public void generateDepthOneTreeRandomlyOld(List <Taxa> TaxaList, string DummyTaxaCharacter, int Level, List <string> _VALID_TAXA_LIST, List <Quartet> inputQuatrets)
{
string DummyTaxa = DummyTaxaCharacter + Level.ToString();
Taxa TaxaDummy = new Taxa();
TaxaDummy._Taxa_Value = DummyTaxa;
FinalPartionPair PartionPair = new FinalPartionPair();
List <Taxa> _LeftPartTaxaList;
List <Taxa> _RightPartTaxaList;
if (CountValidTaxa(TaxaList, _VALID_TAXA_LIST) > 2)
{
_LeftPartTaxaList = new List <Taxa>();
_RightPartTaxaList = new List <Taxa>();
int medianposition = TaxaList.Count / 2 - 1;
for (int i = 0; i <= medianposition; i++)
{
_LeftPartTaxaList.Add(TaxaList[i]);
}
for (int i = medianposition + 1; i < TaxaList.Count; i++)
{
_RightPartTaxaList.Add(TaxaList[i]);
}
_LeftPartTaxaList.Add(TaxaDummy);
_RightPartTaxaList.Add(TaxaDummy);
generateDepthOneTreeRandomly(_LeftPartTaxaList, DummyTaxaCharacter, Level + 1, _VALID_TAXA_LIST, inputQuatrets);
generateDepthOneTreeRandomly(_RightPartTaxaList, DummyTaxaCharacter, Level + 1, _VALID_TAXA_LIST, inputQuatrets);
}
else
{
PartionPair = new FinalPartionPair();
PartionPair._Root = TaxaList;
PartionPair._Q = GetQuatretWithRandomDividedTaxa(TaxaList, inputQuatrets);
PartionPair._InputQuatret = inputQuatrets;
_ListFinalPartionPairRandom.Add(PartionPair);
}
}
public void Divide(PartitionSet pPartitionSet, string DummyTaxaCharacter, int Level, List <string> _VALID_TAXA_LIST)
{
string DummyTaxa = DummyTaxaCharacter + Level.ToString();
Taxa TaxaDummy = new Taxa();
TaxaDummy._Taxa_Value = DummyTaxa;
//Adding Dummy Taxa to the Set PA and PB
FinalPartionPair PartionPair;
List <FinalPartionPair> ListPartionPair = new List <FinalPartionPair>();
foreach (Partition p in pPartitionSet.PartitionList)
{
PartionPair = new FinalPartionPair();
p.TaxaList.Add(TaxaDummy);
PartionPair = SubDivideQuatret(pPartitionSet._ListQuatrets, p, DummyTaxa);
PartionPair._Root = p.TaxaList;
ListPartionPair.Add(PartionPair);
}
foreach (FinalPartionPair pair in ListPartionPair)
{
if (CountValidTaxa(pair._P.TaxaList, _VALID_TAXA_LIST) >= 1 && (pair._Q == null))
{
_ListFinalPartionPair.Add(pair);
}
else if (CountValidTaxa(pair._P.TaxaList, _VALID_TAXA_LIST) >= 3 && (pair._Q != null))
{
InputProcessing input = new InputProcessing(pair._Q, pair._P.TaxaList);
Bipartition bpA = new Bipartition(input);
GainTable GTable = bpA.getFinalGainTable();
Divide(GTable.PartitionSet, DummyTaxaCharacter, Level + 1, _VALID_TAXA_LIST);
}
else if (CountValidTaxa(pair._P.TaxaList, _VALID_TAXA_LIST) < 3 && (pair._Q != null))
{
_ListFinalPartionPair.Add(pair);
}
}
}
public FinalPartionPair SubDivideQuatret(List <Quartet> inputQuatretList, Partition p, string DummyTaxa)
{
List <Quartet> Q = new List <Quartet>();
List <Quartet> QA = new List <Quartet>();
FinalPartionPair PartionPair = new FinalPartionPair();
PartionPair._P = p;
var vDiffered = inputQuatretList.FindAll(x => x._PartitionStatus == PartitionStatus.Differed);
var vIsolated = inputQuatretList.FindAll(x => x._PartitionStatus == PartitionStatus.Isolated);
if (vIsolated != null)
{
if (vIsolated.Count != 0)
{
Q = vIsolated.ToList();
}
}
if (vDiffered != null)
{
if (vDiffered.Count != 0)
{
foreach (Quartet q in vDiffered.ToList())
{
Q.Add(q);
}
}
}
if (Q.Count() != 0)
{
QA = GetQuatretWithDummy(p, Q, DummyTaxa);
PartionPair._Q = QA;
PartionPair._InputQuatret = Q;
}
return(PartionPair);
}
public void generateDepthOneTreeRandomly(List <Taxa> TaxaList, string DummyTaxaCharacter, int Level, List <string> _VALID_TAXA_LIST, List <Quartet> inputQuatrets)
{
string DummyTaxa = DummyTaxaCharacter + Level.ToString();
Taxa TaxaDummy = new Taxa();
TaxaDummy._Taxa_Value = DummyTaxa;
FinalPartionPair PartionPair = new FinalPartionPair();
List <Taxa> _LeftPartTaxaList;
List <Taxa> _RightPartTaxaList;
RandomTaxaListForCalculation = new List <Taxa>(TaxaList);
RandomTaxaListForGeneration = new List <Taxa>();
if (CountValidTaxa(TaxaList, _VALID_TAXA_LIST) > 2)
{
_LeftPartTaxaList = new List <Taxa>();
_RightPartTaxaList = new List <Taxa>();
//
Random rnd = new Random();
int count = 0;
int isLeft = 0;
for (int i = 0; i < TaxaList.Count; i++)
{
getRandomTaxaFromListNew();
}
for (int i = 0; i < RandomTaxaListForGeneration.Count; i++)
{
if (count == 0)
{
int r = rnd.Next(0, TaxaList.Count - 1);
if (r % 2 == 0)
{
_LeftPartTaxaList.Add(RandomTaxaListForGeneration[i]);
isLeft = 0;
}
else
{
_RightPartTaxaList.Add(RandomTaxaListForGeneration[i]);
isLeft = 1;
}
count++;
}
else
{
if (isLeft == 1)
{
_LeftPartTaxaList.Add(RandomTaxaListForGeneration[i]);
isLeft = 0;
}
else
{
_RightPartTaxaList.Add(RandomTaxaListForGeneration[i]);
isLeft = 1;
}
}
}
//RandomTaxaListForGeneration = new List<Taxa>();
//RandomTaxaListForCalculation = new List<Taxa>();
//
_LeftPartTaxaList.Add(TaxaDummy);
_RightPartTaxaList.Add(TaxaDummy);
generateDepthOneTreeRandomly(_LeftPartTaxaList, DummyTaxaCharacter, Level + 1, _VALID_TAXA_LIST, inputQuatrets);
generateDepthOneTreeRandomly(_RightPartTaxaList, DummyTaxaCharacter, Level + 1, _VALID_TAXA_LIST, inputQuatrets);
}
else
{
//RandomTaxaListForGeneration = new List<Taxa>();
//RandomTaxaListForCalculation = new List<Taxa>();
PartionPair = new FinalPartionPair();
PartionPair._Root = TaxaList;
PartionPair._Q = GetQuatretWithRandomDividedTaxa(TaxaList, inputQuatrets);
PartionPair._InputQuatret = inputQuatrets;
_ListFinalPartionPairRandom.Add(PartionPair);
}
}
public void generateDepthOneTreeRandomlyChanged(List <Taxa> TaxaList, string DummyTaxaCharacter, int Level, List <string> _VALID_TAXA_LIST, List <Quartet> inputQuatrets)
{
string DummyTaxa = DummyTaxaCharacter + Level.ToString();
Taxa TaxaDummy = new Taxa();
TaxaDummy._Taxa_Value = DummyTaxa;
FinalPartionPair PartionPair = new FinalPartionPair();
List <Taxa> _LeftPartTaxaList;
List <Taxa> _RightPartTaxaList;
if (TaxaList.Count >= 4 && CountValidTaxa(TaxaList, _VALID_TAXA_LIST) > 0)
{
_LeftPartTaxaList = new List <Taxa>();
_RightPartTaxaList = new List <Taxa>();
this.RandomTaxaListForGeneration = new List <Taxa>(TaxaList);
int randomValue = 0;
Taxa txRandom;
Random rnd = new Random();
int CountRand = 0;
foreach (Taxa ttt in TaxaList)
{
//randomValue = rnd.Next();
if (CountRand == 0)
{
randomValue = rnd.Next();
}
else
{
randomValue = CountRand;
}
if (randomValue % 2 == 0)
{
txRandom = getRandomTaxaFromList(this.RandomTaxaListForGeneration);
_LeftPartTaxaList.Add(txRandom);
this.RandomTaxaListForGeneration.Remove(txRandom);
}
else
{
txRandom = getRandomTaxaFromList(this.RandomTaxaListForGeneration);
_RightPartTaxaList.Add(txRandom);
this.RandomTaxaListForGeneration.Remove(txRandom);
}
randomValue++;
CountRand++;
}
this.RandomTaxaListForGeneration = new List <Taxa>();
_LeftPartTaxaList.Add(TaxaDummy);
generateDepthOneTreeRandomly(_LeftPartTaxaList, DummyTaxaCharacter, Level + 1, _VALID_TAXA_LIST, inputQuatrets);
_RightPartTaxaList.Add(TaxaDummy);
generateDepthOneTreeRandomly(_RightPartTaxaList, DummyTaxaCharacter, Level + 1, _VALID_TAXA_LIST, inputQuatrets);
}
else
{
PartionPair = new FinalPartionPair();
PartionPair._Root = TaxaList;
PartionPair._Q = GetQuatretWithRandomDividedTaxa(TaxaList, inputQuatrets);
PartionPair._InputQuatret = inputQuatrets;
_ListFinalPartionPairRandom.Add(PartionPair);
}
}
