair <string, double> kvp in addQuantEntry.Log2NormalizedSampleValues)
{
string uniqueGroupNameKey = addQuantEntry.FileLocation + kvp.Key;
CombinedLog2NormalizedSampleValues.Add(fileNameAndHeadertoUniqueGroupName[uniqueGroupNameKey], kvp.Value);
}
//Make a combined dictionary for Mean normalized Values
foreach (KeyValuePair <string, double> kvp in addQuantEntry.MeanNormalizedSampleValues)
{
string uniqueGroupNameKey = addQuantEntry.FileLocation + kvp.Key;
CombinedMeanNormalizedSampleValues.Add(fileNameAndHeadertoUniqueGroupName[uniqueGroupNameKey], kvp.Value);
}
//Add to the headers to print list - it will print out values from each file if they are not the same.
foreach (KeyValuePair <string, string> kvp in addQuantEntry.HeadersToPrintDict)
{
List <string> outList = null;
if (CombinedHeadersToPrintSampleValues.TryGetValue(kvp.Key, out outList))
{
if (!outList.Contains(kvp.Value))
{
outList.Add(kvp.Value);
}
}
else
{
List <string> addList = new List <string>();
addList.Add(kvp.Value);
CombinedHeadersToPrintSampleValues.Add(kvp.Key, addList);
}
}
//Populate the Unique Header to Group Number Dictionary that will be used for Grouping the Quant Data
foreach (KeyValuePair <string, string> uniqueGroupNameToNumber in addQuantEntry.UniqueHeaderToGroupString)
{
string outInt = null;
if (!UniqueHeaderToGroupString.TryGetValue(uniqueGroupNameToNumber.Key, out outInt))
{
UniqueHeaderToGroupString.Add(uniqueGroupNameToNumber.Key, uniqueGroupNameToNumber.Value);
}
}
}
public void AddQuantEntry(QuantEntry addQuantEntry, Dictionary<string, string> fileNameAndHeadertoUniqueGroupName)
{
//Make a combined dictionary for Log2Normalized Values
foreach (KeyValuePair<string, double> kvp in addQuantEntry.Log2NormalizedSampleValues)
{
string uniqueGroupNameKey = addQuantEntry.FileLocation + kvp.Key;
CombinedLog2NormalizedSampleValues.Add(fileNameAndHeadertoUniqueGroupName[uniqueGroupNameKey], kvp.Value);
}
//Make a combined dictionary for Mean normalized Values
foreach (KeyValuePair<string, double> kvp in addQuantEntry.MeanNormalizedSampleValues)
{
string uniqueGroupNameKey = addQuantEntry.FileLocation + kvp.Key;
CombinedMeanNormalizedSampleValues.Add(fileNameAndHeadertoUniqueGroupName[uniqueGroupNameKey], kvp.Value);
}
//Add to the headers to print list - it will print out values from each file if they are not the same.
foreach (KeyValuePair<string, string> kvp in addQuantEntry.HeadersToPrintDict)
{
List<string> outList = null;
if (CombinedHeadersToPrintSampleValues.TryGetValue(kvp.Key, out outList))
{
if(!outList.Contains(kvp.Value))
{
outList.Add(kvp.Value);
}
}
else
{
List<string> addList = new List<string>();
addList.Add(kvp.Value);
CombinedHeadersToPrintSampleValues.Add(kvp.Key, addList);
}
}
//Populate the Unique Header to Group Number Dictionary that will be used for Grouping the Quant Data
foreach (KeyValuePair<string, string> uniqueGroupNameToNumber in addQuantEntry.UniqueHeaderToGroupString)
{
string outInt = null;
if(!UniqueHeaderToGroupString.TryGetValue(uniqueGroupNameToNumber.Key, out outInt))
{
UniqueHeaderToGroupString.Add(uniqueGroupNameToNumber.Key, uniqueGroupNameToNumber.Value);
}
}
}
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;
}
public void NormalizeDataSet(bool noNormalize, bool sumNormalize, bool medianNormalize, string uniprotHeader, string normalizationString, List <string> uniprotListForNormalization)
{
if (uniprotListForNormalization.Count == 0)
{
if (noNormalize)
{
DoNotNormalizeDataSet(HeadertoValueDict);
}
else if (medianNormalize)
{
MedianNormalizeDataSet(HeadertoValueDict);
}
else if (sumNormalize)
{
SumNormalizeDataSet(HeadertoValueDict);
}
}
else
{
//this will be a normalization based on a subset of proteins
Dictionary <string, List <double> > subsetDictionary = new Dictionary <string, List <double> >();
foreach (QuantEntry entry in QuantEntries)
{
entry.PopulateUniprotList(uniprotHeader);
foreach (string uniprotID in entry.UniprotIDList)
{
if (uniprotListForNormalization.Contains(uniprotID))
{
QuantEntry outEntry = null;
if (!QuantEntriesForNorm.TryGetValue(entry.UniqueID, out outEntry))
{
QuantEntriesForNorm.Add(entry.UniqueID, entry);
}
foreach (KeyValuePair <string, double> kvp in entry.SampleValues)
{
List <double> outDouble = null;
if (subsetDictionary.TryGetValue(kvp.Key, out outDouble))
{
outDouble.Add(kvp.Value);
}
else
{
List <double> addList = new List <double>();
addList.Add(kvp.Value);
subsetDictionary.Add(kvp.Key, addList);
}
}
}
}
}
if (noNormalize)
{
DoNotNormalizeDataSet(subsetDictionary);
}
else if (medianNormalize)
{
MedianNormalizeDataSet(subsetDictionary);
}
else if (sumNormalize)
{
SumNormalizeDataSet(subsetDictionary);
}
}
}
