public bool CheckDuplication(GroupShare groupA, GroupShare groupB) //true for duplicated region.
{
if (groupA.individualList.Count != groupB.individualList.Count)
{
return(false);
}
for (int i = 0; i < groupA.individualList.Count; i++)
{
if (groupA.individualList[i] != groupB.individualList[i])
{
return(false);
}
}
if ((groupA.allSharedFirstBlockID >= groupB.allSharedFirstBlockID && groupA.allSharedFirstBlockID <= groupB.allSharedLastBlockID) || (groupA.allSharedLastBlockID >= groupB.allSharedFirstBlockID && groupA.allSharedLastBlockID <= groupB.allSharedLastBlockID))
//check the region is overlaped or not
{
return(true);
}
else
{
return(false);
}
}
public bool ChekcSubGroup(GroupShare subGroup)
{
//this.SetIndividualList();
//subGroup.SetIndividualList();
this.individualList.Sort();
subGroup.individualList.Sort();
if (this.individualList.Count < subGroup.individualList.Count)
{
return(false);
}
int thisIndex = 0;
for (int subIndex = 0; subIndex < subGroup.individualList.Count; subIndex++)
{
while (thisIndex < this.individualList.Count)
{
if ((int)(this.individualList[thisIndex]) < (int)(subGroup.individualList[subIndex]))
{
thisIndex++;
}
else if ((int)(this.individualList[thisIndex]) == (int)(subGroup.individualList[subIndex]))
{
thisIndex++;
break;
}
else
{
return(false);
}
if (thisIndex == individualList.Count)
{
return(false);
}
}
}
return(true);
}
public bool GroupShareExtention(ArrayList[] IBDTable, ArrayList newIndividualList, BlockDictionary newBlockDictionary, ArrayList newlyComingSharingList, List <GroupShare> finalResultList, ArrayList newlyAddedList)
{
if (this.allSharedLastBlockID >= IBDTable.GetUpperBound(0)) //the end of the block list, add to result if still some sharing left
{
if (this.individualList.Count > 1 && (this.allSharedLastBlockID - this.allSharedFirstBlockID >= 2)) //add to result list
{
finalResultList.Add((GroupShare)this.MemberwiseClone());
}
}
bool foundNext = false; //if find haplotype that can continue all the individuals in the next block, then "this" will not be added to list
ArrayList passList = new ArrayList();
ArrayList waitingToAddGroupList = new ArrayList();
for (int haplotypeIndex = 0; haplotypeIndex < newlyComingSharingList.Count; haplotypeIndex++)
{
bool foundBefore = false;
ArrayList pairListIntersection;
pairListIntersection = this.GetPairListIntersection(this.sharePairList, ((GroupShare)(newlyComingSharingList[haplotypeIndex])).sharePairList);
if (pairListIntersection.Count == this.sharePairList.Count)
{
foundNext = true;
this.allSharedLastBlockID += 1;
this.haplotypeList.Add(((GroupShare)(newlyComingSharingList[haplotypeIndex])).haplotypeList[0]);
if (pairListIntersection.Count == ((GroupShare)(newlyComingSharingList[haplotypeIndex])).sharePairList.Count)
{
newlyComingSharingList.RemoveAt(haplotypeIndex);
haplotypeIndex--;
}
return(true);
}
foreach (ArrayList eachList in passList) //check this intersection has already go checking next block, so do not need to do again for this subgroup.
{
if (eachList.Count != pairListIntersection.Count)
{
continue;
}
else
{
for (int i = 0; i < pairListIntersection.Count; i++)
{
if (((int[])pairListIntersection[i])[0] != ((int[])(eachList[i]))[0] || ((int[])pairListIntersection[i])[1] != ((int[])(eachList[i]))[1])
{
break;
}
if (i == (pairListIntersection.Count - 1) && ((int[])pairListIntersection[i])[0] == ((int[])(eachList[i]))[0] && ((int[])pairListIntersection[i])[1] == ((int[])(eachList[i]))[1])
{
foundBefore = true;
}
}
}
}
if (foundBefore == true) //checked before, do not need to go checking
{
break;
}
if (pairListIntersection.Count > 1)
{
passList.Add(pairListIntersection.Clone());
GroupShare newGroupShare = new GroupShare();
newGroupShare.sharePairList = (ArrayList)pairListIntersection.Clone();
newGroupShare.allSharedLastBlockID = this.allSharedLastBlockID + 1;
newGroupShare.allSharedFirstBlockID = this.allSharedFirstBlockID;
newGroupShare.haplotypeList = (ArrayList)this.haplotypeList.Clone();
newGroupShare.haplotypeList.Add(((GroupShare)(newlyComingSharingList[haplotypeIndex])).haplotypeList[0]);
newGroupShare.SetIndividualList();
if (newGroupShare.CheckRecombinationRegion(newIndividualList, newBlockDictionary)) // need to check the recombination region first.
{
waitingToAddGroupList.Add(newGroupShare);
}
}
if (foundNext == false && (this.allSharedLastBlockID - this.allSharedFirstBlockID >= 2))
{
finalResultList.Add((GroupShare)(this.MemberwiseClone()));
}
}
MyPrivateResultComparer newPrivateResultComparer = new MyPrivateResultComparer();
waitingToAddGroupList.Sort(newPrivateResultComparer);
for (int i = 0; i < waitingToAddGroupList.Count - 1; i++)
{
for (int j = i + 1; j < waitingToAddGroupList.Count; j++)
{
if (((GroupShare)(waitingToAddGroupList[i])).ChekcSubGroup(((GroupShare)(waitingToAddGroupList[j]))) == true)
{
waitingToAddGroupList.RemoveAt(j);
j--;
}
}
}
foreach (GroupShare newGroupShare in waitingToAddGroupList)
{
if (newlyAddedList.Count == 0)
{
newlyAddedList.Add(newGroupShare);
}
else
{
for (int i = 0; i < newlyAddedList.Count; i++)
{
if (((GroupShare)(newlyAddedList[i])).ChekcSubGroup(newGroupShare) == true)
{
break;
}
if (newGroupShare.ChekcSubGroup((GroupShare)(newlyAddedList[i])) == true)
{
newlyAddedList[i] = newGroupShare;
break;
}
if (i == newlyAddedList.Count - 1)
{
newlyAddedList.Add(newGroupShare);
}
}
}
}
return(false);
}
public void findGroupIBD(ArrayList newIndividualList, BlockDictionary newBlockDictionary, double[,] linkageData, List <GroupShare> result, List <GroupShare> resultList, int windowStart, int windowEnd)
{
ArrayList[] IBDTable = new ArrayList[newBlockDictionary.blockList.Count];
for (int regionIndex = 0; regionIndex < pairwiseRegionList.Count; regionIndex++)//(PairwiseIBDRegion newRegion in this.pairwiseRegionList)
{
PairwiseIBDRegion newRegion = (PairwiseIBDRegion)(pairwiseRegionList[regionIndex]);
for (int blockID = newRegion.GetFirstBlockID(); blockID <= newRegion.GetLastBlockID(); blockID++)
{
foreach (int haplotypeID in newRegion.GetHaplotype(blockID - newRegion.GetFirstBlockID()))
{
if (IBDTable[blockID] == null)
{
int[] newPair = new int[2];
newPair[0] = newRegion.GetFirstIndividual();
newPair[1] = newRegion.GetSecondIndividual();
HaplotypeSharing newHaplotypeShare = new HaplotypeSharing(haplotypeID, newPair);
IBDTable[blockID] = new ArrayList();
IBDTable[blockID].Add(newHaplotypeShare);
}
else
{
bool added = false;
for (int newHaplotypeShare = 0; newHaplotypeShare < IBDTable[blockID].Count; newHaplotypeShare++)
{
if (((HaplotypeSharing)IBDTable[blockID][newHaplotypeShare]).haplotpeID == haplotypeID)
{
int[] newPair = new int[2];
newPair[0] = newRegion.GetFirstIndividual();
newPair[1] = newRegion.GetSecondIndividual();
((HaplotypeSharing)IBDTable[blockID][newHaplotypeShare]).individualList.Add(newPair);
added = true;
}
}
if (!added)
{
int[] newPair = new int[2];
newPair[0] = newRegion.GetFirstIndividual();
newPair[1] = newRegion.GetSecondIndividual();
HaplotypeSharing newHaplotypeShare = new HaplotypeSharing(haplotypeID, newPair);
IBDTable[blockID].Add(newHaplotypeShare);
}
}
}
}
pairwiseRegionList[regionIndex] = null;
}
pairwiseRegionList = null;
GC.Collect();
MyResultComparer newResultComparer = new MyResultComparer();
if (IBDTable[IBDTable.GetUpperBound(0)] == null)
{
IBDTable[IBDTable.GetUpperBound(0)] = new ArrayList();
}
for (int blockIndex = windowStart; blockIndex < windowEnd; blockIndex++)
{
ArrayList newlyComingSharingList = new ArrayList();
if (IBDTable[blockIndex] == null)
{
foreach (GroupShare newGroupShare in resultList)
{
result.Add(newGroupShare);
}
resultList = new List <GroupShare>();
IBDTable[blockIndex] = new ArrayList();
continue;
}
foreach (HaplotypeSharing newHaplotypeSharing in IBDTable[blockIndex])
{
if (newHaplotypeSharing.individualList.Count > 2 && newHaplotypeSharing.individualList.Count < 0.2 * newIndividualList.Count) //at least 2 pairs sharing this haplotype.
{
GroupShare newGroupShare = new GroupShare();
newGroupShare.sharePairList = (ArrayList)newHaplotypeSharing.individualList.Clone();
newGroupShare.allSharedFirstBlockID = blockIndex;
newGroupShare.allSharedLastBlockID = blockIndex;
newGroupShare.haplotypeList = new ArrayList();
newGroupShare.haplotypeList.Add(newHaplotypeSharing.haplotpeID);
newGroupShare.SetIndividualList();
newlyComingSharingList.Add(newGroupShare);
}
}
ArrayList newlyAddedList = new ArrayList();
//for the next block, if no haplotype contains more than 1 pair, stop the extension and record all the region waiting to be extended.
if (newlyComingSharingList.Count == 0)
{
foreach (GroupShare newGroup in resultList)
{
result.Add(newGroup);
}
}
for (int i = 0; i < resultList.Count; i++)
{
GroupShare newGroupshare1 = (GroupShare)(resultList[i]);
if (newGroupshare1.GroupShareExtention(IBDTable, newIndividualList, newBlockDictionary, newlyComingSharingList, result, newlyAddedList) == false)
{
resultList.RemoveAt(i);
i--;
}
}
foreach (GroupShare newGroupShare in newlyAddedList)
{
bool found = false;
foreach (GroupShare checkingGroup in resultList)
{
if (checkingGroup.ChekcSubGroup(newGroupShare) == true)
{
found = true;
break;
}
}
if (found == false)
{
resultList.Add(newGroupShare);
}
}
foreach (GroupShare newGroupShare in newlyComingSharingList)
{
bool found = false;
foreach (GroupShare checkingGroup in resultList)
{
if (checkingGroup.ChekcSubGroup(newGroupShare) == true)
{
found = true;
break;
}
}
if (found == false)
{
resultList.Add(newGroupShare);
}
}
resultList.Sort(newResultComparer);
}
foreach (GroupShare newShare in result)
{
newShare.SetIndividualList();
}
result.Sort(newResultComparer);
for (int i = 0; i < result.Count - 1; i++)
{
if (((GroupShare)(result[i])).CheckContain((GroupShare)(result[i + 1])) == true)
{
result.RemoveAt(i + 1);
i--;
}
else if (((GroupShare)(result[i + 1])).CheckContain(((GroupShare)(result[i]))) == true)
{
result.RemoveAt(i);
i--;
}
}
for (int i = 0; i < result.Count - 1; i++)
{
if (((GroupShare)(result[i])).CheckOverlap((GroupShare)(result[i + 1])))
{
result.RemoveAt(i + 1);
i--;
}
}
foreach (GroupShare newShare in result)
{
newShare.SetIndividualList();
}
for (int i = 0; i < result.Count; i++)
{
((GroupShare)(result[i])).SetPartiallySharedRegion(IBDTable, newBlockDictionary, newIndividualList, windowStart, windowEnd);
Console.SetCursorPosition(16, Console.CursorTop);
Console.Write("{0} / {1}", i + 1, result.Count);
}
for (int i = 0; i < result.Count; i++)
{
((GroupShare)(result[i])).SetAllSharedSnpHaplotype(newIndividualList, newBlockDictionary);
}
for (int i = 0; i < result.Count; i++)
{
((GroupShare)(result[i])).SetPartiallySharedSnpHaplotype(newIndividualList, newBlockDictionary);
}
for (int i = 0; i < result.Count; i++)
{
((GroupShare)(result[i])).SetAValue(newBlockDictionary, newIndividualList, linkageData);
}
Console.WriteLine("\t\t\t\t\tFinished.");
result.Sort(newResultComparer);
for (int i = 0; i < result.Count - 1; i++)
{
if (((GroupShare)(result[i])).CheckContain((GroupShare)(result[i + 1])))
{
result.RemoveAt(i + 1);
i--;
}
}
for (int i = 0; i < result.Count - 1; i++)
{
if (((GroupShare)(result[i])).CheckOverlap((GroupShare)(result[i + 1])))
{
result.RemoveAt(i + 1);
i--;
}
}
}
