/// <summary>
/// Deserialize from a binary file
/// </summary>
public static AssayDict DeserializeFromFile(
string fileName)
{
FileStream fs = null;
try
{
int t0 = TimeOfDay.Milliseconds();
AssayDict tad = new AssayDict();
if (File.Exists(fileName))
{
fs = File.Open(fileName, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
BinaryFormatter bf = new BinaryFormatter();
List <AssayAttributes> taaList = bf.Deserialize(fs) as List <AssayAttributes>;
fs.Close();
fs = null;
foreach (AssayAttributes taa in taaList)
{
tad.SetMaps(taa);
}
}
t0 = TimeOfDay.Milliseconds() - t0;
return(tad);
}
catch (Exception ex)
{ // be sure file is closed
if (fs != null)
{
fs.Close();
fs = null;
}
throw new Exception(ex.Message, ex);
}
}
/// <summary>
/// Convert a value objectarray into a TargetAssayAttributes
/// </summary>
/// <param name="vo"></param>
/// <param name="voMap"></param>
/// <returns></returns>
public void FromValueObject(
object[] vo,
TargetAssayAttrsFieldPositionMap voMap)
{
string key;
AssayAttributes row = this;
row.Id = GetIntVo(vo, voMap.Id.Voi);
row.GeneSymbol = GetStringVo(vo, voMap.TargetSymbol.Voi);
row.GeneId = GetIntVo(vo, voMap.TargetId.Voi);
row.GeneDescription = GetStringVo(vo, voMap.TargetDescription.Voi);
row.GeneFamily = GetStringVo(vo, voMap.GeneFamily.Voi);
row.GeneFamilyTargetSymbol = GetStringVo(vo, voMap.GeneFamilyTargetSymbol.Voi);
row.AssayType = GetStringVo(vo, voMap.AssayType.Voi);
row.AssayMode = GetStringVo(vo, voMap.AssayMode.Voi);
object obj = GetObjectVo(vo, voMap.AssayName.Voi);
if (obj != null)
{
if (obj is string)
{
row.AssayName = (string)obj;
}
else if (obj is StringMx)
{
StringMx sx = obj as StringMx;
row.AssayName = sx.Value;
if (sx.DbLink.Contains(","))
{
string mtName = sx.DbLink.Replace(",", "_").ToUpper();
row.AssayMetaTableName = mtName;
}
}
}
row.AssayDesc = GetStringVo(vo, voMap.AssayDesc.Voi);
row.AssayDatabase = GetStringVo(vo, voMap.AssayDatabase.Voi);
row.AssaySource = GetStringVo(vo, voMap.AssayLocation.Voi);
row.AssayId2 = GetIntVo(vo, voMap.AssayId2.Voi);
row.AssayIdNbr = GetIntVo(vo, voMap.AssayIdNbr.Voi);
row.AssayIdTxt = GetStringVo(vo, voMap.AssayIdTxt.Voi);
string txt = GetStringVo(vo, voMap.AssayMetaTableName.Voi);
if (txt != null)
{
row.AssayMetaTableName = txt;
}
row.AssayStatus = GetStringVo(vo, voMap.AssayStatus.Voi);
row.GeneCount = GetIntVo(vo, voMap.AssayGeneCount.Voi);
row.ResultName = GetStringVo(vo, voMap.ResultName.Voi);
row.ResultTypeId2 = GetIntVo(vo, voMap.ResultTypeId2.Voi);
row.ResultTypeIdNbr = GetIntVo(vo, voMap.ResultTypeIdNbr.Voi);
row.ResultTypeIdTxt = GetStringVo(vo, voMap.ResultTypeIdTxt.Voi);
row.ResultTypeConcType = GetStringVo(vo, voMap.ResultTypeConcType.Voi);
row.ResultTypeUnits = GetStringVo(vo, voMap.ResultTypeUnits.Voi);
row.ResultTypeConcUnits = GetStringVo(vo, voMap.ResultTypeConcUnits.Voi);
row.TopLevelResult = GetStringVo(vo, voMap.TopLevelResult.Voi);
row.Remapped = GetStringVo(vo, voMap.Remapped.Voi);
row.Multiplexed = GetStringVo(vo, voMap.Multiplexed.Voi);
row.Reviewed = GetStringVo(vo, voMap.Reviewed.Voi);
row.ProfilingAssay = GetStringVo(vo, voMap.ProfilingAssay.Voi);
row.CompoundsAssayed = GetIntVo(vo, voMap.CompoundsAssayed.Voi);
row.ResultCount = GetIntVo(vo, voMap.ResultCount.Voi);
row.AssayUpdateDate = GetDateVo(vo, voMap.AssayUpdateDate.Voi);
row.AssociationSource = GetStringVo(vo, voMap.AssociationSource.Voi);
row.AssociationConflict = GetStringVo(vo, voMap.AssociationConflict.Voi);
row.TargetMapX = GetDoubleVo(vo, voMap.TargetMapX.Voi);
row.TargetMapY = GetDoubleVo(vo, voMap.TargetMapY.Voi);
row.TargetMapZ = GetDoubleVo(vo, voMap.TargetMapZ.Voi);
// Complete assignment any missing assay database and/or assay id information
AssayDict tad = AssayDict.Instance; // dict used for various lookups
if (Lex.IsNullOrEmpty(row.AssayIdTxt) && row.AssayId2 == NullValue.NullNumber)
{ // try to assign from assay name
if (!Lex.IsNullOrEmpty(row.AssayName) && tad != null)
{
key = row.AssayName.Trim().ToUpper();
if (tad.AssayNameMap.ContainsKey(key))
{
AssayAttributes taa = tad.AssayNameMap[key];
row.AssayDatabase = taa.AssayDatabase;
row.AssayId2 = taa.AssayId2;
row.AssayIdNbr = taa.AssayIdNbr;
row.AssayIdTxt = taa.AssayIdTxt;
}
}
}
else if (Lex.IsNullOrEmpty(row.AssayIdTxt))
{
row.AssayIdTxt = row.AssayId2.ToString();
}
else if (row.AssayId2 == NullValue.NullNumber)
{
int.TryParse(row.AssayIdTxt, out row.AssayId2);
}
// Complete any missing target information if target dict is available
if (tad != null)
{
if (Lex.IsNullOrEmpty(row.GeneSymbol) && row.GeneId == NullValue.NullNumber) // assign target from assay info
{
if (!Lex.IsNullOrEmpty(row.AssayDatabase) && !Lex.IsNullOrEmpty(row.AssayIdTxt))
{
key = row.AssayDatabase.ToUpper() + "-" + row.AssayIdTxt.ToUpper();
if (tad.DatabaseAssayIdMap.ContainsKey(key))
{
row.GeneSymbol = tad.DatabaseAssayIdMap[key].GeneSymbol;
row.GeneId = tad.DatabaseAssayIdMap[key].GeneId;
}
}
}
else if (Lex.IsNullOrEmpty(row.GeneSymbol)) // assign symbol from targetid
{
if (tad.TargetIdMap.ContainsKey(row.GeneId))
{
row.GeneSymbol = tad.TargetIdMap[row.GeneId].GeneSymbol;
}
}
else if (row.GeneId == NullValue.NullNumber) // assign targetId from symbol
{
string geneSymbol = row.GeneSymbol.ToUpper();
if (tad.TargetSymbolMap.ContainsKey(geneSymbol))
{
//geneSymbol = "EPHB1"; // debug
//geneSymbol = "AKT3"; // debug
row.GeneId = tad.TargetSymbolMap[geneSymbol].GeneId;
}
}
}
return;
}
