/// <summary>
/// parses the relevant data from each intron object
/// </summary>
private static void ParseReference(ObjectValue objectValue, DataStructures.VEP.Intron intron, ImportDataStore dataStore)
{
// loop over all of the key/value pairs in the intron object
foreach (AbstractData ad in objectValue)
{
// skip normal entries
if (!DumperUtilities.IsReference(ad))
{
continue;
}
// handle each key
switch (ad.Key)
{
case Transcript.SliceKey:
var referenceKeyValue = ad as ReferenceKeyValue;
if (referenceKeyValue != null)
{
intron.Slice = Slice.ParseReference(referenceKeyValue.Value, dataStore);
}
break;
default:
throw new GeneralException($"Found an unhandled reference in the intron object: {ad.Key}");
}
}
}
/// <summary>
/// parses the relevant data from each intron object
/// </summary>
public static DataStructures.VEP.Intron[] ParseList(List <AbstractData> abstractDataList, ImportDataStore dataStore)
{
var introns = new DataStructures.VEP.Intron[abstractDataList.Count];
// loop over all of the introns
for (int intronIndex = 0; intronIndex < abstractDataList.Count; intronIndex++)
{
var objectValue = abstractDataList[intronIndex] as ObjectValue;
if (objectValue == null)
{
throw new GeneralException(
$"Could not transform the AbstractData object into an ObjectValue: [{abstractDataList[intronIndex].GetType()}]");
}
introns[intronIndex] = Parse(objectValue, dataStore);
}
return(introns);
}
/// <summary>
/// returns a new exon given an ObjectValue
/// </summary>
private static DataStructures.VEP.Intron Parse(ObjectValue objectValue, ImportDataStore dataStore)
{
var intron = new DataStructures.VEP.Intron();
// loop over all of the key/value pairs in the intron object
foreach (AbstractData ad in objectValue)
{
// sanity check: make sure we know about the keys are used for
if (!KnownKeys.Contains(ad.Key))
{
throw new GeneralException($"Encountered an unknown key in the dumper mapper object: {ad.Key}");
}
// handle each key
switch (ad.Key)
{
case Transcript.EndKey:
intron.End = DumperUtilities.GetInt32(ad);
break;
case Transcript.SliceKey:
var sliceNode = ad as ObjectKeyValue;
if (sliceNode != null)
{
var newSlice = Slice.Parse(sliceNode.Value, dataStore.CurrentReferenceIndex);
// DS.VEP.Slice oldSlice;
// if (dataStore.Slices.TryGetValue(newSlice, out oldSlice))
//{
// intron.Slice = oldSlice;
//}
// else
//{
intron.Slice = newSlice;
// dataStore.Slices[newSlice] = newSlice;
//}
}
else if (DumperUtilities.IsReference(ad))
{
// skip references until the second pass
}
else
{
throw new GeneralException(
$"Could not transform the AbstractData object into an ObjectKeyValue or ReferenceKeyValue: [{ad.GetType()}]");
}
break;
case Transcript.StartKey:
intron.Start = DumperUtilities.GetInt32(ad);
break;
case Transcript.StrandKey:
TranscriptUtilities.GetStrand(ad);
break;
default:
throw new GeneralException($"Unknown key found: {ad.Key}");
}
}
return(intron);
}