/// <summary>
/// returns an array of exons given a list of ObjectValues (AbstractData)
/// </summary>
public static MutableExon[] ParseList(IImportNode importNode, IChromosome chromosome)
{
var listMembers = importNode.GetListMembers();
if (listMembers == null)
{
throw new InvalidDataException("Encountered an exon node that could not be converted to a member list.");
}
var exons = new MutableExon[listMembers.Count];
for (var exonIndex = 0; exonIndex < listMembers.Count; exonIndex++)
{
if (listMembers[exonIndex] is ObjectValueNode objectValue)
{
exons[exonIndex] = Parse(objectValue, chromosome);
}
else
{
throw new InvalidDataException($"Could not transform the AbstractData object into an ObjectValue: [{listMembers[exonIndex].GetType()}]");
}
}
return(exons);
}
/// <summary>
/// returns an array of miRNAs given a list of ObjectValues (AbstractData)
/// </summary>
public static (IInterval[] MicroRnas, IRnaEdit[] RnaEdits, bool CdsStartNotFound, bool CdsEndNotFound) ParseList(
IImportNode importNode)
{
var listMembers = importNode.GetListMembers();
if (listMembers == null)
{
throw new InvalidDataException("Encountered an attribute node that could not be converted to a member list.");
}
var microRnaList = new List <IInterval>();
var rnaEditList = new List <IRnaEdit>();
var cdsStartNotFound = false;
var cdsEndNotFound = false;
foreach (var node in listMembers)
{
if (!(node is ObjectValueNode objectValue))
{
throw new InvalidDataException($"Could not transform the AbstractData object into an ObjectValue: [{node.GetType()}]");
}
(var key, var value) = ParseKeyValue(objectValue);
if (key == null)
{
continue;
}
// ReSharper disable once SwitchStatementMissingSomeCases
switch (key)
{
case "miRNA":
microRnaList.Add(GetInterval(value));
break;
case "_rna_edit":
rnaEditList.Add(GetRnaEdit(value));
break;
case "cds_start_NF":
cdsStartNotFound = true;
break;
case "cds_end_NF":
cdsEndNotFound = true;
break;
}
}
var microRnas = microRnaList.Count == 0 ? null : microRnaList.ToArray();
var rnaEdits = rnaEditList.Count == 0 ? null : rnaEditList.ToArray();
return(microRnas, rnaEdits, cdsStartNotFound, cdsEndNotFound);
}
