public static void AddToList(List <OverlappedChipSeqItem> currResult, ChipSeqItem chipSeqItem)
{
var maxpercentage = 0.0;
OverlappedChipSeqItem maxcr = null;
foreach (var cr in currResult)
{
foreach (var item in cr)
{
var oc = item.GetOverlapPercentage(chipSeqItem);
if (oc > maxpercentage)
{
maxcr = cr;
maxpercentage = oc;
}
}
}
if (maxcr != null)
{
maxcr.Add(chipSeqItem);
}
else
{
maxcr = new OverlappedChipSeqItem();
maxcr.Add(chipSeqItem);
currResult.Add(maxcr);
}
}
public static Dictionary <string, List <OverlappedChipSeqItem> > ReadItems(List <string> sourceFiles)
{
if (sourceFiles.Count <= 2)
{
throw new ArgumentException("Input at least two data files first!");
}
var firstFile = ReadInGeneItem(sourceFiles[0]);
var curResult = OverlappedChipSeqItem.Build(firstFile);
for (int i = 1; i < sourceFiles.Count; i++)
{
var curFile = ReadInGeneItem(sourceFiles[i]);
foreach (var item in curFile)
{
if (!curResult.ContainsKey(item.GeneSymbol))
{
var oi = new OverlappedChipSeqItem();
oi.Add(item);
var oil = new List <OverlappedChipSeqItem>();
oil.Add(oi);
curResult[item.GeneSymbol] = oil;
continue;
}
var curGroup = curResult[item.GeneSymbol];
OverlappedChipSeqItem.AddToList(curGroup, item);
}
}
return(curResult);
}
public void AddItem(string key, ChipSeqItem item)
{
if (!_itemMap.ContainsKey(key))
{
_itemMap[key] = new OverlappedChipSeqItem();
}
_itemMap[key].Add(item);
}
public static OverlappedChipSeqComparisonItem Build(OverlappedChipSeqItem item, Dictionary <string, string> fileNameGroup)
{
var result = new OverlappedChipSeqComparisonItem();
foreach (var csi in item)
{
var key = fileNameGroup[csi.Filename];
result.AddItem(key, csi);
}
return(result);
}
public static Dictionary <string, List <OverlappedChipSeqItem> > Build(List <ChipSeqItem> items)
{
var result = new Dictionary <string, List <OverlappedChipSeqItem> >();
var grp = items.GroupBy(m => m.GeneSymbol);
foreach (var g in grp)
{
var currResult = new List <OverlappedChipSeqItem>();
var cs = g.OrderBy(m => m.Start).ToList();
var r = new OverlappedChipSeqItem();
r.Add(cs[0]);
currResult.Add(r);
for (int i = 1; i < cs.Count; i++)
{
AddToList(currResult, cs[i]);
}
result[g.Key] = currResult;
}
return(result);
}
