/// <summary>
/// loads the items from the VEP reader
/// </summary>
private static void Load <T>(IVepReader <T> reader, List <T> values)
{
while (true)
{
var value = reader.Next();
if (value == null)
{
break;
}
values.Add(value);
}
}
/// <summary>
/// constructor
/// </summary>
public NirvanaDatabaseCreator(VepTranscriptReader transcriptReader, VepRegulatoryReader regulatoryReader,
VepGeneReader geneReader, VepCombinedGeneReader mergedGeneReader, VepSimpleIntervalReader intronReader,
VepSimpleIntervalReader mirnaReader, VepSequenceReader peptideReader, ChromosomeRenamer renamer)
{
_transcriptReader = transcriptReader;
_regulatoryReader = regulatoryReader;
_geneReader = geneReader;
_mergedGeneReader = mergedGeneReader;
_intronReader = intronReader;
_microRnaReader = mirnaReader;
_peptideReader = peptideReader;
_renamer = renamer;
_transcripts = new List <VD.Transcript>();
_regulatoryElements = new List <VD.RegulatoryElement>();
_genes = new List <MutableGene>();
_mergedGenes = new List <MutableGene>();
_introns = new List <VD.SimpleInterval>();
_microRnas = new List <VD.SimpleInterval>();
_peptideSeqs = new List <string>();
}
