public override void WriteToFile(string fileName, List<FeatureItemGroup> groups)
{
UTF8Encoding utf8 = new UTF8Encoding(false);
Progress.SetMessage("Creating xml writer ... ");
using (XmlTextWriter xw = new XmlTextWriter(fileName, utf8))
{
Progress.SetMessage("Start writing ... ");
xw.WriteStartDocument();
xw.WriteStartElement("root");
Progress.SetMessage("Getting queries ... ");
var queries = groups.GetQueries();
Progress.SetMessage("Writing {0} queries ...", queries.Count);
SAMAlignedItemUtils.WriteTo(xw, queries);
Progress.SetMessage("Writing {0} subjects ...", groups.Count);
xw.WriteStartElement("subjectResult");
foreach (var itemgroup in groups)
{
xw.WriteStartElement("subjectGroup");
foreach (var item in itemgroup)
{
xw.WriteStartElement("subject");
xw.WriteAttribute("name", item.Name);
foreach (var region in item.Locations)
{
xw.WriteStartElement("region");
xw.WriteAttribute("seqname", region.Seqname);
xw.WriteAttribute("start", region.Start);
xw.WriteAttribute("end", region.End);
xw.WriteAttribute("strand", region.Strand);
xw.WriteAttribute("sequence", XmlUtils.ToXml(region.Sequence));
if (this.exportPValue)
{
xw.WriteAttribute("query_count_before_filter", region.QueryCountBeforeFilter);
xw.WriteAttribute("query_count", region.QueryCount);
xw.WriteAttribute("pvalue", region.PValue);
}
xw.WriteAttribute("size", region.Length);
foreach (var sl in region.SamLocations)
{
var loc = sl.SamLocation;
xw.WriteStartElement("query");
xw.WriteAttribute("qname", loc.Parent.Qname);
xw.WriteAttribute("loc", loc.GetLocation());
xw.WriteAttribute("overlap", string.Format("{0:0.##}", sl.OverlapPercentage));
xw.WriteAttribute("offset", sl.Offset);
xw.WriteAttribute("query_count", loc.Parent.QueryCount);
xw.WriteAttribute("seq_len", loc.Parent.Sequence.Length);
xw.WriteAttribute("nmi", loc.NumberOfMismatch);
xw.WriteAttribute("nnpm", loc.NumberOfNoPenaltyMutation);
xw.WriteEndElement();
}
xw.WriteEndElement();
}
xw.WriteEndElement();
}
xw.WriteEndElement();
}
xw.WriteEndElement();
xw.WriteEndElement();
xw.WriteEndDocument();
Progress.SetMessage("Writing xml file finished.");
}
}