internal static NEC GetInstance(NEC input, int flankSize)
{
SpecialFunctions.CheckCondition(input.N.Length >= flankSize && input.C.Length >= flankSize, "The input flank size should not be larger than the new flank size");
NEC output = NEC.GetInstance(input.N.Remove(0, input.N.Length - flankSize), input.E, input.C.Substring(0, flankSize));
return(output);
}
public static NEC GetInstanceWithPossibleNulls(int flankingSize, string mer, string protein, int position)
{
string e = protein.Substring(position, mer.Length);
string n;
if (position - flankingSize < 0)
{
//Console.WriteLine("Warning: matching position in protein too close to start to create left flanking region");
n = null;
}
else
{
n = protein.Substring(position - flankingSize, flankingSize);
}
string c;
if (position + mer.Length + flankingSize > protein.Length)
{
//Console.WriteLine("Warning: matching position in protein too close to end to create right flanking region");
c = null;
}
else
{
c = protein.Substring(position + mer.Length, flankingSize);
}
NEC nec = NEC.GetInstance(n, e, c);
return(nec);
}
public static NEC GetRandomInstance(NEC sample, Dictionary <char, int> aaToCount, ref Random random)
{
string n = RandomAAString(aaToCount, sample.N.Length, ref random);
string e = RandomAAString(aaToCount, sample.E.Length, ref random);
string c = RandomAAString(aaToCount, sample.C.Length, ref random);
return(NEC.GetInstance(n, e, c));
}
public static NEC GetConsensusInstanceWithPossibleNullFlanks(string mer, Set <NEC> necSet, ref Random random)
{
DebugCheckMerSameLengthAsEInSet(mer, necSet);
string n = FindConsensusOrNull(necSet, GetN, ref random);
string c = FindConsensusOrNull(necSet, GetC, ref random);
NEC nec = NEC.GetInstance(n, mer, c);
return(nec);
}
public static NEC GetInstance(string necString)
{
string[] fieldCollection = necString.Split(',');
SpecialFunctions.CheckCondition(fieldCollection.Length == 3);
for (int iField = 0; iField < fieldCollection.Length; ++iField)
{
if (fieldCollection[iField] == "null")
{
fieldCollection[iField] = null;
}
}
NEC nec = NEC.GetInstance(fieldCollection[0], fieldCollection[1], fieldCollection[2]);
return(nec);
}
//static private Dictionary<Pair<NEC, Hla>, bool> CloseHuman = null;
//GeneratorType.Hla | GeneratorType.Position | GeneratorType.Property | GeneratorType.AndHla | GeneratorType.Zero6Supertype | GeneratorType.AndZero6Supertype
private static Set <IHashableFeature> GenerateFeatureSet(
object entity, string supertypeTableSource,
int?flankSizeOrNull,
bool includeFlankNECFeatures,
bool includeChemicalProperties, bool includeAAFeatures,
bool addEiFeatures
)
{
bool includeAndHlaAndSTWithEpitopeAdjFeatures = false;
bool subtractSupertypeFeatures = false;
bool subtractHlaFeatures = false;
bool substractChemAACrissCrossFeatures = false;
SpecialFunctions.CheckCondition(!includeAndHlaAndSTWithEpitopeAdjFeatures || includeFlankNECFeatures);
Pair <NEC, Hla> necAndHlaX = (Pair <NEC, Hla>)entity;
NEC nec = (null == flankSizeOrNull) ? necAndHlaX.First : NEC.GetInstance(necAndHlaX.First, (int)flankSizeOrNull);
Hla hla = necAndHlaX.Second;
Debug.Assert(nec.N.Length == nec.C.Length); // real assert
Pair <NEC, Hla> necAndHla = new Pair <NEC, Hla>(nec, hla);
Set <IHashableFeature> hlaishFeatureSet = new Set <IHashableFeature>();
CreateAndAddHlaFeature(subtractHlaFeatures, hla, necAndHla, ref hlaishFeatureSet);
CreateAndAddFeatureSupertype(supertypeTableSource, subtractSupertypeFeatures, hla, necAndHla, ref hlaishFeatureSet, Assembly.GetExecutingAssembly(), Predictor.ResourceString);
Set <IHashableFeature> featureSet = Set <IHashableFeature> .GetInstance(hlaishFeatureSet);
if (addEiFeatures)
{
AddEiFeatures(includeChemicalProperties, includeAAFeatures, substractChemAACrissCrossFeatures, nec, necAndHla, hlaishFeatureSet, featureSet);
}
if (includeFlankNECFeatures)
{
List <IHashableFeature> aaInNFlankFeatureList = new List <IHashableFeature>(In.GetAASeqInRegionInstance(1, necAndHla, NFlank.GetInstance()));
DebugCheckThatEvaluatesToTrue(necAndHla, aaInNFlankFeatureList);
if (includeAAFeatures)
{
featureSet.AddNewRange(aaInNFlankFeatureList); //AA in N flank
featureSet.AddNewRange(In.GetAASeqInRegionInstance(2, necAndHla, NFlank.GetInstance())); //AA1-AA2 in Nflank
featureSet.AddNewRange(SubSeq.GetInSubSeqEnumeration(NFlank.GetInstance(), false, 1, necAndHla)); //AA@x in N flank (numbering is 5 4 3 2 1)
featureSet.AddNewRange(SubSeq.GetInSubSeqEnumeration(NFlank.GetInstance(), false, 2, necAndHla)); //AA1-AA2@x in Nflank (x is position of AA2, i.e., the smaller number)
featureSet.AddNewRange(In.GetAASeqInRegionInstance(1, necAndHla, CFlank.GetInstance())); //AA in Cflank
featureSet.AddNewRange(In.GetAASeqInRegionInstance(2, necAndHla, CFlank.GetInstance())); //AA1-AA2 in Cflank
featureSet.AddNewRange(SubSeq.GetInSubSeqEnumeration(CFlank.GetInstance(), true, 1, necAndHla)); //AA@x in C flank (numbering is 1 2 3 4 5)
featureSet.AddNewRange(SubSeq.GetInSubSeqEnumeration(CFlank.GetInstance(), true, 2, necAndHla)); //AA1-AA2@x in Cflank (x is position of AA1, i.e., the smaller number)
}
if (includeChemicalProperties)
{
featureSet.AddNewOrOldRange(InProperty.GetPropertySeqInRegionInstance(1, necAndHla, NFlank.GetInstance()));
featureSet.AddNewOrOldRange(SubSeq.GetInPropertySubSeqEnumeration(NFlank.GetInstance(), false, 1, necAndHla));
featureSet.AddNewOrOldRange(InProperty.GetPropertySeqInRegionInstance(1, necAndHla, CFlank.GetInstance()));
featureSet.AddNewOrOldRange(SubSeq.GetInPropertySubSeqEnumeration(CFlank.GetInstance(), true, 1, necAndHla));
featureSet.AddNewOrOldRange(InProperty.GetPropertySeqInRegionInstance(2, necAndHla, NFlank.GetInstance()));
featureSet.AddNewOrOldRange(SubSeq.GetInPropertySubSeqEnumeration(NFlank.GetInstance(), false, 2, necAndHla));
featureSet.AddNewOrOldRange(InProperty.GetPropertySeqInRegionInstance(2, necAndHla, CFlank.GetInstance()));
featureSet.AddNewOrOldRange(SubSeq.GetInPropertySubSeqEnumeration(CFlank.GetInstance(), true, 2, necAndHla));
}
}
if (includeFlankNECFeatures)
{
if (includeAAFeatures)
{
//EV in Epitope
AddFeatureWithOptionalAndHlaAndST(In.GetAASeqInRegionInstance(2, necAndHla, Epitope.GetInstance()), includeAndHlaAndSTWithEpitopeAdjFeatures, hlaishFeatureSet, false, ref featureSet);//AA1-AA2 in Epitope
//RR in Epitope[@1-2]
AddFeatureWithOptionalAndHlaAndST(SubSeq.GetInSubSeqEnumeration(Epitope.GetInstance(), true, 2, necAndHla), includeAndHlaAndSTWithEpitopeAdjFeatures, hlaishFeatureSet, false, ref featureSet);//AA1-AA2@x in Epitope (x is position of AA1, i.e., the smaller number)
}
if (includeChemicalProperties)
{
//polar,cyclic in Epitope
AddFeatureWithOptionalAndHlaAndST(InProperty.GetPropertySeqInRegionInstance(2, necAndHla, Epitope.GetInstance()), includeAndHlaAndSTWithEpitopeAdjFeatures, hlaishFeatureSet, false, ref featureSet);
//polar,large in Epitope[@8-9]
AddFeatureWithOptionalAndHlaAndST(SubSeq.GetInPropertySubSeqEnumeration(Epitope.GetInstance(), true, 2, necAndHla), includeAndHlaAndSTWithEpitopeAdjFeatures, hlaishFeatureSet, false, ref featureSet);
}
//AA1-AA2 in Nflank,Epitope, etc
if (null != flankSizeOrNull && (int)flankSizeOrNull > 0)
{
string epitope = (string)Epitope.GetInstance().Evaluate(entity);
SubSeq lastNAAFeature = SubSeq.GetInstance(1, 1, false, NFlank.GetInstance());
string lastNAA = (string)lastNAAFeature.Evaluate(entity);
In inLastNAA = In.GetInstance(lastNAA, lastNAAFeature);
SubSeq firstEAAFeature = SubSeq.GetInstance(1, 1, true, Epitope.GetInstance());
string firstEAA = (string)firstEAAFeature.Evaluate(entity);
Debug.Assert(firstEAA == epitope.Substring(0, 1));// real assert
In inFirstEAA = In.GetInstance(firstEAA, firstEAAFeature);
SubSeq lastEAAFeature = SubSeq.GetInstance(epitope.Length, epitope.Length, true, Epitope.GetInstance());
string lastEAA = (string)lastEAAFeature.Evaluate(entity);
In inLastEAA = In.GetInstance(lastEAA, lastEAAFeature);
SubSeq firstCAAFeature = SubSeq.GetInstance(1, 1, true, CFlank.GetInstance());
string firstCAA = (string)firstCAAFeature.Evaluate(entity);
In inFirstCAA = In.GetInstance(firstCAA, firstCAAFeature);
if (includeAAFeatures)
{
And andLastNNAAFirstEAA = And.GetInstance(inLastNAA, inFirstEAA);
AddFeatureWithOptionalAndHlaAndST(andLastNNAAFirstEAA, includeAndHlaAndSTWithEpitopeAdjFeatures, hlaishFeatureSet, /*checkThatNew*/ true, ref featureSet);
And andLastEAAFirstCAA = And.GetInstance(inLastEAA, inFirstCAA);
AddFeatureWithOptionalAndHlaAndST(andLastEAAFirstCAA, includeAndHlaAndSTWithEpitopeAdjFeatures, hlaishFeatureSet, /*checkThatNew*/ true, ref featureSet);
}
if (includeChemicalProperties)
{
foreach (string lastNProperty in KmerProperties.AaToPropList[Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter[lastNAA[0]]])
{
InProperty inLastNProperty = InProperty.GetInstance(lastNProperty, lastNAAFeature);
foreach (string firstEProperty in KmerProperties.AaToPropList[Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter[firstEAA[0]]])
{
InProperty inFirstEProperty = InProperty.GetInstance(firstEProperty, firstEAAFeature); //!!!get this out of the loop?
And andLastNPropertyFirstEProperty = And.GetInstance(inLastNProperty, inFirstEProperty);
AddFeatureWithOptionalAndHlaAndST(andLastNPropertyFirstEProperty, includeAndHlaAndSTWithEpitopeAdjFeatures, hlaishFeatureSet, /*checkThatNew*/ false, ref featureSet);
Debug.Assert((bool)andLastNPropertyFirstEProperty.Evaluate(necAndHla));
}
}
foreach (string lastEProperty in KmerProperties.AaToPropList[Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter[lastEAA[0]]])
{
InProperty inlastEProperty = InProperty.GetInstance(lastEProperty, lastEAAFeature);
foreach (string firstCProperty in KmerProperties.AaToPropList[Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter[firstCAA[0]]])
{
InProperty infirstCProperty = InProperty.GetInstance(firstCProperty, firstCAAFeature); //!!!get this out of the loop?
And andlastEPropertyfirstCProperty = And.GetInstance(inlastEProperty, infirstCProperty);
AddFeatureWithOptionalAndHlaAndST(andlastEPropertyfirstCProperty, includeAndHlaAndSTWithEpitopeAdjFeatures, hlaishFeatureSet, /*checkThatNew*/ false, ref featureSet);
Debug.Assert((bool)andlastEPropertyfirstCProperty.Evaluate(necAndHla));
}
}
}
}
}
return(featureSet);
}
public static bool TryCreateInstance(string epitopeString, int aa1PosStart, int aa1PosLast, AASeq aaSeqConsensus, out NEC nec)
{
AASeq aaSeqSubConsensus = aaSeqConsensus.SubSeqAA1Pos(aa1PosStart, epitopeString.Length);
Debug.Assert(aaSeqSubConsensus.OriginalAA1Position(0) == aa1PosStart.ToString()); // real assert
string consensusAsString = aaSeqConsensus.ToString();
int flankingSize = 5;
//Create a string builder to file from back to front
StringBuilder sbN = new StringBuilder(new string(' ', flankingSize));
int sbNIndex = flankingSize - 1;
//Look at the characters of the concensus moving to the left
for (int aa1Pos = aa1PosStart - 1;; --aa1Pos)
{
if (aa1Pos < 1)
{
Console.WriteLine("Warning: for epitope {0}, the epitope position is too close to the left of the protein to create a c region of length 5. Skipping epitope", epitopeString);
nec = null;
return(false);
}
char aa = consensusAsString[aa1Pos - 1];
if (aa == '-')
{
continue;
}
sbN[sbNIndex] = aa;
--sbNIndex;
if (sbNIndex < 0)
{
break;
}
}
StringBuilder sbC = new StringBuilder();
//Look at the characters of the concensus moving to the right
for (int aa1Pos = aa1PosLast + 1; ; ++aa1Pos)
{
if (aa1Pos > consensusAsString.Length)
{
Console.WriteLine("Warning: for epitope {0}, the epitope position is too close to the right of the protein to create a n region of length 5. Skipping epitope", epitopeString);
nec = null;
return(false);
}
char aa = consensusAsString[aa1Pos - 1];
if (aa == '-')
{
continue;
}
sbC.Append(aa);
if (sbC.Length == flankingSize)
{
break;
}
}
nec = NEC.GetInstance(sbN.ToString(), epitopeString, sbC.ToString());
return(true);
}
