/// <summary>
/// parses the relevant data from each mapper
/// </summary>
public static void ParseReference(ObjectValue objectValue, DataStructures.VEP.Mapper mapper, ImportDataStore dataStore)
{
// loop over all of the key/value pairs in the mapper object
foreach (AbstractData ad in objectValue)
{
switch (ad.Key)
{
case PairCodingDnaKey:
var pairCodingDnaNode = ad as ObjectKeyValue;
if (pairCodingDnaNode != null)
{
PairCodingDna.ParseReference(pairCodingDnaNode.Value, mapper.PairCodingDna, dataStore);
}
break;
case PairGenomicKey:
var pairGenomicNode = ad as ObjectKeyValue;
if (pairGenomicNode != null)
{
PairGenomic.ParseReference(pairGenomicNode.Value, mapper.PairGenomic, dataStore);
}
break;
}
}
}
/// <summary>
/// parses the relevant data from each exon coordinate mapper object
/// </summary>
public static DataStructures.VEP.Mapper Parse(ObjectValue objectValue, ImportDataStore dataStore)
{
var mapper = new DataStructures.VEP.Mapper();
// loop over all of the key/value pairs in the exon coordinate mapper 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 FromCoordSystemKey:
if (!DumperUtilities.IsUndefined(ad))
{
throw new GeneralException("Found an unexpected value in FromCoordSystemKey");
}
break;
case FromNameKey:
mapper.FromType = DumperUtilities.GetString(ad);
break;
case IsSortedKey:
mapper.IsSorted = DumperUtilities.GetBool(ad);
break;
case PairCodingDnaKey:
var pairCodingDnaNode = ad as ObjectKeyValue;
if (pairCodingDnaNode != null)
{
mapper.PairCodingDna = PairCodingDna.Parse(pairCodingDnaNode.Value, dataStore);
}
else if (DumperUtilities.IsUndefined(ad))
{
mapper.PairCodingDna = null;
}
else
{
throw new GeneralException(
$"Could not transform the AbstractData object into an ObjectKeyValue: [{ad.GetType()}]");
}
break;
case PairCountKey:
mapper.PairCount = DumperUtilities.GetInt32(ad);
break;
case PairGenomicKey:
var pairGenomicNode = ad as ObjectKeyValue;
if (pairGenomicNode != null)
{
mapper.PairGenomic = PairGenomic.Parse(pairGenomicNode.Value, dataStore);
}
else if (DumperUtilities.IsUndefined(ad))
{
mapper.PairGenomic = null;
}
else
{
throw new GeneralException(
$"Could not transform the AbstractData object into an ObjectKeyValue: [{ad.GetType()}]");
}
break;
case ToCoordSystemKey:
if (!DumperUtilities.IsUndefined(ad))
{
throw new GeneralException("Found an unexpected value in ToCoordSystemKey");
}
break;
case ToNameKey:
mapper.ToType = DumperUtilities.GetString(ad);
break;
default:
throw new GeneralException($"Unknown key found: {ad.Key}");
}
}
return(mapper);
}