private static void fillScans(binStack[] stackIndex, string fileXml, string schemaFile, BinStackOptions options)
{
DataSet ds = new DataSet();
ds.ReadXmlSchema(schemaFile);
ds.ReadXml(fileXml);
DataView dv = new DataView(ds.Tables["peptide_match"]);
scanIndexStrt newScan = new scanIndexStrt();
int spectrumIndex = 1;
for (int i = 0; i <= stackIndex.GetUpperBound(0); i++)
{
for (int j = 0; j < dv.Count; j++)
{
String RAWfilename = dv[j]["RAWFileName"].ToString().Trim();
if (RAWfilename == stackIndex[i].rawFileName.Trim())
{
int firstscan = int.Parse(dv[j]["FirstScan"].ToString(), CultureInfo.InvariantCulture.NumberFormat);
newScan.FirstScan = firstscan;
newScan.spectrumIndex = spectrumIndex;
dv[j]["spectrumIndex"] = spectrumIndex;
if (options.useParentalMass)
{
try
{
int charge = int.Parse(dv[j]["Charge"].ToString(), CultureInfo.InvariantCulture.NumberFormat);
newScan.parentMass = (double)dv[j]["PrecursorMass"];
newScan.parentMass = (newScan.parentMass + charge) / charge;
}
catch { }
}
stackIndex[i].insert(newScan);
spectrumIndex++;
}
}
}
//Save the QuiXML with the new index (spectrumIndex)
DataSet dsSave = new DataSet();
dsSave = ds.Copy();
try
{
dsSave.WriteXml(fileXml);
}
catch
{
FileInfo f = new FileInfo(fileXml);
string quiXMLfilenew = f.DirectoryName + "\\" + f.Name + "_binStackProcessed" + f.Extension;
dsSave.WriteXml(quiXMLfilenew);
}
}
private static void fillScans(binStack[] stackIndex, string fileXml)
{
//Initialize necessary objets for XML reading
XmlTextReader reader = new XmlTextReader(fileXml);
XmlNodeType nType = reader.NodeType;
XmlDocument xmldoc = new XmlDocument();
xmldoc.Load(reader);
XmlNodeList xmlnodeMatch = xmldoc.GetElementsByTagName("peptide_match");
scanIndexStrt newScan = new scanIndexStrt();
for (int i = 0; i <= stackIndex.GetUpperBound(0); i++)
{
foreach (XmlNode node in xmlnodeMatch)
{
if (node["RAWFileName"].InnerText.ToString().Trim() == stackIndex[i].rawFileName.Trim())
{
newScan.FirstScan = int.Parse(node["FirstScan"].InnerText.ToString(), System.Globalization.CultureInfo.InvariantCulture);
stackIndex[i].insert(newScan);
}
}
}
}
/// <summary>
/// insert a new element in the chemical composition
/// </summary>
/// <param name="newComp">(Comb.compStrt)Element + Number of atoms</param>
public void insert(scanIndexStrt newScan)
{
// if insert won't overflow list
if (theSize < scan.Length)
{
// increment start and set element
scan[start = (start + 1) % scan.Length] = newScan;
// increment list size (we've added an element)
theSize++;
}
}
/// <summary>
/// peek at an element in the list
/// </summary>
/// <param name="offset">(int)array index to point</param>
/// <returns>(Comb.compStrt)Element + Number of atoms</returns>
public scanIndexStrt peek(int offset)
{
scanIndexStrt ret = new scanIndexStrt();
// is someone trying to peek beyond our size?
if (offset >= theSize)
{
return(ret);
}
// get object we're peeking at (do not remove it)
return(scan[(end + offset + 1) % scan.Length]);
}
private static void fillScans(binStack[] stackIndex,
DataView dv,
BinStackOptions options)
{
double protonMass = 1.007276466812; // source: http://physics.nist.gov/cgi-bin/cuu/Value?mpu
//associate the dataset to a dataview
string filter = "";
scanIndexStrt newScan = new scanIndexStrt();
int spectrumIndex = 0;
for (int i = 0; i <= stackIndex.GetUpperBound(0); i++)
{
filter = "RAWFileName = '" + stackIndex[i].rawFileName.Trim() + "'";
dv.RowFilter = filter;
for (int j = 0; j < dv.Count; j++)
{
int firstScan = int.Parse(dv[j]["FirstScan"].ToString());
newScan.scanNumbers[0] = firstScan;
newScan.FirstScan = firstScan;
newScan.spectrumIndex = spectrumIndex;
dv[j]["spectrumIndex"] = spectrumIndex;
if (!(options.averagingMethod == averagingMethod.mostIntense ||
options.averagingMethod == averagingMethod.none))
{
newScan.peakStart = int.Parse(dv[j]["PeakStart"].ToString());
newScan.peakEnd = int.Parse(dv[j]["PeakEnd"].ToString());
}
spectrumIndex++;
if (options.useParentalMass)
{
try
{
int charge = int.Parse(dv[j]["Charge"].ToString());
newScan.parentMass = double.Parse(dv[j]["PrecursorMass"].ToString());
newScan.parentMass = (newScan.parentMass + (charge - 1) * protonMass) / charge;
}
catch { }
}
stackIndex[i].insert(newScan);
}
}
}
/// <summary>
/// insert a new element in the chemical composition
/// </summary>
/// <param name="newComp">(Comb.compStrt)Element + Number of atoms</param>
public void insert(scanIndexStrt newScan)
{
// if insert won't overflow list
if (theSize < scan.Length)
{
// increment start and set element
start = (start + 1) % scan.Length;
scan[start].frame = newScan.frame;
scan[start].parentMass = newScan.parentMass;
scan[start].scanNumbers = (int[])newScan.scanNumbers.Clone();
scan[start].FirstScan = newScan.FirstScan;
scan[start].spectrumIndex = newScan.spectrumIndex;
scan[start].peakStart = newScan.peakStart;
scan[start].peakEnd = newScan.peakEnd;
// increment list size (we've added an element)
theSize++;
}
}
