private static void Add(ref List <DbParameter> list, object data, ParamListType ParamType)
{
Type objType = data.GetType();
List <PropertyInfo> propertyList = new List <PropertyInfo>(objType.GetProperties());
System.Attribute[] AttributeList = System.Attribute.GetCustomAttributes(objType);
for (int i = 0; i < propertyList.Count; ++i)
{
var prop = propertyList.ToArray()[i];
DBKeyField keyAttr = (DBKeyField)AttributeList[i];
DBField attr = (DBField)AttributeList[i];
DbParameter param = new DbParameter();
object propValue = prop.GetValue(data, null);
param.Name = prop.Name;
param.Value = propValue;
param.Direction = DbDirection.Input;
param.SqlType = keyAttr == null ? attr.SqlDbType : keyAttr.SqlDbType;
if (ParamType == ParamListType.Key)
{
if (keyAttr != null)
{
list.Add(param);
}
}
else
{
list.Add(param);
}
}
}
public static List <DbParameter> CreateParam(object objClass, ParamListType ParamType)
{
var list = new List <DbParameter>();
Add(ref list, objClass, ParamType);
return(list);
}
/// <summary>
/// Creates a list of parametrs based off of the object class and it's values
/// </summary>
/// <param name="objClass">Class to be reflected into parameters</param>
/// <param name="ListType">Value determines all columns, or just the key values should be parameterized</param>
/// <returns></returns>
public List <DbParameter> CreateParamList(object objClass, ParamListType ListType)
{
//Update to allow differeny ListTypes (Save = All columns, Get is Just PK)
List <DbParameter> result = ClassToDbParameter.CreateParam(objClass, ListType);
return(result);
}
private void LoadSeqScores() {
m_GreenTh = new double[4];
m_YellowTh = new double[4];
ParamListType ParamList = m_mzid.Data.AnalysisProtocolCollection.SpectrumIdentificationProtocol[0].AdditionalSearchParams;
if( ParamList == null )
return;
int ProteomeDiscovererSequestXcorr = 0;
foreach( AbstractParamType param in ParamList.Items ) {
if( !(param is CVParamType) )
continue;
CVParamType cv = param as CVParamType;
switch( cv.accession ) {
case "MS:1001712": // ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1
m_GreenTh[0] = double.Parse(cv.value, m_Format);
ProteomeDiscovererSequestXcorr++;
break;
case "MS:1001713": // ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2
m_GreenTh[1] = double.Parse(cv.value, m_Format);
ProteomeDiscovererSequestXcorr++;
break;
case "MS:1001714": // ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3
m_GreenTh[2] = double.Parse(cv.value, m_Format);
ProteomeDiscovererSequestXcorr++;
break;
case "MS:1001715": // ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4
m_GreenTh[3] = double.Parse(cv.value, m_Format);
ProteomeDiscovererSequestXcorr++;
break;
case "MS:1001716": // ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1
m_YellowTh[0] = double.Parse(cv.value, m_Format);
ProteomeDiscovererSequestXcorr++;
break;
case "MS:1001717": // ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2
m_YellowTh[1] = double.Parse(cv.value, m_Format);
ProteomeDiscovererSequestXcorr++;
break;
case "MS:1001718": // ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3
m_YellowTh[2] = double.Parse(cv.value, m_Format);
ProteomeDiscovererSequestXcorr++;
break;
case "MS:1001719": // ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4
m_YellowTh[3] = double.Parse(cv.value, m_Format);
ProteomeDiscovererSequestXcorr++;
break;
}
}
if( ProteomeDiscovererSequestXcorr >= 8 ) {
string yellow = "\t* Red-Yellow thresholds:";
string green = "\t* Yellow-Green thresholds:";
for( int i = 0; i < 4; i++ ) {
green += " " + m_GreenTh[i] + "(" + (i+1) + ")";
yellow += " " + m_YellowTh[i] + "(" + (i+1) + ")";
}
Notify( "Using ProteomeDiscoverer/SEQUEST XCorr values:");
Notify( yellow );
Notify( green );
SeqThreshold = Peptide.ConfidenceType.Yellow;
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="pl"></param>
/// <param name="idata"></param>
public ParamListObj(ParamListType pl, IdentDataObj idata)
: base(idata)
{
_items = null;
if (pl != null && pl.Items.Count > 0)
{
Items = new IdentDataList <ParamBaseObj>();
foreach (var p in pl.Items)
{
if (p is CVParamType)
{
Items.Add(new CVParamObj(p as CVParamType, IdentData));
}
else if (p is UserParamType)
{
Items.Add(new UserParamObj(p as UserParamType, IdentData));
}
}
}
}
/// <summary>
/// Create an object using the contents of the corresponding MzIdentML object
/// </summary>
/// <param name="pl"></param>
/// <param name="idata"></param>
public ParamListObj(ParamListType pl, IdentDataObj idata)
: base(idata)
{
Items = new IdentDataList <ParamBaseObj>(1);
if (pl?.Items.Count > 0)
{
Items.AddRange(pl.Items, p =>
{
if (p is CVParamType cvp)
{
return(new CVParamObj(cvp, IdentData));
}
if (p is UserParamType up)
{
return(new UserParamObj(up, IdentData));
}
return(null);
});
}
}
