//public static IEnumerable<ISorterStage> ReplaceAtIndex(this IEnumerable<ISorterStage> source, int index,
// ISorterStage replacement)
//{
// var lst = source.ToList();
// lst[index] = replacement;
// return lst;
//}
public static Tuple <bool, IPermutation> Sort(this ISorterStage stage, IPermutation perm)
{
var aRet = new uint[stage.Order];
for (uint i = 0; i < stage.Order; i++)
{
aRet[i] = perm[i];
}
var wasUsed = false;
for (uint i = 0; i < stage.Order; i++)
{
var m = stage[i];
if (m > i)
{
var llv = perm[i];
var hlv = perm[m];
if (llv > hlv)
{
aRet[m] = llv;
aRet[i] = hlv;
wasUsed = true;
}
}
}
return(new Tuple <bool, IPermutation>(wasUsed, PermutationEx.MakePermutation(aRet)));
}
public GenomeSorterConjOrbit(Guid id, IPermutation twoCycle, IPermutation conj, uint order, uint stageCount)
{
Id = id;
TwoCycle = twoCycle;
Conj = conj;
Order = order;
Stagecount = stageCount;
}
public SortResult(ISorter sorter, double sortedness, bool[] stageUse,
ISortable sortable, IPermutation result)
{
Sortedness = sortedness;
StageUse = stageUse;
Sortable = sortable;
Result = result;
Sorter = sorter;
}
public static int GetHashCode(this IPermutation perm)
{
uint hCode = 0;
for (uint i = 0; i < perm.Order; i++)
{
hCode ^= perm[i];
}
return((int)hCode);
}
public static uint SortednessSq(this IPermutation perm)
{
var tot = 0u;
for (uint i = 0; i < perm.Order; i++)
{
tot += (uint)Math.Pow((i - perm[i]), 2);
}
return(tot);
}
public static IPermutation ToInverse(this IPermutation perm)
{
var invs = new uint[perm.Order];
for (uint i = 0; i < perm.Order; i++)
{
invs[perm[i]] = i;
}
return(new Permutation(order: perm.Order, terms: invs));
}
public override ISolution Apply(ISolution solution, Configuration configuration)
{
IPermutation permutation = (IPermutation)solution;
TwoOperands operands = (TwoOperands)configuration;
List <int> swapped = new List <int>(permutation.Order)
{
[operands.First] = permutation.Order[operands.Second],
[operands.Second] = permutation.Order[operands.First]
};
return(permutation.FetchPermutation(swapped, "swap"));
}
/// <summary>
/// Swaps the content of the indices according to the given permutation.
/// </summary>
/// <param name="permutation">The given permutation that specifies how the content should be permutated.</param>
public void Swap(IPermutation permutation)
{
int[] ia = this.Indices;
int l = ia.Length, lp = permutation.Length, f;
for (int i = 0x00; i < l; i++)
{
f = ia [i];
if (f < lp)
{
ia [i] = permutation.GetTransitionOfIndex(f);
}
}
}
public static IPermutation Multiply(this IPermutation lhs, IPermutation rhs)
{
if (lhs.Order != rhs.Order)
{
throw new ArgumentException("The two Permutation must have the same Order");
}
var aRet = new uint[lhs.Order];
for (uint i = 0; i < lhs.Order; i++)
{
aRet[i] = lhs[rhs[i]];
}
return(new Permutation(order: lhs.Order, terms: aRet));
}
internal BaseSPN(ISubstitution substitution, IPermutation permutation, IKeyScheduler keyScheduler)
{
Substitution = substitution;
Permutation = permutation;
KeyScheduler = keyScheduler;
RoundCount = 4;
SubstitutionBoxCount = 4;
BlockLength = 16;
if (BlockLength / SubstitutionBoxCount != Substitution.InputLength)
{
throw new Exception("ISubstitution is not compatible with SPN.");
}
}
public static bool IsEqualTo(this IPermutation lhs, IPermutation rhs)
{
if (lhs.Order != rhs.Order)
{
return(false);
}
for (uint i = 0; i < lhs.Order; i++)
{
if (lhs[i] != rhs[i])
{
return(false);
}
}
return(true);
}
/// <summary>
/// Saves "u" to the "Output"
/// </summary>
public static void Save(BinaryWriter Output, IPermutation u)
{
var type = u.GetType ();
byte idType = 255;
for (byte i = 0; i < Catalog.Count; i++) {
if (type == Catalog [i]) {
idType = i;
break;
}
}
if (idType == 255) {
var s = String.Format ("Type {0} is not a recognized IPerms, please add it to " +
"PermsGenericIO.Catalog", type);
throw new ArgumentException (s);
}
Output.Write (idType);
u.Save (Output);
}
public static CompositeDictionary <IPermutation, int> GetOrbit(
this IPermutation perm, uint maxSize = 1000)
{
var pd = PermutationEx.PermutationDictionary(perm.Order);
var cume = perm;
for (var i = 0; i < maxSize; i++)
{
if (pd.ContainsKey(cume))
{
return(pd);
}
pd.Add(cume, 1);
cume = cume.Multiply(perm);
}
return(pd);
}
public static CompositeDictionary <IPermutation, int> GetConjOrbit(
this IPermutation perm, IPermutation conj, uint maxSize = 1000)
{
var pd = PermutationEx.PermutationDictionary(perm.Order);
var curConj = conj;
var curRes = perm;
for (var i = 0; i < maxSize; i++)
{
if (pd.ContainsKey(curRes))
{
return(pd);
}
pd.Add(curRes, 1);
curRes = perm.ConjugateBy(curConj);
curConj = curConj.Multiply(conj);
}
return(pd);
}
public override ISolution Apply(ISolution solution, Configuration configuration)
{
IPermutation permutation = (IPermutation)solution;
TwoOperands operands = (TwoOperands)configuration;
List <int> shifted = new List <int>(permutation.Order);
int shiftedItem = shifted[operands.First];
shifted.RemoveAt(operands.First);
if (operands.Second <= operands.First)
{
shifted.Insert(operands.Second, shiftedItem);
}
else
{
shifted.Insert(operands.Second - 1, shiftedItem);
}
return(permutation.FetchPermutation(shifted, "shift"));
}
public override ISolution Apply(ISolution solution, Configuration configuration)
{
IPermutation permutation = (IPermutation)solution;
TwoOperands operands = (TwoOperands)configuration;
List <int> twoOpted;
if (operands.First < operands.Second)
{
twoOpted = new List <int>(permutation.Order);
twoOpted.Reverse(operands.First, operands.Second - operands.First + 1);
}
else
{
twoOpted = permutation.Order.GetRange(operands.First, permutation.Order.Count - operands.First);
twoOpted.AddRange(permutation.Order.GetRange(0, operands.First));
twoOpted.Reverse(0, operands.Second + twoOpted.Count - operands.First + 1);
}
return(permutation.FetchPermutation(twoOpted, "2opt"));
}
public Sponge(int bitRate, IPermutation permutation)
{
if (permutation == null)
{
throw new ArgumentNullException("permutation");
}
if (bitRate <= 0 || bitRate > 1600)
{
throw new ArgumentOutOfRangeException("bitRate", "The bit rate must be betwen 1 and 1600, inclusive");
}
this.permutation = permutation;
this.bitRate = bitRate;
state = new[]
{
new ulong[] { 0, 0, 0, 0, 0 },
new ulong[] { 0, 0, 0, 0, 0 },
new ulong[] { 0, 0, 0, 0, 0 },
new ulong[] { 0, 0, 0, 0, 0 },
new ulong[] { 0, 0, 0, 0, 0 }
};
}
public Sponge(int bitRate, IPermutation permutation)
{
if (permutation == null)
{
throw new ArgumentNullException("permutation");
}
if (bitRate <= 0 || bitRate > 1600)
{
throw new ArgumentOutOfRangeException("bitRate", "The bit rate must be betwen 1 and 1600, inclusive");
}
this.permutation = permutation;
this.bitRate = bitRate;
state = new[]
{
new ulong[] { 0, 0, 0, 0, 0 },
new ulong[] { 0, 0, 0, 0, 0 },
new ulong[] { 0, 0, 0, 0, 0 },
new ulong[] { 0, 0, 0, 0, 0 },
new ulong[] { 0, 0, 0, 0, 0 }
};
}
public static ISortable ToSortable(this IPermutation perm)
{
return(new Sortable(Guid.NewGuid(), perm.Order, perm.GetMap()));
}
public Sponge(IPermutation permutation)
: this(defaultBitRate, permutation)
{
}
/// <summary>
/// Swaps the content of the indices according to the given permutation.
/// </summary>
/// <param name="permutation">The given permutation that specifies how the content should be permutated.</param>
public void Swap(IPermutation permutation)
{
int[] ia = this.Indices;
int l = ia.Length, lp = permutation.Length, f;
for (int i = 0x00; i < l; i++) {
f = ia [i];
if (f < lp) {
ia [i] = permutation.GetTransitionOfIndex (f);
}
}
}
public static SortablePool OrbitSortablePool(IPermutation seed, uint maxSize)
{
return new SortablePool(Guid.NewGuid(),
seed.GetOrbit(maxSize).Keys.Select(p => p.ToSortable()));
}
public void FixtureSetUp()
{
TestFixtureBaseSetup();
mockPermutation = Create<IPermutation>();
defaultBitRate = 1024;
}
public void Build(IList<int> seq, int sigma, PermutationBuilder perm_builder, BitmapFromBitStream bitmap_builder)
{
// A counting sort construction of the permutation
var counters = new int[sigma];
foreach (var s in seq) {
if (s + 1 < sigma) {
counters [s + 1]++;
}
}
for (int i = 1; i < sigma; i++) {
counters [i] += counters [i - 1];
}
var n = seq.Count;
var P = new int[n];
for (int i = 0; i < n; i++) {
var sym = seq [i];
var pos = counters [sym];
P [pos] = i;
counters [sym] = pos + 1;
}
// the bitmap to save the lengths
var lens = new BitStream32 ();
int prevc = 0;
foreach (var c in counters) {
var len = c - prevc;
prevc = c;
lens.Write (true);
lens.Write (false, len);
}
// an additional 1 to the end, to simplify source code
lens.Write (true);
var bb_lens = new FakeBitmap (lens);
this.LENS = bitmap_builder(bb_lens);
this.PERM = perm_builder(P);
}
public void Load(BinaryReader Input)
{
this.PERM = GenericIO<IPermutation>.Load (Input);
this.LENS = GenericIO<Bitmap>.Load (Input);
}
public void Load(BinaryReader Input)
{
this.PERM = PermutationGenericIO.Load (Input);
this.LENS = RankSelectGenericIO.Load (Input);
}
public static int OrbitLengthFor(this IPermutation perm, uint maxSize = 1000)
{
return(GetOrbit(perm, maxSize).Count);
}
public static uint[] GetMap(this IPermutation permutation)
{
return(0u.CountUp(permutation.Order)
.Select(i => permutation[i])
.ToArray());
}
public static int ConjOrbitLengthFor(this IPermutation perm,
IPermutation conj, uint maxSize = 1000)
{
return(GetConjOrbit(perm, conj, maxSize).Count);
}
static void Main(string[] args)
{
//FloorplanProblem problem = new FloorplanProblem(50);
//FloorplanSolution solution = new FloorplanSolution(problem);
//Swap swap = new Swap(problem.Dimension);
//Shift shift = new Shift(problem.Dimension);
//FullLeafMove leaf = new FullLeafMove(problem.Dimension);
//List<Operator> operations = new List<Operator> { swap, shift, leaf };
TspProblem problem = new TspProblem(100);
TspSolution solution = new TspSolution(problem);
Swap swap = new Swap(problem.Dimension, 1);
Shift shift = new Shift(problem.Dimension, 2);
TwoOpt twoOpt = new TwoOpt(problem.Dimension, 3);
List <Operator> operations = new List <Operator> {
swap, shift, twoOpt
};
MultistartParameters multistartOptions = new MultistartParameters()
{
InstancesNumber = 1,
OutputFrequency = 500,
};
LocalDescentParameters ldParameters = new LocalDescentParameters()
{
DetailedOutput = true,
Seed = 0,
Operators = operations,
IsSteepestDescent = false
};
SimulatedAnnealingParameters saParameters = new SimulatedAnnealingParameters()
{
InitProbability = 0.3,
TemperatureCooling = 0.97,
UseWeightedNeighborhood = true,
DetailedOutput = false,
Seed = 0,
Operators = operations,
};
MultistartParameters ldMultistartParameters = (MultistartParameters)multistartOptions.Clone();
ldMultistartParameters.Parameters = ldParameters;
MultistartParameters saMultistartParameters = (MultistartParameters)multistartOptions.Clone();
saMultistartParameters.Parameters = saParameters;
LocalDescent ld = new LocalDescent(ldParameters);
SimulatedAnnealing sa = new SimulatedAnnealing(saParameters);
ParallelMultistart pld = new ParallelMultistart(ldMultistartParameters);
ParallelMultistart psa = new ParallelMultistart(saMultistartParameters);
List <string> operators = new List <string>();
IPermutation sol = solution;
foreach (IPermutation s in ld.Minimize(solution))
{
Console.WriteLine("{0}, {1:f}s, {2}, {3}, {4}, {5}", s.CostValue, s.TimeInSeconds, s.IterationNumber, s.IsCurrentBest, s.IsFinal, sol.CostValue - s.CostValue);
sol = s;
operators.Add(s.OperatorTag);
}
//var groups = operators.GroupBy(s => s).Select(s => new { Operator = s.Key, Count = s.Count() });
//var dictionary = groups.ToDictionary(g => g.Operator, g => g.Count);
//foreach (var o in groups)
//{
// Console.WriteLine("{0} = {1}", o.Operator, o.Count);
//}
Console.WriteLine("Done");
Console.ReadLine();
}
public static IPermutation ConjugateBy(this IPermutation perm, IPermutation conj)
{
return(conj.ToInverse().Multiply(perm.Multiply(conj)));
}
public Sponge(IPermutation permutation)
: this(defaultBitRate, permutation)
{
}
public void Build(IList<int> seq, int sigma, int t = 16, BitmapFromList64 bitmap_builder = null)
{
this.sigma = sigma;
long n = seq.Count;
var L = new long[n];
var counters = new int[sigma + 1];
// counters.Add (0, sigma); <- if ListIFS
for (int i = 0; i < n; ++i) {
var sym = seq [i];
counters [sym + 1] += 1;
}
for (int i = 1; i <= sigma; ++i) {
counters [i] += counters [i - 1];
}
for (int i = 0; i < n; ++i) {
var sym = seq [i];
long long_sym = n * ((long)sym) + i;
L [counters [sym]] = long_sym;
counters [sym] += 1;
}
counters = null;
/**** slow construction ****/
/*****
for (int i = 0; i < n; ++i) {
long s = seq [i];
L [i] = n * s + i;
//L.Add (n * s + i);
}
Array.Sort (L);
*****/
if (bitmap_builder == null) {
bitmap_builder = BitmapBuilders.GetSArray64 ();
}
this.xl_bitmap = bitmap_builder (L, n * sigma);
// now building the permutation for access
var p = new ListGen_MRRR ();
p.Build (this.GetNotIdxPERM (), t, null);
this.perm = p;
}
public static IPermutation ConjugateByRandomSingleTwoCycle(this IPermutation perm, IRando randy)
{
return(perm.ConjugateBy(randy.ToSingleTwoCyclePermutation(perm.Order)));
// return perm.ConjugateBy(randy.ToFullTwoCyclePermutation(perm.Order));
}
public static IPermutation ConjugateByRandomPermutation(this IPermutation perm, IRando randy)
{
return(perm.ConjugateBy(randy.ToPermutation(perm.Order)));
}
public void FixtureSetUp()
{
TestFixtureBaseSetup();
mockPermutation = Create <IPermutation>();
defaultBitRate = 1024;
}
void Print1Perm(IPermutation p)
{
for (int i = 0; i < p.Count; ++i) {
Console.Write ("<{0}>, ", p.Direct(i));
}
Console.WriteLine ("<END>");
}
public void Load(BinaryReader Input)
{
this.sigma = Input.ReadInt32 ();
this.xl_bitmap = RankSelect64GenericIO.Load (Input);
var p = new ListGen_MRRR ();
p.Load (Input);
p.SetPERM (this.GetNotIdxPERM ());
this.perm = p;
}
public static ISorterStage ToSorterStage(this IPermutation permutation,
uint stageNumber)
{
return(new SorterStage(permutation.Order, permutation.GetMap(), stageNumber));
}
public void Load(BinaryReader Input)
{
this.N = Input.ReadInt32 ();
int vocsize = Input.ReadInt32 ();
this.InvIndex = new Bitmap[vocsize];
for (int i = 0; i < vocsize; i++) {
this.InvIndex [i] = GenericIO<Bitmap>.Load (Input);
}
this.Lens = GenericIO<Bitmap>.Load (Input);
var p = new ListGen_MRRR ();
p.Load (Input);
p.SetPERM (this.GetNotIdxPERM ());
this.Perm = p;
}
/// <summary>
/// Builds the index for the sequence
/// </summary>
public void Build(IList<int> sequence, int alphabet_size, int t = 16,
BitmapFromList rowbuilder = null, BitmapFromBitStream lenbuilder = null)
{
if (rowbuilder == null) {
rowbuilder = BitmapBuilders.GetSArray ();
}
if (lenbuilder == null) {
lenbuilder = BitmapBuilders.GetGGMN_wt (12);
}
var invindex = new IList<int>[alphabet_size];
for (int i = 0; i < alphabet_size; i++) {
invindex [i] = new List<int> ();
}
int pos = 0;
foreach (var c in sequence) {
invindex [c].Add (pos);
pos++;
}
pos = 0;
this.N = sequence.Count;
this.InvIndex = new Bitmap[alphabet_size];
var lens = new BitStream32 ();
for (int i = 0; i < alphabet_size; i++) {
if (i % 1000 == 0) {
if (i % 10000 == 0) {
Console.WriteLine ();
Console.Write ("*** InvIndexXLBSeq {0}/{1}", i, alphabet_size);
} else {
Console.Write (", {0}", i);
}
}
this.InvIndex [i] = rowbuilder (invindex [i]);
lens.Write (true);
lens.Write (false, invindex [i].Count);
invindex [i] = null;
}
lens.Write (true);
Console.WriteLine ();
Console.WriteLine ("done, now saving permutation and the Len bitmap");
this.Lens = lenbuilder (new FakeBitmap (lens));
var p = new ListGen_MRRR ();
p.Build (this.GetNotIdxPERM (), t, null);
Console.WriteLine ("done");
this.Perm = p;
}
public StageDimer(IPermutation stage1, IPermutation stage2, IPermutation modifier)
{
Stage1 = stage1;
Stage2 = stage2;
Modifier = modifier;
}