public List <FeatureItemGroup> ReadFromFile(string fileName)
{
Console.WriteLine("read file {0} ...", fileName);
var result = new List <FeatureItemGroup>();
XElement root = XElement.Load(fileName);
//Console.WriteLine("read locations ...");
Dictionary <string, SAMAlignedLocation> qmmap = root.ToSAMAlignedItems().ToSAMAlignedLocationMap();
//Console.WriteLine("read mapped items ...");
foreach (XElement groupEle in root.Element("subjectResult").Elements("subjectGroup"))
{
var group = new FeatureItemGroup();
result.Add(group);
foreach (XElement featureEle in groupEle.Elements("subject"))
{
var item = new FeatureItem();
group.Add(item);
item.Name = featureEle.Attribute("name").Value;
foreach (XElement locEle in featureEle.Elements("region"))
{
var fl = new FeatureLocation();
item.Locations.Add(fl);
fl.Name = item.Name;
fl.ParseLocation(locEle);
if (locEle.Attribute("sequence") != null)
{
fl.Sequence = locEle.Attribute("sequence").Value;
}
if (locEle.Attribute("query_count_before_filter") != null)
{
fl.QueryCountBeforeFilter = int.Parse(locEle.Attribute("query_count_before_filter").Value);
}
if (locEle.Attribute("pvalue") != null)
{
fl.PValue = double.Parse(locEle.Attribute("pvalue").Value);
}
foreach (XElement queryEle in locEle.Elements("query"))
{
string qname = queryEle.Attribute("qname").Value;
string loc = queryEle.Attribute("loc").Value;
string key = SAMAlignedLocation.GetKey(qname, loc);
SAMAlignedLocation query = qmmap[key];
FeatureSamLocation fsl = new FeatureSamLocation(fl);
fsl.SamLocation = query;
var attr = queryEle.FindAttribute("overlap");
if (attr == null)
{
fsl.OverlapPercentage = query.OverlapPercentage(fl);
}
else
{
fsl.OverlapPercentage = double.Parse(attr.Value);
}
var nnpm = queryEle.FindAttribute("nnpm");
if (nnpm == null)
{
nnpm = queryEle.FindAttribute("nnmp");
}
if (nnpm != null)
{
fsl.NumberOfNoPenaltyMutation = int.Parse(nnpm.Value);
}
var nmi = queryEle.FindAttribute("nmi");
if (nmi != null)
{
fsl.NumberOfMismatch = int.Parse(nmi.Value);
}
}
}
}
}
qmmap.Clear();
return(result);
}
