public void Extend(SnpDataSet dataSet)
{
int newStart = this.GetStart();
int newEnd = this.GetEnd();
ArrayList newEndingSequence = new ArrayList();
while (newEnd < dataSet.GetSnpCount() - 1)
{
int data = -1;
bool flag = false;
for (int i = 1; i < this.group.Length; i++)
{
if (data == -1)
{
if (dataSet.GetSnp(this.group[i], newEnd + 1) != 1)
{
data = dataSet.GetSnp(this.group[i], newEnd + 1);
}
}
else if (Math.Abs(dataSet.GetSnp(this.group[i], newEnd + 1) - data) == 2)
{
flag = true;
break;
}
}
if (flag)
{
break;
}
if (data == -1)
{
newEndingSequence.Add(1);
}
else if (data == 0)
{
newEndingSequence.Add(0);
}
else
{
newEndingSequence.Add(2);
}
newEnd++;
}
ArrayList newStartingSequence = new ArrayList();
while (newStart > 0)
{
int data = -1;
bool flag = false;
for (int i = 1; i < this.GetGroup().Length; i++)
{
if (data == -1)
{
if (dataSet.GetSnp(this.group[i], newStart - 1) != 1)
{
data = dataSet.GetSnp(this.group[i], newStart - 1);
}
}
else if (Math.Abs(dataSet.GetSnp(this.group[i], newStart - 1) - data) == 2)
{
flag = true;
break;
}
}
if (flag)
{
break;
}
if (data == -1)
{
newStartingSequence.Add(1);
}
else if (data == 0)
{
newStartingSequence.Add(0);
}
else
{
newStartingSequence.Add(2);
}
newStart--;
}
newStartingSequence.Reverse();
int[] newWholeSequence = new int[this.sequence.Length + newStartingSequence.Count + newEndingSequence.Count];
newStartingSequence.CopyTo(newWholeSequence);
this.GetSequence().CopyTo(newWholeSequence, newStartingSequence.Count);
newEndingSequence.CopyTo(newWholeSequence, newStartingSequence.Count + this.sequence.Length);
this.SetSequence(newWholeSequence);
this.SetStart(newStart);
this.SetEnd(newEnd);
if (this.GetEnd() - this.GetEnd() > 170)
{
;
}
while (newEnd < dataSet.GetSnpCount())
{
ArrayList group0 = new ArrayList();
ArrayList group1 = new ArrayList();
ArrayList group2 = new ArrayList();
for (int i = 0; i < this.GetGroup().Length; i++)
{
if (this.GetGroup(i) == 0)
{
group0.Add(this.GetGroup(i));
}
else if (this.GetGroup(i) == 2)
{
group2.Add(this.GetGroup(i));
}
else
{
group1.Add(this.GetGroup(i));
}
}
}
}
public void inWindowExtend(ArrayList group, int snpPosition, SnpDataSet dataSet, ArrayList shareWindowListRef)
{
if (snpPosition == this.end) //when it reached the end of the window
{
ShareWindow newShareWindow = new ShareWindow(); //construct a shareWindow object
newShareWindow.windowStart = this;
newShareWindow.windowLast = this;
newShareWindow.group = group;
group.Sort();
shareWindowListRef.Add(newShareWindow); // Add newShareWindow to shareWindow List;
return;
}
ArrayList group0 = new ArrayList(); //store the individuals that the data of this snp is 0
ArrayList group1 = new ArrayList(); //store the individuals that the data of this snp is 1
ArrayList group2 = new ArrayList(); //store the individuals that the data of this snp is 2
foreach (int individual in group)
{
if (dataSet.GetSnp(individual, snpPosition) == 0) // the data is 0
{
group0.Add(individual);
}
else if (dataSet.GetSnp(individual, snpPosition) == 1) //the data is 1
{
group1.Add(individual);
}
else //the data is 2
{
group2.Add(individual);
}
}
if (group2.Count + group1.Count >= 3) // construct a new group if group2+group1>=3
{
ArrayList group12 = new ArrayList();
foreach (int ind in group2) //add group2 and group1 into group21
{
group12.Add(ind);
}
foreach (int ind in group1)
{
group12.Add(ind);
}
//group12.ToArray();
inWindowExtend(group12, snpPosition + 1, dataSet, shareWindowListRef); //use group21 to do the next Extend
}
if (group0.Count + group1.Count >= 3) // construct a new group if group0+group1>=3, similar to last.
{
ArrayList group01 = new ArrayList();
foreach (int ind in group0)
{
group01.Add(ind);
}
foreach (int ind in group1)
{
group01.Add(ind);
}
//group01.ToArray();
inWindowExtend(group01, snpPosition + 1, dataSet, shareWindowListRef); //do the next Extend
}
}
private bool CheckCommon(SnpDataSet dataSet) //check snp data between rare blocks
{
int[] error = new int[this.group.Length]; //error data.
this.sequence = new int[this.end - this.start + 1];
for (int e = 0; e < error.Length; e++) // all is 0 at the begining.
{
error[e] = 0;
}
for (int i = start; i < end; i++) //loop from start to end for snp
{
int count0 = 0; //count how many 0
int count2 = 0; //count how many 2
int[] dataTmp = new int[this.group.Length]; //store the data, avoid multi data accessing
//for (int d = 0; d < dataTmp.Length; d++) //
// d = 0;
int j = 0;
foreach (int ind in this.group) // for each guy in group ,check this snp data
{
int data = dataSet.GetSnp(ind, i);
if (data == 2)
{
count2++;
}
else if (data == 0)
{
count0++;
}
dataTmp[j] = data; //store the data.
j++;
}
if (count2 <= count0) //two minor allele is the outlier in the group
{
for (int m = 0; m < this.group.Length; m++)
{
if (dataTmp[m] == 2)
{
error[m]++;
}
}
sequence[i - start] = 0;
}
else //two major allele is the outlier in the group
{
for (int m = 0; m < this.group.Length; m++)
{
if (dataTmp[m] == 0)
{
error[m]++;
}
}
sequence[i - start] = 2;
}
if (count2 == 0 && count0 == 0)
{
sequence[i - start] = 1;
}
}
ArrayList newGroup = new ArrayList();
for (int n = 0; n < this.group.Length; n++)
{
if (!(error[n] > 0)) //no error or little error, keep this guy.
{
newGroup.Add(this.group[n]);
}
}
if (newGroup.Count < 3)
{
return(false);
}
else
{
this.group = (int[])newGroup.ToArray(typeof(int));
return(true);
}
}