public void Tabulate(string directory, string caseName, List <KeyValuePair <int, int> > firstNullAndLastNullList)
{
List <Dictionary <string, string> > realRowCollectionToSort = new List <Dictionary <string, string> >();
List <double> nullDiffCollectionToBeSorted = new List <double>();
//!!!move VirusCount.PhyloTree.RangeCollection to a more general place
RangeCollection rangeCollection = RangeCollection.GetInstance();
int minFirstNull = int.MaxValue;
int maxLastNull = int.MinValue;
foreach (KeyValuePair <int, int> firstNullAndLastNull in firstNullAndLastNullList)
{
int firstNull = firstNullAndLastNull.Key;
minFirstNull = Math.Min(minFirstNull, firstNull);
int lastNull = firstNullAndLastNull.Value;
maxLastNull = Math.Max(maxLastNull, lastNull);
//!!!string repeated elsewere
//!!!what "new" or not?
string inputFileName = string.Format(@"{0}\{1}.{2}.{3}-{4}.pValues.new.txt", directory, SelectionName, CaseName, firstNull, lastNull); //!!!const
int maxNullSeen = int.MinValue;
//foreach (Dictionary<string, string> row in SpecialFunctions.TabFileTable(inputFileName, true))
foreach (Dictionary <string, string> row in SpecialFunctions.TabFileTable(inputFileName, PValueDetails.Header, true))
{
int nullIndex = int.Parse(row["NullIndex"]);
rangeCollection.TryAdd(nullIndex);
if (nullIndex == -1)
{
realRowCollectionToSort.Add(row);
}
else
{
double value = AccessPValueFromRow(row);
nullDiffCollectionToBeSorted.Add(value);
maxNullSeen = Math.Max(maxNullSeen, nullIndex);
}
}
}
SpecialFunctions.CheckCondition(realRowCollectionToSort.Count != 0);
SpecialFunctions.CheckCondition(rangeCollection.IsComplete(minFirstNull, maxLastNull));
int nullCount = maxLastNull - Math.Max(0, minFirstNull) + 1;
Dictionary <Dictionary <string, string>, double>
qValueList = SpecialFunctions.ComputeQValues(ref realRowCollectionToSort, AccessPValueFromRow, ref nullDiffCollectionToBeSorted, nullCount);
string outputFile = string.Format(@"{0}\{1}.{2}.{3}.qValues.new.txt", directory, SelectionName, CaseName, nullCount); //!!!const
using (StreamWriter outputStream = File.CreateText(outputFile))
{
outputStream.WriteLine(SpecialFunctions.CreateTabString(PValueDetails.Header, "qValue"));
foreach (Dictionary <string, string> row in realRowCollectionToSort)
{
double qValue = qValueList[row];
outputStream.WriteLine(SpecialFunctions.CreateTabString(row[""], qValue));
}
}
}
//!!!!somehow combine with Tabulate
static public void TabulateForTwo(LrtForHla lrtForHlaA, string directoryA, string caseNameA, List <KeyValuePair <int, int> > firstNullAndLastNullListA,
LrtForHla lrtForHlaB, string directoryB, string caseNameB, List <KeyValuePair <int, int> > firstNullAndLastNullListB)
{
SpecialFunctions.CheckCondition(lrtForHlaA.SelectionName == lrtForHlaB.SelectionName);
List <Dictionary <string, string> > realRowCollectionToSort = new List <Dictionary <string, string> >();
List <double> nullDiffCollectionToBeSorted = new List <double>();
//!!!move VirusCount.PhyloTree.RangeCollection to a more general place
RangeCollection rangeCollection = RangeCollection.GetInstance();
int minFirstNullx = int.MaxValue;
int maxLastNullx = int.MinValue;
foreach (char which in new char[] { 'A', 'B' })
{
List <KeyValuePair <int, int> > firstNullAndLastNullList;
string directory;
LrtForHla lrtForHla;
if (which == 'A')
{
firstNullAndLastNullList = firstNullAndLastNullListA;
directory = directoryA;
lrtForHla = lrtForHlaA;
}
else
{
Debug.Assert(which == 'B');
firstNullAndLastNullList = firstNullAndLastNullListB;
directory = directoryB;
lrtForHla = lrtForHlaB;
}
int minFirstNull = int.MaxValue;
int maxLastNull = int.MinValue;
foreach (KeyValuePair <int, int> firstNullAndLastNull in firstNullAndLastNullList)
{
int firstNull = firstNullAndLastNull.Key;
minFirstNull = Math.Min(minFirstNull, firstNull);
int lastNull = firstNullAndLastNull.Value;
maxLastNull = Math.Max(maxLastNull, lastNull);
//!!!string repeated elsewere
//!!!what "new" or not?
string inputFileName = string.Format(@"{0}\{1}.{2}.{3}-{4}.pValues.new.txt", directory, lrtForHla.SelectionName, lrtForHla.CaseName, firstNull, lastNull); //!!!const
int maxNullSeen = int.MinValue;
//foreach (Dictionary<string, string> row in SpecialFunctions.TabFileTable(inputFileName, true))
foreach (Dictionary <string, string> row in SpecialFunctions.TabFileTable(inputFileName, PValueDetails.Header, true))
{
int nullIndex = int.Parse(row["NullIndex"]);
rangeCollection.TryAdd(nullIndex);
if (nullIndex == -1)
{
realRowCollectionToSort.Add(row);
}
else
{
double value = AccessPValueFromRow(row);
nullDiffCollectionToBeSorted.Add(value);
maxNullSeen = Math.Max(maxNullSeen, nullIndex);
}
}
}
if (minFirstNullx == int.MaxValue)
{
minFirstNullx = minFirstNull;
Debug.Assert(maxLastNullx == int.MinValue);
maxLastNullx = maxLastNull;
}
else
{
SpecialFunctions.CheckCondition(minFirstNullx == minFirstNull);
SpecialFunctions.CheckCondition(maxLastNullx == maxLastNull);
}
}
SpecialFunctions.CheckCondition(realRowCollectionToSort.Count != 0);
SpecialFunctions.CheckCondition(rangeCollection.IsComplete(minFirstNullx, maxLastNullx));
int nullCount = maxLastNullx - Math.Max(0, minFirstNullx) + 1;
//Dictionary<string,string> realRowCollectionToSortNAAs0 = new List<double>();
//foreach (Dictionary<string,string> row in realRowCollectionToSort)
//{
// double r = AccessPValueFromRow(row);
// if (double.IsNaN(r))
// {
// Dictionary<string, string> row2 = new Dictionary<string, string>();
// foreach (KeyValuePair<string, string> keyAndValue in row)
// {
// }
// realRowCollectionToSortNAAs0.Add(0.0);
// }
// else
// {
// realRowCollectionToSortNAAs0.Add(row);
// }
//}
Dictionary <Dictionary <string, string>, double>
qValueList = SpecialFunctions.ComputeQValues(ref realRowCollectionToSort, AccessPValueFromRow, ref nullDiffCollectionToBeSorted, nullCount);
string outputFile = string.Format(@"{0}\{1}.{2}-{3}.{4}.qValues.new.txt", directoryB, lrtForHlaA.SelectionName, lrtForHlaA.CaseName, lrtForHlaB.CaseName, nullCount); //!!!const
using (StreamWriter outputStream = File.CreateText(outputFile))
{
outputStream.WriteLine(SpecialFunctions.CreateTabString(PValueDetails.Header, "qValue"));
foreach (Dictionary <string, string> row in realRowCollectionToSort)
{
double qValue = qValueList[row];
outputStream.WriteLine(SpecialFunctions.CreateTabString(row[""], qValue));
}
}
}
//Similar to the other tabulators, but can work with multiple sets of pValues files
//!!!would be better if could cut off really bad pValues to save memory
//!!! also would be nice to have filters
public static void CreateTabulateReport(ICollection <string> inputFilePatternCollection, string outputFileName,
KeepTest <Dictionary <string, string> > keepTest, double maxPValue, bool auditRowIndexValues)
{
//SpecialFunctions.CheckCondition(!File.Exists(outputFileName), "Output file already exists: " + outputFileName);
using (TextWriter textWriter = File.CreateText(outputFileName)) // Do this early so that if it fails, well know
{
List <Dictionary <string, string> > realRowCollectionToSort = new List <Dictionary <string, string> >();
List <double> nullValueCollectionToBeSorted = new List <double>();
string headerSoFar = null;
Set <int> broadRealAndNullIndexSetSoFar = null;
foreach (string broadInputFilePattern in inputFilePatternCollection)
{
Set <int> narrowRealAndNullIndexSetSetSoFar = Set <int> .GetInstance();
foreach (string narrowInputFilePattern in broadInputFilePattern.Split('+'))
{
Set <int> realAndNullIndexSet =
CreateTabulateReportInternal(narrowInputFilePattern, keepTest, maxPValue, auditRowIndexValues,
ref realRowCollectionToSort, ref nullValueCollectionToBeSorted, ref headerSoFar);
//Instead of throwing an error, we could filter out the duplicated null indexes
SpecialFunctions.CheckCondition(narrowRealAndNullIndexSetSetSoFar.IntersectionIsEmpty(realAndNullIndexSet),
string.Format("Within inputFilePattern {0}, multiple '+'-connected parts cover the same nullIndex(s), {1}",
broadInputFilePattern,
narrowRealAndNullIndexSetSetSoFar.Intersection(realAndNullIndexSet)));
narrowRealAndNullIndexSetSetSoFar.AddNewRange(realAndNullIndexSet);
}
SpecialFunctions.CheckCondition(!auditRowIndexValues || narrowRealAndNullIndexSetSetSoFar.Contains(-1),
string.Format("The 'null' index -1 for the real data was not seen in {0}", broadInputFilePattern));
if (broadRealAndNullIndexSetSoFar == null)
{
broadRealAndNullIndexSetSoFar = narrowRealAndNullIndexSetSetSoFar;
}
else
{
SpecialFunctions.CheckCondition(broadRealAndNullIndexSetSoFar.Equals(narrowRealAndNullIndexSetSetSoFar),
string.Format("The broad inputFilePattern {0} covers a different set of nullIndexes ({1}) than its predecessors ({2})",
broadInputFilePattern, narrowRealAndNullIndexSetSetSoFar, broadRealAndNullIndexSetSoFar));
}
}
double numberOfRandomizationRuns = broadRealAndNullIndexSetSoFar.Count - 1;
Console.WriteLine("Detected {0} randomized runs relative to the number of real runs.", numberOfRandomizationRuns);
Dictionary <Dictionary <string, string>, double> qValueList = SpecialFunctions.ComputeQValues(ref realRowCollectionToSort, AccessPValueFromPhylotreeRow, ref nullValueCollectionToBeSorted, numberOfRandomizationRuns);
//!!!this code is repeated elsewhere
textWriter.WriteLine(SpecialFunctions.CreateTabString(headerSoFar, "qValue"));
foreach (Dictionary <string, string> row in realRowCollectionToSort)
{
double qValue = qValueList[row];
textWriter.WriteLine(SpecialFunctions.CreateTabString(row[""], qValue));
}
}
}
