private static List <string> ProcessLine(ShowBy showBy, PredictorCollection predictorCollection, string line,
MerLength merLength, int?dOfCenter, HlaSetSpecification hlaSetSpecification, bool modelOnly)
{
try
{
string hlaOrSupertypeOrNull;
string inputPeptide = ExtractInputs(hlaSetSpecification, line, predictorCollection, out hlaOrSupertypeOrNull);
List <string> output = new List <string>();
foreach (List <Prediction> predictionList in predictorCollection.MaxProbabilityPredictions(showBy, inputPeptide, merLength, dOfCenter, hlaSetSpecification, hlaOrSupertypeOrNull, modelOnly).Values)
{
string outputLine = InsertMaterial(line, hlaSetSpecification.InputHeaderCollection().Length, Prediction.CollectionToString(predictionList, false, hlaSetSpecification.IncludeHlaInOutput()));
output.Add(outputLine);
}
return(output);
}
catch (Exception exception)
{
string errorString = SpecialFunctions.CreateTabString(
line,
string.Format("Error: {0}{1}", exception.Message, exception.InnerException == null ? "" : string.Format(" ({0})", exception.InnerException)));
List <string> output = new List <string>();
output.Add(errorString);
return(output);
}
}
/// <summary>
/// Returns a list with one item per unique "GroupBy" key (e.g. each hla, each length, etc). Each item is a list of the predictions
/// that tie for maximum probability.
///
/// Most of the inputs are the same as for PredictionEnumeration.
/// </summary>
/// <param name="showBy"></param>
/// <param name="inputPeptide"></param>
/// <param name="merLength"></param>
/// <param name="hlaSetSpecification"></param>
/// <param name="hlaOrSupertypeOrNull"></param>
/// <param name="modelOnly"></param>
/// <returns></returns>
public Dictionary <object, List <Prediction> > MaxProbabilityPredictions(ShowBy showBy, string inputPeptide,
MerLength merLength, int?dOfCenter, HlaSetSpecification hlaSetSpecification, string hlaOrSupertypeOrNull, bool modelOnly)
{
Dictionary <object, BestSoFarWithTies <double, Prediction> > keyToBest =
ForEachKeyFindTheBestResults(showBy, inputPeptide, merLength, dOfCenter, hlaSetSpecification, hlaOrSupertypeOrNull, modelOnly);
Dictionary <object, List <Prediction> > maxProbabilityPredictionsPerKey = FindResultsPerKey(keyToBest);
return(maxProbabilityPredictionsPerKey);
}
private Dictionary <object, BestSoFarWithTies <double, Prediction> > ForEachKeyFindTheBestResults(
ShowBy showBy,
string inputPeptide, MerLength merLength, int?dOfCenter, HlaSetSpecification hlaSetSpecification, string hlaOrSupertypeOrNull, bool modelOnly)
{
Dictionary <object, BestSoFarWithTies <double, Prediction> > keyToBest = new Dictionary <object, BestSoFarWithTies <double, Prediction> >();
foreach (Prediction prediction in PredictionEnumeration(inputPeptide, merLength, dOfCenter, hlaSetSpecification, hlaOrSupertypeOrNull, modelOnly))
{
object key = prediction.GroupByKey(showBy); //!!!would be nice if this were typed, rather than just using 'string'
BestSoFarWithTies <double, Prediction> bestSoFarWithTies = SpecialFunctions.GetValueOrDefault(keyToBest, key, BestSoFarWithTies <double, Prediction> .GetInstance(SpecialFunctions.DoubleGreaterThan));
bestSoFarWithTies.Compare(prediction.WeightOfEvidence, prediction);
}
return(keyToBest);
}
public static void Main(string[] args)
{
try
{
// Parse arguments
ArgCollection argCollection = ArgCollection.GetInstance(args);
if (argCollection.ExtractOptionalFlag("Help"))
{
Console.WriteLine(HelpString);
return;
}
string modelName = argCollection.ExtractOptional("model", "LANLIEDB03062007");
bool modelOnly = argCollection.ExtractOptionalFlag("modelOnly");
bool inputHasHeader = argCollection.ExtractOptionalFlag("inputHasHeader");
MerLength merLength = argCollection.ExtractOptional <MerLength>("merLength", MerLength.scan);
int? dOfCenter = argCollection.ExtractOptional <int?>("withinDOfCenter", null);
ShowBy showBy = argCollection.ExtractOptional <ShowBy>("showBy", ShowBy.all);
string hlaSetName = argCollection.ExtractOptional <string>("hlaSet", "singleton");
HlaSetSpecification hlaSetSpecification = HlaSetSpecification.GetInstance(hlaSetName);
argCollection.CheckNoMoreOptions();
string inputFileName = argCollection.ExtractNext <string>("inputFile");
string outputFileName = argCollection.ExtractNext <string>("outputFile");
argCollection.CheckThatEmpty();
ReadInputCreatingOutput(showBy, modelName, inputHasHeader, merLength, dOfCenter, hlaSetSpecification, modelOnly, inputFileName, outputFileName);
}
catch (Exception exception)
{
Console.WriteLine("");
Console.WriteLine(exception.Message);
if (exception.InnerException != null)
{
Console.WriteLine(exception.InnerException.Message);
}
Console.Error.WriteLine("");
Console.Error.WriteLine(@"For more help:
Epipred -help");
System.Environment.Exit(-1);
}
}
internal object GroupByKey(ShowBy showBy)
{
switch (showBy)
{
case ShowBy.all:
return("all");
case ShowBy.hla:
return(Hla);
case ShowBy.length:
return(NEC.E.Length);
case ShowBy.hlaAndLength:
return(new Pair <Hla, int>(Hla, NEC.E.Length));
case ShowBy.doNotGroup:
return(this);
default:
SpecialFunctions.CheckCondition(false, "Don't know how to showBy " + showBy.ToString());
return(null);
}
}
private static void ReadInputCreatingOutput(ShowBy showBy, string modelName,
bool inputHasHeader, MerLength merLength, int?dOfCenter,
HlaSetSpecification hlaSetSpecification, bool modelOnly, string inputFileName, string outputFileName)
{
using (TextReader textReader = File.OpenText(inputFileName))
{
using (TextWriter textWriter = File.CreateText(outputFileName))
{
string header = CreateHeader(hlaSetSpecification, textReader, inputHasHeader);
textWriter.WriteLine(header);
PredictorCollection predictorCollection = PredictorCollection.GetInstance(modelName);
foreach (string line in SpecialFunctions.ReadEachLine(textReader))
{
foreach (string outputLine in ProcessLine(showBy, predictorCollection, line, merLength, dOfCenter, hlaSetSpecification, modelOnly))
{
textWriter.WriteLine(outputLine);
textWriter.Flush();
}
}
}
}
}
/// <summary>
/// Displays the show by.
/// </summary>
/// <param name="showBy">The show by.</param>
private void DisplayShowBy(ShowBy showBy)
{
hfShowBy.Value = showBy.ConvertToInt().ToString();
pnlChart.Visible = showBy == ShowBy.Chart;
pnlDetails.Visible = showBy == ShowBy.Attendees;
}
/// <summary>
/// Loads the attendance reporting settings from user preferences.
/// </summary>
private void LoadSettingsFromUserPreferences()
{
string keyPrefix = string.Format("giving-analytics-{0}-", this.BlockId);
string slidingDateRangeSettings = this.GetUserPreference(keyPrefix + "SlidingDateRange");
if (string.IsNullOrWhiteSpace(slidingDateRangeSettings))
{
// default to current year
drpSlidingDateRange.SlidingDateRangeMode = SlidingDateRangePicker.SlidingDateRangeType.Current;
drpSlidingDateRange.TimeUnit = SlidingDateRangePicker.TimeUnitType.Year;
}
else
{
drpSlidingDateRange.DelimitedValues = slidingDateRangeSettings;
}
hfGroupBy.Value = this.GetUserPreference(keyPrefix + "GroupBy");
nreAmount.DelimitedValues = this.GetUserPreference(keyPrefix + "AmountRange");
var currencyTypeIdList = this.GetUserPreference(keyPrefix + "CurrencyTypeIds").Split(',').ToList();
cblCurrencyTypes.SetValues(currencyTypeIdList);
var sourceIdList = this.GetUserPreference(keyPrefix + "SourceIds").Split(',').ToList();
cblTransactionSource.SetValues(sourceIdList);
var accountIdList = this.GetUserPreference(keyPrefix + "AccountIds").Split(',').ToList();
foreach (var cblAccounts in phAccounts.Controls.OfType <RockCheckBoxList>())
{
cblAccounts.SetValues(accountIdList);
}
dvpDataView.SetValue(this.GetUserPreference(keyPrefix + "DataView"));
HideShowDataViewResultOption();
rblDataViewAction.SetValue(this.GetUserPreference(keyPrefix + "DataViewAction"));
hfGraphBy.Value = this.GetUserPreference(keyPrefix + "GraphBy");
ShowBy showBy = this.GetUserPreference(keyPrefix + "ShowBy").ConvertToEnumOrNull <ShowBy>() ?? ShowBy.Chart;
DisplayShowBy(showBy);
GiversViewBy viewBy = this.GetUserPreference(keyPrefix + "ViewBy").ConvertToEnumOrNull <GiversViewBy>() ?? GiversViewBy.Giver;
hfViewBy.Value = viewBy.ConvertToInt().ToString();
GiversFilterBy giversFilterby = this.GetUserPreference(keyPrefix + "GiversFilterByType").ConvertToEnumOrNull <GiversFilterBy>() ?? GiversFilterBy.All;
switch (giversFilterby)
{
case GiversFilterBy.FirstTime:
radFirstTime.Checked = true;
break;
case GiversFilterBy.Pattern:
radByPattern.Checked = true;
break;
default:
radAllGivers.Checked = true;
break;
}
string attendeesFilterByPattern = this.GetUserPreference(keyPrefix + "GiversFilterByPattern");
string[] attendeesFilterByPatternValues = attendeesFilterByPattern.Split('|');
if (attendeesFilterByPatternValues.Length == 3)
{
tbPatternXTimes.Text = attendeesFilterByPatternValues[0];
cbPatternAndMissed.Checked = attendeesFilterByPatternValues[1].AsBooleanOrNull() ?? false;
drpPatternDateRange.DelimitedValues = attendeesFilterByPatternValues[2];
}
}
/// <summary>
/// Displays the show by.
/// </summary>
/// <param name="showBy">The show by.</param>
private void DisplayShowBy( ShowBy showBy )
{
hfShowBy.Value = showBy.ConvertToInt().ToString();
pnlShowByChart.Visible = showBy == ShowBy.Chart;
pnlShowByAttendees.Visible = showBy == ShowBy.Attendees;
}
/// <summary>
/// Displays the show by.
/// </summary>
/// <param name="showBy">The show by.</param>
private void DisplayShowBy( ShowBy showBy )
{
hfShowBy.Value = showBy.ConvertToInt().ToString();
pnlChart.Visible = showBy == ShowBy.Chart;
pnlDetails.Visible = showBy == ShowBy.Details;
}
