/// <summary>
/// Set coords based on gene symbol & current target map
/// </summary>
/// <param name="rr"></param>
void SetCoordinates(UnpivotedAssayResult rr)
{
UnpivotedAssayResult rr2;
int tci;
if (TargetMap == null || !TargetMap.Coords.ContainsKey(rr.GeneId))
{
return;
}
//if (rr.TargetSymbol != "CHRM5") rr = rr; // debug
List <TargetMapCoords> coordList = TargetMap.Coords[rr.GeneId];
for (tci = 0; tci < coordList.Count; tci++)
{
if (tci == 0)
{
rr2 = rr;
}
else
{
rr2 = rr.CloneUnpivotedAssayResult();
}
TargetMapCoords tmc = coordList[tci];
rr2.TargetMapX = tmc.X;
rr2.TargetMapY = -tmc.Y; // use negative value for y
if (tci > 0)
{
BufferedRows.Add(rr2); // add to buffer
}
}
}
/// <summary>
/// Get a map by name with coordinates
/// </summary>
/// <param name="name"></param>
/// <returns></returns>
public static TargetMap GetMapWithCoords(
string name)
{
if (TargetMapDict == null)
{
ReadTargetMapDict();
}
string key = name.ToUpper();
if (!TargetMapDict.ContainsKey(key))
{
throw new Exception("Target map doesn't exist: " + name);
}
TargetMap tm = TargetMapDict[key];
if (tm.Coords != null)
{
return(tm); // have coords?
}
tm.Coords = new Dictionary <int, List <TargetMapCoords> >();
StreamReader sr = new StreamReader(TargetMapDir + @"\" + tm.CoordsFile);
while (true)
{
string rec = sr.ReadLine();
try
{
if (rec == null)
{
break;
}
if (rec.Trim().StartsWith(";"))
{
continue;
}
if (rec.Trim() == "")
{
continue;
}
string[] sa = rec.Split('\t');
int targetId = int.Parse(sa[0]);
if (!tm.Coords.ContainsKey(targetId))
{
tm.Coords[targetId] = new List <TargetMapCoords>();
}
List <TargetMapCoords> tml = tm.Coords[targetId];
TargetMapCoords tmc = new TargetMapCoords();
tml.Add(tmc);
tmc.TargetId = targetId;
tmc.X = int.Parse(sa[1]);
tmc.Y = int.Parse(sa[2]);
if (sa.Length > 3 && !String.IsNullOrEmpty(sa[3]))
{
tmc.X2 = int.Parse(sa[3]);
}
if (sa.Length > 4 && !String.IsNullOrEmpty(sa[4]))
{
tmc.Y2 = int.Parse(sa[4]);
}
}
catch (Exception ex) { throw new Exception(ex.Message, ex); }
}
sr.Close();
return(tm);
}
