/// <summary>
/// writes the annotations to the current database file
/// </summary>
internal void Write(Prediction.Entry[] lut, Prediction[][] predictionsPerRef)
{
_blockStream.WriteHeader(_header.Write);
WriteLookupTable(_writer, lut);
_blockStream.Flush();
WritePredictions(predictionsPerRef);
}
private static void WriteBlockStream(ICompressionAlgorithm compressionAlgorithm, CacheHeader header,
DemoCustomHeader customHeader, MemoryStream ms, string s)
{
using (var blockStream = new BlockStream(compressionAlgorithm, ms, CompressionMode.Compress, true))
using (var writer = new ExtendedBinaryWriter(blockStream))
{
CheckReadException(blockStream);
blockStream.WriteHeader(header.Write);
var bp = new BlockStream.BlockPosition();
// detect that we have written a block
blockStream.GetBlockPosition(bp);
writer.WriteOptAscii(s);
blockStream.GetBlockPosition(bp);
// here we write a test string that won't invoke a new block
blockStream.GetBlockPosition(customHeader.DemoPosition);
writer.WriteOptAscii(SmallString);
blockStream.GetBlockPosition(bp);
Assert.Equal(customHeader.DemoPosition.FileOffset, blockStream.Position);
blockStream.Flush();
// this will be flushed during dispose
writer.WriteOptAscii(FinalString);
}
}
/// <summary>
/// writes the annotations to the current database file
/// </summary>
public void Write(Prediction.Entry[] lut, Prediction[][] predictionsPerRef)
{
// write the header
_blockStream.WriteHeader(_header);
// write the LUT
WriteLookupTable(_writer, lut);
_blockStream.Flush();
// write the predictions
WritePredictions(predictionsPerRef);
}
/// <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 the annotations to the current database file
/// </summary>
public void Write(TranscriptCacheData cacheData)
{
_blockStream.WriteHeader(_header.Write);
WriteItems(_writer, cacheData.Genes, x => x.Write(_writer));
WriteItems(_writer, cacheData.TranscriptRegions, x => x.Write(_writer));
WriteItems(_writer, cacheData.Mirnas, x => x.Write(_writer));
WriteItems(_writer, cacheData.PeptideSeqs, x => _writer.WriteOptAscii(x));
var geneComparer = new GeneComparer();
var transcriptRegionComparer = new TranscriptRegionComparer();
var intervalComparer = new IntervalComparer();
var geneIndices = CreateIndex(cacheData.Genes, geneComparer);
var transcriptRegionIndices = CreateIndex(cacheData.TranscriptRegions, transcriptRegionComparer);
var microRnaIndices = CreateIndex(cacheData.Mirnas, intervalComparer);
var peptideIndices = CreateIndex(cacheData.PeptideSeqs, EqualityComparer <string> .Default);
WriteIntervals(_writer, cacheData.RegulatoryRegionIntervalArrays, x => x.Write(_writer));
WriteIntervals(_writer, cacheData.TranscriptIntervalArrays, x => x.Write(_writer, geneIndices, transcriptRegionIndices, microRnaIndices, peptideIndices));
}
private static void WriteBlockStream(ICompressionAlgorithm compressionAlgorithm, DemoHeader header,
DemoCustomHeader customHeader, Stream ms, string s)
{
using (var blockStream = new BlockStream(compressionAlgorithm, ms, CompressionMode.Compress, true))
using (var writer = new ExtendedBinaryWriter(blockStream))
{
CheckReadException(blockStream);
blockStream.WriteHeader(header.Write);
writer.WriteOptAscii(s);
(customHeader.FileOffset, customHeader.InternalOffset) = blockStream.GetBlockPosition();
Assert.Equal(customHeader.FileOffset, blockStream.Position);
writer.WriteOptAscii(SmallString);
blockStream.Flush();
// this will be flushed during dispose
writer.WriteOptAscii(FinalString);
}
}
