public List <MappedMirnaGroup> ReadFromFile(string fileName)
{
List <MappedMirnaGroup> result = new List <MappedMirnaGroup>();
XElement root = XElement.Load(fileName);
var qmmap = root.ToSAMAlignedItems().ToSAMAlignedLocationMap();
foreach (var mirnaGroupEle in root.Element("mirnas").Elements("mirnagroup"))
{
var group = new MappedMirnaGroup();
result.Add(group);
foreach (var mirnaEle in mirnaGroupEle.Elements("mirna"))
{
var mirna = new MappedMirna();
group.Add(mirna);
mirna.Name = mirnaEle.Attribute("name").Value;
mirna.Sequence = mirnaEle.Attribute("sequence").Value;
foreach (var regionEle in mirnaEle.Elements("region"))
{
var region = new MappedMirnaRegion();
mirna.MappedRegions.Add(region);
region.Region.Name = mirna.Name;
ParseLocation(regionEle, region.Region);
foreach (var posEle in regionEle.Elements("position"))
{
var position = new SequenceRegionMapped();
position.Region = region.Region;
position.Offset = int.Parse(posEle.Attribute("offset").Value);
region.Mapped[position.Offset] = position;
foreach (var queryEle in posEle.Elements("query"))
{
var qname = queryEle.Attribute("qname").Value;
var loc = queryEle.Attribute("loc").Value;
var key = GenerateKey(qname, loc);
var query = qmmap[key];
position.AlignedLocations.Add(query);
query.Features.Add(region.Region);
}
}
}
}
}
qmmap.Clear();
return(result);
}
public MappedMirnaRegion FindOrCreateRegion(string loc)
{
foreach (var region in MappedRegions)
{
if (region.Region.GetLocation().Equals(loc))
{
return region;
}
}
var result = new MappedMirnaRegion();
result.Region = SequenceRegionUtils.ParseLocation<SequenceRegion>(loc);
this.MappedRegions.Add(result);
return result;
}
public MappedMirnaRegion FindOrCreateRegion(string loc)
{
foreach (var region in MappedRegions)
{
if (region.Region.GetLocation().Equals(loc))
{
return(region);
}
}
var result = new MappedMirnaRegion();
result.Region = SequenceRegionUtils.ParseLocation <SequenceRegion>(loc);
this.MappedRegions.Add(result);
return(result);
}
private void FindLocation(List<SAMAlignedLocation> list, List<MappedMirnaRegion> list_2, out SAMAlignedLocation loc, out MappedMirnaRegion reg)
{
throw new NotImplementedException();
}
private void FindLocation(List <SAMAlignedLocation> list, List <MappedMirnaRegion> list_2, out SAMAlignedLocation loc, out MappedMirnaRegion reg)
{
throw new NotImplementedException();
}
