/// <summary>
/// parses the relevant data from each protein function prediction object
/// </summary>
public static void ParseReference(ObjectValue objectValue, DataStructures.VEP.ProteinFunctionPredictions cache, ImportDataStore dataStore)
{
// loop over all of the key/value pairs in the cache object
foreach (AbstractData ad in objectValue)
{
if (!DumperUtilities.IsReference(ad))
{
continue;
}
// handle each key
var referenceKeyValue = ad as ReferenceKeyValue;
if (referenceKeyValue == null)
{
continue;
}
switch (referenceKeyValue.Key)
{
case PolyPhenHumVarKey:
cache.PolyPhen = PolyPhen.ParseReference(referenceKeyValue.Value, dataStore);
break;
case SiftKey:
cache.Sift = Sift.ParseReference(referenceKeyValue.Value, dataStore);
break;
default:
throw new GeneralException(
$"Found an unhandled reference in the protein function prediction object: {ad.Key}");
}
}
}
/// <summary>
/// parses the relevant data from each protein function predictions object
/// </summary>
public static DataStructures.VEP.ProteinFunctionPredictions Parse(ObjectValue objectValue)
{
var predictions = new DataStructures.VEP.ProteinFunctionPredictions();
// loop over all of the key/value pairs in the protein function predictions object
foreach (AbstractData ad in objectValue)
{
// sanity check: make sure we know about the keys are used for
if (!KnownKeys.Contains(ad.Key))
{
throw new GeneralException($"Encountered an unknown key in the dumper mapper object: {ad.Key}");
}
// handle each key
switch (ad.Key)
{
case PolyPhenHumDivKey:
// not used by default
break;
case PolyPhenKey:
if (DumperUtilities.IsUndefined(ad))
{
// do nothing
}
else
{
throw new GeneralException($"Could not handle the PolyPhen key: [{ad.GetType()}]");
}
break;
case PolyPhenHumVarKey:
// used by default
var polyPhenHumVarNode = ad as ObjectKeyValue;
if (polyPhenHumVarNode != null)
{
predictions.PolyPhen = PolyPhen.Parse(polyPhenHumVarNode.Value);
}
else if (DumperUtilities.IsUndefined(ad))
{
predictions.PolyPhen = null;
}
else if (DumperUtilities.IsReference(ad))
{
// skip references for now
}
else
{
throw new GeneralException(
$"Could not transform the AbstractData object into an ObjectKeyValue: [{ad.GetType()}]");
}
break;
case SiftKey:
var siftNode = ad as ObjectKeyValue;
if (siftNode != null)
{
predictions.Sift = Sift.Parse(siftNode.Value);
}
else if (DumperUtilities.IsUndefined(ad))
{
predictions.Sift = null;
}
else if (DumperUtilities.IsReference(ad))
{
// skip references for now
}
else
{
throw new GeneralException(
$"Could not transform the AbstractData object into an ObjectKeyValue: [{ad.GetType()}]");
}
break;
default:
throw new GeneralException($"Unknown key found: {ad.Key}");
}
}
return(predictions);
}
