public override bool Equals(object obj)
        {
            InProperty other = obj as InProperty;

            if (other == null)
            {
                return(false);
            }
            else
            {
                if (PropertySeq != other.PropertySeq || FeatureCollection.Length != other.FeatureCollection.Length)
                {
                    Debug.Assert(obj.ToString() != ToString()); // real assert
                    return(false);
                }
                if (FeatureCollection.Length > 0)
                {
                    bool b = FeatureCollection[0].Equals(other.FeatureCollection[0]);
                    Debug.Assert(b == (obj.ToString() == ToString())); // real assert
                    return(b);
                }
                Debug.Assert(obj.ToString() == ToString()); // real assert
                return(true);
            }
        }
        static public InProperty GetInstance(string propertySeq, IHashableFeature subFeature)
        {
            InProperty feature = new InProperty();

            feature.PropertySeq       = propertySeq;
            feature.FeatureCollection = new Feature[] { (Feature)subFeature };
            return(feature);
        }
 public static IEnumerable <IHashableFeature> GetInPropertySubSeqEnumeration(IHashableFeature regionFeature, bool fromLeft, IEnumerable <IHashableFeature> epitopeSubSeqEnumeration, Pair <NEC, Hla> entity, int littleLength)
 {
     foreach (IHashableFeature epitopeSubSeq in epitopeSubSeqEnumeration)
     {
         string aaSeqFull = (string)((Feature)epitopeSubSeq).Evaluate(entity);
         foreach (string aaSeqLittle in SpecialFunctions.SubstringEnumeration(aaSeqFull, littleLength))
         {
             foreach (List <string> propertyCombination in KmerProperties.EveryPropertyCombination(aaSeqLittle))
             {
                 string     propertySeq = SpecialFunctions.Join(",", propertyCombination);
                 InProperty feature     = InProperty.GetInstance(propertySeq, epitopeSubSeq);
                 Debug.Assert((bool)feature.Evaluate(entity)); // real assert - must only generate true features
                 yield return(feature);
             }
         }
     }
 }
        public static IEnumerable <IHashableFeature> GetPropertySeqInRegionInstance(int k, Pair <NEC, Hla> necAndHla, IHashableFeature regionFeature)
        {
            NEC nec = necAndHla.First;

            string       region   = (string)((Feature)regionFeature).Evaluate(necAndHla);
            Set <string> aaSeqSet = Set <string> .GetInstance(SpecialFunctions.SubstringEnumeration(region, k));

            foreach (string aaSeq in aaSeqSet)
            {
                foreach (List <string> propertyCombination in KmerProperties.EveryPropertyCombination(aaSeq))
                {
                    string     propertySeq = SpecialFunctions.Join(",", propertyCombination);
                    InProperty feature     = InProperty.GetInstance(propertySeq, regionFeature);
                    Debug.Assert((bool)feature.Evaluate(necAndHla)); // real assert - must only generate true features
                    yield return(feature);
                }
            }
        }
        //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);
        }