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);
}
public virtual List <FeatureItemGroup> ReadFromFile(string fileName)
{
var result = new List <FeatureItemGroup>();
using (XmlReader source = XmlReader.Create(fileName))
{
Progress.SetMessage("reading queries ...");
List <SAMAlignedItem> queries = SAMAlignedItemUtils.ReadFrom(source);
Progress.SetMessage("{0} queries read.", queries.Count);
var qmmap = queries.ToSAMAlignedLocationMap();
queries.Clear();
Progress.SetMessage("reading subjects ...");
string value;
source.ReadToFollowing("subjectResult");
if (source.ReadToDescendant("subjectGroup"))
{
do
{
var featureGroup = new FeatureItemGroup();
result.Add(featureGroup);
if (source.ReadToDescendant("subject"))
{
do
{
var item = new FeatureItem();
featureGroup.Add(item);
item.Name = source.GetAttribute("name");
if (source.ReadToDescendant("region"))
{
do
{
var fl = new FeatureLocation();
item.Locations.Add(fl);
fl.Name = item.Name;
fl.Seqname = source.GetAttribute("seqname");
fl.Start = long.Parse(source.GetAttribute("start"));
fl.End = long.Parse(source.GetAttribute("end"));
fl.Strand = source.GetAttribute("strand")[0];
fl.Sequence = source.GetAttribute("sequence");
value = source.GetAttribute("query_count_before_filter");
if (value != null)
{
fl.QueryCountBeforeFilter = int.Parse(value);
}
value = source.GetAttribute("pvalue");
if (value != null)
{
fl.PValue = double.Parse(value);
}
if (source.ReadToDescendant("query"))
{
do
{
string qname = source.GetAttribute("qname");
string loc = source.GetAttribute("loc");
string key = SAMAlignedLocation.GetKey(qname, loc);
SAMAlignedLocation query = qmmap[key];
FeatureSamLocation fsl = new FeatureSamLocation(fl);
fsl.SamLocation = query;
fsl.Offset = int.Parse(source.GetAttribute("offset"));
var attr = source.GetAttribute("overlap");
if (attr == null)
{
fsl.OverlapPercentage = query.OverlapPercentage(fl);
}
else
{
fsl.OverlapPercentage = double.Parse(attr);
}
var nmi = source.GetAttribute("nmi");
if (nmi != null)
{
fsl.NumberOfMismatch = int.Parse(nmi);
}
var nnpm = source.GetAttribute("nnpm");
if (nnpm != null)
{
fsl.NumberOfNoPenaltyMutation = int.Parse(nnpm);
}
} while (source.ReadToNextSibling("query"));
}
} while (source.ReadToNextSibling("region"));
}
} while (source.ReadToNextSibling("subject"));
}
} while (source.ReadToNextSibling("subjectGroup"));
}
qmmap.Clear();
}
Progress.SetMessage("{0} subjects read.", result.Count);
return(result);
}
public override bool AcceptLocus(SAMAlignedLocation loc)
{
var result = false;
if (!loc.Seqname.Equals(lastSeqname))
{
if (!featureMap.TryGetValue(loc.Seqname, out lastFeatures))
{
return false;
}
lastSeqname = loc.Seqname;
}
foreach (var feature in lastFeatures)
{
if (feature.End < loc.Start)
{
continue;
}
if (feature.Start > loc.End)
{
break;
}
if (feature.Overlap(loc, this.minOverlapPercentage))
{
result = true;
var samloc = new FeatureSamLocation(feature);
samloc.SamLocation = loc;
feature.SamLocations.Add(samloc);
}
}
return result;
}
