/// <summary>
/// parses the relevant data from each transcript mapper cache
/// </summary>
public static void ParseReference(ObjectValue objectValue, DataStructures.VEP.TranscriptMapper transcriptMapper, ImportDataStore dataStore)
{
// loop over all of the key/value pairs in the transcript mapper object
foreach (AbstractData ad in objectValue)
{
if (ad.Key != ExonCoordinateMapperKey)
{
continue;
}
var exonMapperNode = ad as ObjectKeyValue;
if (exonMapperNode != null)
{
Mapper.ParseReference(exonMapperNode.Value, transcriptMapper.ExonCoordinateMapper, dataStore);
}
}
}
/// <summary>
/// parses the relevant data from each transcript mapper
/// </summary>
public static DataStructures.VEP.TranscriptMapper Parse(ObjectValue objectValue, ImportDataStore dataStore)
{
var mapper = new DataStructures.VEP.TranscriptMapper();
// loop over all of the key/value pairs in the transcript 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 transcript mapper object: {ad.Key}");
}
// handle each key
switch (ad.Key)
{
case CodingDnaCodingEndKey:
case CodingDnaCodingStartKey:
case StartPhaseKey:
break;
case ExonCoordinateMapperKey:
var exonCoordMapperNode = ad as ObjectKeyValue;
if (exonCoordMapperNode != null)
{
mapper.ExonCoordinateMapper = Mapper.Parse(exonCoordMapperNode.Value, dataStore);
}
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(mapper);
}
