public override void WriteToFile(string fileName, List<FeatureItemGroup> groups)
{
UTF8Encoding utf8 = new UTF8Encoding(false);
Progress.SetMessage("Ready for writing ...");
using (var ft = new FileStream(fileName, FileMode.Create))
using (var xw = new StreamWriter(ft, utf8))
//using (var xw = new StreamWriter(ft))
{
//Console.WriteLine("Start writing ... ");
Progress.SetMessage("Start writing ... ");
//xw.WriteLine("<?xml version=\"1.0\" encoding=\"utf-8\"?>");
xw.WriteLine("<?xml version=\"1.0\"?>");
xw.WriteLine("<root>");
Progress.SetMessage("Getting queries ... ");
var queries = groups.GetQueries();
Progress.SetMessage("Writing {0} queries ...", queries.Count);
xw.WriteLine(" <queries>");
foreach (var query in queries)
{
xw.WriteLine(@" <query name=""{0}"" sequence=""{1}"" count=""{2}"">", query.Qname, query.Sequence, query.QueryCount);
foreach (var loc in query.Locations)
{
xw.WriteLine(@" <location seqname=""{0}"" start=""{1}"" end=""{2}"" strand=""{3}"" cigar=""{4}"" score=""{5}"" mdz=""{6}"" nmi=""{7}"" nnpm=""{8}"" />",
loc.Seqname,
loc.Start,
loc.End,
loc.Strand,
loc.Cigar,
loc.AlignmentScore,
loc.MismatchPositions,
loc.NumberOfMismatch,
loc.NumberOfNoPenaltyMutation);
}
xw.WriteLine(" </query>");
}
xw.WriteLine(" </queries>");
Progress.SetMessage("Writing {0} subjects ...", groups.Count);
xw.WriteLine(" <subjectResult>");
foreach (var itemgroup in groups)
{
xw.WriteLine(" <subjectGroup>");
foreach (var item in itemgroup)
{
xw.WriteLine(" <subject name=\"{0}\">", item.Name);
foreach (var region in item.Locations)
{
xw.Write(" <region seqname=\"{0}\" start=\"{1}\" end=\"{2}\" strand=\"{3}\" sequence=\"{4}\"",
region.Seqname,
region.Start,
region.End,
region.Strand,
XmlUtils.ToXml(region.Sequence));
if (this.exportPValue)
{
xw.Write(" query_count_before_filter=\"{0}\"", region.QueryCountBeforeFilter);
xw.Write(" query_count=\"{0}\"", region.QueryCount);
xw.Write(" pvalue=\"{0}\"", region.PValue);
}
xw.WriteLine(" size=\"{0}\">", region.Length);
foreach (var sl in region.SamLocations)
{
var loc = sl.SamLocation;
xw.Write(" <query qname=\"{0}\"", loc.Parent.Qname);
xw.Write(" loc=\"{0}\"", loc.GetLocation());
xw.Write(" overlap=\"{0}\"", string.Format("{0:0.##}", sl.OverlapPercentage));
xw.Write(" offset=\"{0}\"", sl.Offset);
xw.Write(" query_count=\"{0}\"", loc.Parent.QueryCount);
xw.Write(" seq_len=\"{0}\"", loc.Parent.Sequence.Length);
xw.Write(" nmi=\"{0}\"", loc.NumberOfMismatch);
xw.WriteLine(" nnpm=\"{0}\" />", loc.NumberOfNoPenaltyMutation);
}
xw.WriteLine(" </region>");
}
xw.WriteLine(" </subject>");
}
xw.WriteLine(" </subjectGroup>");
}
xw.WriteLine(" </subjectResult>");
xw.Write("</root>");
}
Progress.SetMessage("Writing xml file finished.");
}
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.");
}
}
