private static void WriteCvParam(XmlTextWriter w, string accession, string name)
{
w.WriteStartElement("cvParam");
w.WriteAttribute("accession", accession);
w.WriteAttribute("name", name);
w.WriteAttribute("cvRef", "PSI-MS");
w.WriteEndElement();
}
private static void StartDocument(XmlTextWriter w)
{
w.WriteStartDocument();
w.WriteStartElement("MzIdentML");
w.WriteAttribute("id", 1);
w.WriteAttribute("version", "1.1.0");
w.WriteAttribute("xmlns", "http://psidev.info/psi/pi/mzIdentML/1.1");
w.WriteAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
w.WriteAttribute("xsi:schemaLocation", "http://www.psidev.info/files/mzIdentML1.1.0.xsd");
w.WriteAttributeFormat("creationDate", "{0:s}", DateTime.Now);
}
public static void StartWriteDocument(XmlTextWriter w, String mode)
{
w.Formatting = Formatting.Indented;
w.WriteStartDocument();
w.WriteStartElement("ITraqResult");
w.WriteAttribute("Mode", mode);
}
public void StartWriteDocument(XmlTextWriter w, IsobaricResult ir)
{
w.Formatting = Formatting.Indented;
w.WriteStartDocument();
w.WriteStartElement("IsobaricResult");
w.WriteAttribute("IsobaricType", ir.PlexType.ToString());
//Write used channels
if (ir.UsedChannels != null && ir.UsedChannels.Count > 0)
{
w.WriteAttribute("HasUsedChannel", true.ToString());
w.WriteStartElement("UsedChannels");
foreach (var channel in ir.UsedChannels)
{
w.WriteStartElement("UsedChannel");
w.WriteAttribute("Index", channel.Index);
w.WriteAttribute("Name", channel.Name);
w.WriteAttribute("Mz", channel.Mz);
w.WriteEndElement();
}
w.WriteEndElement();
}
//Write comments, including parameters
w.WriteStartElement("Comments");
foreach (var comment in ir.Comments)
{
w.WriteStartElement("Comment");
w.WriteAttribute("Key", comment.Key);
w.WriteAttribute("Value", comment.Value);
w.WriteEndElement();
}
w.WriteEndElement();
}
private void WriteSoftwareList(XmlTextWriter w, IIdentifiedResult t, Dictionary <string, string> engineMap)
{
w.WriteStartElement("AnalysisSoftwareList");
var engines = (from g in t
from p in g
from pep in p.Peptides
select pep.Spectrum.Engine).Distinct().ToList();
Dictionary <string, string> map = new Dictionary <string, string>();
engines.ForEach(m => map[m] = "unknown");
map[softname] = softversion;
foreach (var item in map)
{
var name = item.Key;
var version = item.Value;
var id = name.Replace(' ', '_').Replace('\t', '_');
engineMap[name] = id;
w.WriteStartElement("AnalysisSoftware");
w.WriteAttribute("id", id);
w.WriteAttribute("name", name);
w.WriteAttribute("version", version);
w.WriteStartElement("SoftwareName");
WriteCvParam(w, GetAccessionOfSoftware(name), name);
w.WriteEndElement();
w.WriteEndElement();
}
w.WriteEndElement();
}
private static void WriteCvList(XmlTextWriter w)
{
w.WriteStartElement("cvList");
w.WriteAttribute("xmlns", "http://psidev.info/psi/pi/mzIdentML/1.1");
w.WriteStartElement("cv");
w.WriteAttribute("id", "PSI-MS");
w.WriteAttribute("uri", "http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo");
w.WriteAttribute("version", "2.25.0");
w.WriteAttribute("fullName", "PSI-MS");
w.WriteEndElement();
w.WriteStartElement("cv");
w.WriteAttribute("id", "UNIMOD");
w.WriteAttribute("uri", "http://www.unimod.org/obo/unimod.obo");
w.WriteAttribute("fullName", "UNIMOD");
w.WriteEndElement();
w.WriteEndElement();
}
private XmlTextWriter CreateWriter(string path, IChat chat)
{
XmlTextWriter writer = new XmlTextWriter(
storage.GetWriter(path + ".xml"))
{
Formatting = Formatting.Indented,
Indentation = 4,
IndentChar = ' '
};
writer.WriteStartDocument();
writer.WriteStartElement("Chat");
writer.WriteAttribute("ExportStartTime", DateTime.Now);
writer.WriteAttribute("SkypeHistorianVersion", App.Version);
Action action =
delegate
{
writer.WriteAttribute("Description", chat.Description);
writer.WriteAttribute("FriendlyName", chat.FriendlyName);
writer.WriteAttribute("MyRole", chat.MyRole);
writer.WriteAttribute("MyStatus", chat.MyStatus);
writer.WriteAttribute("Name", chat.Name);
writer.WriteAttribute("Topic", chat.Topic);
writer.WriteAttribute("Type", chat.Type);
writer.WriteStartElement("Members");
foreach (IUser user in chat.Members)
{
writer.WriteStartElement("Member");
writer.WriteAttribute("Handle", user.Handle);
writer.WriteAttribute("FullName", user.FullName);
writer.WriteEndElement();
}
writer.WriteEndElement();
};
if (!SafeInvoker.Invoke(action))
{
Logger.Error("Couldn't store chat properties.");
return(null);
}
writer.WriteStartElement("Messages");
return(writer);
}
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))
{
xw.Formatting = Formatting.Indented;
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.");
}
}