/// <summary>
/// Get TargetSummaryOptions from QueryTable criteria values
/// </summary>
/// <param name="targetSumTable"></param>
/// <returns></returns>
public static TargetSummaryOptions GetFromQueryTable(
QueryTable targetSumTable)
{
QueryTable qt = targetSumTable;
TargetSummaryOptions tso = GetFromMdbAssayOptionsColumn(qt);
if (tso == null)
{
tso = new TargetSummaryOptions(); // use default values
}
if (qt == null)
{
return(tso);
}
if (qt.Query != null)
{
tso.CidCriteria = qt.Query.KeyCriteria;
}
else
{
tso.CidCriteria = qt.KeyQueryColumn.Criteria; // keep in variable criteria form
}
tso.TargetList = GetListFromColCriteria(qt, MultiDbAssayDataNames.GeneSymbol);
tso.GeneFamilies = GetListFromColCriteria(qt, MultiDbAssayDataNames.GeneFamily);
tso.AssayTypesToInclude = GetListFromColCriteria(qt, MultiDbAssayDataNames.AssayType);
tso.AssayModesToInclude = GetListFromColCriteria(qt, MultiDbAssayDataNames.AssayMode);
tso.ResultTypesToInclude = GetListFromColCriteria(qt, MultiDbAssayDataNames.ResultType);
//string criteria = qt.GetQueryColumnByName("top_lvl_rslt").Criteria;
//tso.UseTopLevelResultTypeOnly = Lex.IsNullOrEmpty(criteria) || Lex.Contains(criteria, "'Y'");
return(tso);
}
/// <summary>
/// Get any existing target summary options from option column
/// </summary>
/// <param name="qt"></param>
/// <returns></returns>
public static TargetSummaryOptions GetFromMdbAssayOptionsColumn(
QueryTable qt)
{
TargetSummaryOptions tso = null;
if (qt == null)
{
return(null);
}
QueryColumn qc = qt.GetQueryColumnByName(MultiDbAssayDataNames.MultiDbViewOptions);
if (qc == null)
{
return(null);
}
ParsedSingleCriteria psc = MqlUtil.ParseSingleCriteria(qc.Criteria);
if (psc == null)
{
return(null);
}
string tsoString = Lex.RemoveSingleQuotes(psc.Value);
if (Lex.IsNullOrEmpty(tsoString))
{
return(null);
}
tso = TargetSummaryOptions.Deserialize(tsoString);
return(tso);
}
/// <summary>
/// Deserialize
/// </summary>
/// <param name="serializedForm"></param>
/// <returns></returns>
public static TargetSummaryOptions Deserialize(string serializedForm)
{
XmlMemoryStreamTextReader mstr = new XmlMemoryStreamTextReader(serializedForm);
XmlTextReader tr = mstr.Reader;
tr.Read();
tr.MoveToContent();
TargetSummaryOptions p = Deserialize(tr);
mstr.Close();
return(p);
}
/// <summary>
/// Deserialize from XmlTextReader
/// </summary>
/// <param name="tr"></param>
/// <returns></returns>
public static TargetSummaryOptions Deserialize(XmlTextReader tr)
{
TargetSummaryOptions p = new TargetSummaryOptions();
if (!Lex.Eq(tr.Name, "MultiDbViewerPrefs") && // new name
!Lex.Eq(tr.Name, "TargetResultsViewerParms")) // old name
{
throw new Exception("\"MultiDbViewerPrefs\" element not found");
}
XmlUtil.GetStringAttribute(tr, "DbName", ref p.DbName);
XmlUtil.GetStringAttribute(tr, "CidCriteria", ref p.CidCriteria);
XmlUtil.GetStringAttribute(tr, "TargetList", ref p.TargetList);
XmlUtil.GetStringAttribute(tr, "GeneFamilies", ref p.GeneFamilies);
if (Lex.Contains(p.GeneFamilies, "Ion, channel")) // fixup
{
p.GeneFamilies = Lex.Replace(p.GeneFamilies, "Ion, channel", "Ion channel");
}
if (Lex.Contains(p.GeneFamilies, "Nuclear, hormone, receptor"))
{
p.GeneFamilies = Lex.Replace(p.GeneFamilies, "Nuclear, hormone, receptor", "Nuclear hormone receptor");
}
XmlUtil.GetStringAttribute(tr, "AssayTypesToInclude", ref p.AssayTypesToInclude);
XmlUtil.GetStringAttribute(tr, "AssayTypesToInclude", ref p.AssayTypesToInclude);
XmlUtil.GetStringAttribute(tr, "ResultTypesToInclude", ref p.ResultTypesToInclude);
XmlUtil.GetBoolAttribute(tr, "UseTopLevelResultTypeOnly", ref p.UseTopLevelResultTypeOnly);
XmlUtil.GetBoolAttribute(tr, "TargetsWithActivesOnly", ref p.TargetsWithActivesOnly);
XmlUtil.GetStringAttribute(tr, "CrcUpperBound", ref p.CrcUpperBound);
XmlUtil.GetStringAttribute(tr, "SpLowerBound", ref p.SpLowerBound);
XmlUtil.GetBoolAttribute(tr, "UseMeans", ref p.UseMeans);
XmlUtil.GetBoolAttribute(tr, "IncludeStructures", ref p.IncludeStructures);
XmlUtil.GetStringAttribute(tr, "FilterableTargets", ref p.FilterableTargets);
XmlUtil.GetStringAttribute(tr, "TargetMap", ref p.TargetMapName);
XmlUtil.GetStringAttribute(tr, "UserMapNames", ref p.UserMapNames);
XmlUtil.GetStringAttribute(tr, "OutputFormat", ref p.PreferredView);
XmlUtil.GetBoolAttribute(tr, "FormatForMobius", ref p.FormatForMobius);
XmlUtil.GetBoolAttribute(tr, "ShowAdvancedDialog", ref p.ShowAdvancedDialog);
return(p);
}