public bool CkeckSubGroup(RareBlock rareBlockToCheck)
{
if (this.GetStart() != rareBlockToCheck.GetStart() || this.GetEnd() != rareBlockToCheck.GetEnd() || this.GetGroup().Length <= rareBlockToCheck.GetGroup().Length)
{
return(false);
}
int i = 0;
int j = 0;
while (j < rareBlockToCheck.GetGroup().Length)
{
if (this.GetGroup(i) == rareBlockToCheck.GetGroup(j))
{
i++;
j++;
}
else if (this.GetGroup(i) < rareBlockToCheck.GetGroup(j))
{
i++;
}
else
{
return(false);
}
if (i == this.GetGroup().Length&& j != rareBlockToCheck.GetGroup().Length)
{
return(false);
}
}
return(true);
}
public bool CheckContain(RareBlock rareBlockToCheck) //check if RareBlockToCheck is in the region of "this" with same group.
{
if (this.GetGroup().Length != rareBlockToCheck.GetGroup().Length)
{
return(false);
}
if (this.GetEnd() > rareBlockToCheck.GetEnd())
{
return(false);
}
if (this.GetStart() < rareBlockToCheck.GetStart())
{
return(false);
}
for (int i = 0; i < this.GetGroup().Length; i++)
{
if (this.GetGroup(i) != rareBlockToCheck.GetGroup(i))
{
return(false);
}
}
return(true);
}
public bool CheckSame(RareBlock rareBlockToCheck) //check if two rare blocks are the same or not.
{
if (this.GetStart() != rareBlockToCheck.GetStart())
{
return(false);
}
if (this.GetEnd() != rareBlockToCheck.GetEnd())
{
return(false);
}
if (this.GetGroup().Length != rareBlockToCheck.GetGroup().Length)
{
return(false);
}
for (int i = 0; i < this.GetGroup().Length; i++)
{
if (this.GetGroup(i) != rareBlockToCheck.GetGroup(i))
{
return(false);
}
}
return(true);
}
public void Combine(int i, ArrayList rareBlockList, ArrayList combinedBlockList, SnpDataSet dataSet)
{
if (i == rareBlockList.Count - 1)
{
return; //reach the end of the rareBlockList.
}
ArrayList newGroup = new ArrayList();
ArrayList remainGroup = new ArrayList();
bool flag = true;
for (int j = i + 1; j < i + 50 && j < rareBlockList.Count; j++) // find combined block from this block to 100 blocks away.
{
RareBlock block = new RareBlock();
//Console.WriteLine("{0} {1}", i, j);
block = (RareBlock)((RareBlock)rareBlockList[j]).MemberwiseClone();
if (block.GetStart() < this.GetEnd())
{
continue;
}
int m = 0;
int n = 0;
newGroup.Clear();
remainGroup.Clear();
for (m = 0; m < this.GetGroup().Length; m++) //find the intersection of the two group of individuals.
{
if (n == block.GetGroup().Length)
{
remainGroup.Add(this.GetGroup(m));
break;
}
if (this.group[m] == block.GetGroup(n))
{
newGroup.Add(this.group[m]);
n++;
}
else if (this.group[m] > block.GetGroup(n))
{
n++;
m--;
}
else
{
remainGroup.Add(this.GetGroup(m));
}
}
if (newGroup.Count > 2) //more than 1 guys appare in the two rare blocks
{
//Console.Write("{0} {1} {2}\t", i, j, newGroup.Count);
//foreach (int ind in newGroup)
// Console.Write("{0} ",ind);
//Console.WriteLine();
//Console.ReadKey();
RareBlock newRareBlock = new RareBlock();
newRareBlock.SetStart(this.GetStart());
newRareBlock.SetEnd(block.GetEnd());
newRareBlock.SetGroup((int[])newGroup.ToArray(typeof(int)));
if (newRareBlock.CheckCommon(dataSet)) //check the snp data between the rare blocks
//if (true)
{
if (newRareBlock.GetGroup().Length == 3)
{
newRareBlock.Extend(dataSet);
if (newRareBlock.GetEnd() - newRareBlock.GetStart() > 170)
{
if (combinedBlockList.Count > 0)
{
RareBlock lastRareBlock = (RareBlock)((RareBlock)combinedBlockList[combinedBlockList.Count - 1]).MemberwiseClone();
if (!lastRareBlock.CheckSame(this))
{
if (this.CheckContain(lastRareBlock))
{
combinedBlockList[combinedBlockList.Count - 1] = this.GetCopy();
}
else
{
combinedBlockList.Add(this.GetCopy());
}
}
}
else
{
combinedBlockList.Add(this.GetCopy());
}
}
}
else
{
newRareBlock.Combine(j, rareBlockList, combinedBlockList, dataSet);//if pass, continue combining.
}
//break; //When we find another block to combine to this block ,stop searching for this block.
//Time saving a lot, can miss some, discuss later on.
if (this.group.Length - newRareBlock.group.Length == 0)
{
flag = false;
break;
}
//else if (newRareBlock.group.Length / (this.group.Length - newRareBlock.group.Length) >= 3) break;
}
/*
* if (this.group.Length - newRareBlock.group.Length >= 3)
* {
* RareBlock remainGroupBlock = new RareBlock();
* remainGroupBlock.start = this.start;
* remainGroupBlock.end = this.end;
* remainGroupBlock.sequence = this.sequence;
* remainGroupBlock.group = (int[])remainGroup.ToArray(typeof(int));
* remainGroupBlock.Combine(j, rareBlockList, combinedBlockList, dataSet);
* }
*/
}
}
if (flag && (this.GetEnd() - this.GetEnd()) > 70)
{
if (combinedBlockList.Count > 0)
{
RareBlock lastRareBlock = (RareBlock)combinedBlockList[combinedBlockList.Count - 1];
if (!lastRareBlock.CheckSame(this))
{
if (this.CheckContain(lastRareBlock))
{
combinedBlockList[combinedBlockList.Count - 1] = this.GetCopy();
}
else
{
combinedBlockList.Add(this.GetCopy());
}
}
}
else
{
combinedBlockList.Add(this.GetCopy());
}
}
}