public void Combine(ArrayList shareWindowList, ArrayList combinedShareWindowList) //combine a sharewindow with next window(id+1)
{
foreach (ShareWindow shareWindowItem in shareWindowList)
{
if (shareWindowItem.windowStart.id == this.windowLast.id + 1)
{
//Console.Write("{0}\t{1}\t{2}\r\n", shareWindowItem.windowStart.id,this.group.Count,shareWindowItem.group.Count);
//Console.ReadKey();
ArrayList newGroup = new ArrayList();
foreach (int individualA in this.group) //find the share individuals between two groups
{
foreach (int individualB in shareWindowItem.group)
{
if (individualA == individualB)
{
newGroup.Add(individualA);
}
}
}
if (newGroup.Count >= 5) //gourp size should be >=3 for combined window
{
ShareWindow newShareWindow = new ShareWindow();
newShareWindow.group = newGroup;
newShareWindow.windowStart = this.windowStart;
newShareWindow.windowLast = shareWindowItem.windowLast;
newShareWindow.Combine(shareWindowList, combinedShareWindowList);
if ((this.group.Count - newGroup.Count > 1) && (newShareWindow.windowLast.id - newShareWindow.windowStart.id) > 3)
{
combinedShareWindowList.Add(newShareWindow);
Console.Write("{0}\t{1}\t{2}\r\n", newShareWindow.group.Count, newShareWindow.windowStart.id, newShareWindow.windowLast.id);
}
}
else
{
if (this.windowLast.id - this.windowStart.id > 0)
{
combinedShareWindowList.Add(this);
}
}
}
else if (shareWindowItem.windowStart.id - this.windowLast.id > 3)
{
break;
}
}
}
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
}
}