public static IsobaricType ReadIsobaricType(XElement iso)
{
var item = new IsobaricType();
item.Name = iso.FindElement("name").Value;
foreach (var tag in iso.FindElements("tag_mz"))
{
item.TagMassH.Add(double.Parse(tag.Value));
}
var channels = iso.FindElements("channel");
for (int index = 0; index < channels.Count; index++)
{
var channel = channels[index];
var cha = new IsobaricChannel();
cha.Index = index;
cha.Name = channel.FindAttribute("name").Value;
cha.Mz = double.Parse(channel.FindAttribute("mz").Value);
cha.Percentage = double.Parse(channel.FindAttribute("percentage").Value);
item.Channels.Add(cha);
foreach (var isotopic in channel.FindElements("isotopic"))
{
var isot = new IsobaricIsotope();
isot.Name = isotopic.FindAttribute("name").Value;
isot.Percentage = double.Parse(isotopic.FindAttribute("percentage").Value);
cha.Isotopics.Add(isot);
}
}
item.Initialize();
return(item);
}
public static List <UsedChannel> GetUsedChannels(string fileName, IsobaricType isobaricType)
{
using (var stream = new FileStream(fileName, FileMode.Open))
{
using (var reader = XmlReader.Create(stream))
{
if (reader.MoveToElement("IsobaricResult"))
{
if (reader.HasAttributes)
{
var hasUsedChannel = reader.GetAttribute("HasUsedChannel");
if (!string.IsNullOrEmpty(hasUsedChannel) && hasUsedChannel.Equals(true.ToString()))
{
reader.MoveToElement("UsedChannels");
XElement el = XNode.ReadFrom(reader) as XElement;
List <UsedChannel> result = new List <UsedChannel>();
foreach (var ele in el.FindElements("UsedChannel"))
{
var item = new UsedChannel();
item.Index = int.Parse(ele.Attribute("Index").Value);
item.Name = ele.Attribute("Name").Value;
item.Mz = double.Parse(ele.Attribute("Mz").Value);
result.Add(item);
}
return(result);
}
}
}
}
}
return(null);
}
public IsobaricPurityCorrectionRCalculator(IsobaricType plexType, List <UsedChannel> used, string rExecute, bool performPurityCorrection, bool performGraph)
{
this.plexType = plexType;
this.used = used;
this.rExecute = rExecute;
if (this.rExecute == null)
{
throw new Exception("Define R location first!");
}
this.performPurityCorrection = performPurityCorrection;
this.performGraph = performGraph;
}
public object Clone()
{
var result = new IsobaricType();
result.Name = Name;
result.TagMassH = TagMassH;
result.Channels = (from channel in Channels
select channel.Clone() as IsobaricChannel).ToList();
result.IsotopicTable = IsotopicTable;
result.NameIndexMap = NameIndexMap;
return(result);
}
public static void WriteIsobaricType(XElement iso, IsobaricType item)
{
iso.Add(new XElement("name", item.Name));
foreach (var tag in item.TagMassH)
{
iso.Add(new XElement("tag_mass", tag));
}
foreach (var channel in item.Channels)
{
iso.Add(new XElement("channel",
new XAttribute("name", channel.Name),
new XAttribute("mz", channel.Mz),
new XAttribute("percentage", channel.Percentage),
(from isotopic in channel.Isotopics
select new XElement("isotopic",
new XAttribute("name", isotopic.Name),
new XAttribute("percentage", isotopic.Percentage)))));
}
}
public IsobaricPurityCorrectionRCalculator(IsobaricType plexType, List <UsedChannel> used, bool performPurityCorrection, bool performGraph)
: this(plexType, used, ExternalProgramConfig.GetExternalProgram("R"), performPurityCorrection, performGraph)
{
}