/// <summary>
/// writes the annotations to the current database file
/// </summary>
public void Write(DataStructures.GlobalCache cache)
{
// write the header
_blockStream.WriteHeader(_header);
// write out each of our arrays
WriteItems(cache.RegulatoryElements);
WriteItems(cache.Genes);
WriteItems(cache.Introns);
WriteItems(cache.MicroRnas);
WriteItems(cache.PeptideSeqs);
// write our transcripts
WriteTranscripts(cache);
}
/// <summary>
/// writes out each transcript in the cache
/// </summary>
private void WriteTranscripts(DataStructures.GlobalCache cache)
{
if (cache.Transcripts == null)
{
_writer.WriteOpt(0);
}
else
{
// create index dictionaries for each data type
var geneIndices = CreateIndex(cache.Genes);
var intronIndices = CreateIndex(cache.Introns);
var microRnaIndices = CreateIndex(cache.MicroRnas);
var peptideIndices = CreateIndex(cache.PeptideSeqs);
// write the transcripts
_writer.WriteOpt(cache.Transcripts.Length);
foreach (var transcript in cache.Transcripts)
{
transcript.Write(_writer, geneIndices, intronIndices, microRnaIndices, peptideIndices);
}
}
_writer.Write(CacheConstants.GuardInt);
}
