public static CacheFormat FromVersion(CacheFormatVersion formatVersion)
{
if (formatVersion > CacheFormatVersion.CURRENT)
{
throw new NotSupportedException();
}
CacheFormatVersion versionRequired;
if (formatVersion.CompareTo(CacheHeaderStruct.WithStructSizes) >= 0)
{
versionRequired = CacheHeaderStruct.WithStructSizes;
}
else
{
versionRequired = formatVersion;
}
return(new CacheFormat
{
FormatVersion = formatVersion,
VersionRequired = versionRequired,
ChromPeakSize = ChromPeak.GetStructSize(formatVersion),
ChromTransitionSize = ChromTransition.GetStructSize(formatVersion),
CachedFileSize = CachedFileHeaderStruct.GetStructSize(formatVersion),
ChromGroupHeaderSize = ChromGroupHeaderInfo.GetStructSize(formatVersion)
});
}
public void TestChromTransitionMissingMassErrors()
{
foreach (var chromSource in ListChromSourceValues())
{
ChromTransition chromTransition = MakeChromTransition(chromSource);
Assert.AreEqual(chromSource, chromTransition.Source);
Assert.IsFalse(chromTransition.MissingMassErrors);
chromTransition.MissingMassErrors = true;
Assert.IsTrue(chromTransition.MissingMassErrors);
Assert.AreEqual(chromSource, chromTransition.Source);
chromTransition.MissingMassErrors = false;
Assert.IsFalse(chromTransition.MissingMassErrors);
Assert.AreEqual(chromSource, chromTransition.Source);
}
}
public IItemSerializer <ChromTransition> ChromTransitionSerializer()
{
if (FormatVersion > CacheFormatVersion.Six)
{
return(ChromTransition.StructSerializer(ChromTransitionSize));
}
if (FormatVersion > CacheFormatVersion.Four)
{
return(ConvertedItemSerializer.Create(
ChromTransition5.StructSerializer(),
chromTransition5 => new ChromTransition(chromTransition5),
chromTransition => new ChromTransition5(chromTransition)));
}
return(ConvertedItemSerializer.Create(ChromTransition4.StructSerializer(),
chromTransition4 => new ChromTransition(chromTransition4),
chromTransiton => new ChromTransition4(chromTransiton)));
}
public static long CacheSize(SrmDocument docInitial, long format3Size, int groupCount, int tranCount, int peakCount)
{
long cacheSize = format3Size;
int fileCachedCount = docInitial.Settings.MeasuredResults.MSDataFileInfos.Count();
if (ChromatogramCache.FORMAT_VERSION_CACHE > ChromatogramCache.FORMAT_VERSION_CACHE_3)
{
// Cache version 4 stores instrument information, and is bigger in size.
cacheSize += sizeof(int) * fileCachedCount;
}
if (ChromatogramCache.FORMAT_VERSION_CACHE > ChromatogramCache.FORMAT_VERSION_CACHE_4)
{
// Cache version 5 adds an int for flags for each file
// Allow for a difference in sizes due to the extra information.
int fileFlagsSize = sizeof(int) * fileCachedCount;
// And SeqIndex, SeqCount, StartScoreIndex and padding
var deltaSize5 = ChromGroupHeaderInfo.GetStructSize(CacheFormatVersion.Five) -
ChromGroupHeaderInfo.GetStructSize(CacheFormatVersion.Four);
int groupHeadersSize = deltaSize5 * groupCount;
// And flags for each transition
int transitionFlagsSize = ChromTransition5.DeltaSize5 * tranCount;
// And num seq byte count, seq location, score types, num scores and score location
const int headerScoreSize = sizeof(int) + sizeof(long) + sizeof(int) + sizeof(int) + sizeof(long);
cacheSize += groupHeadersSize + fileFlagsSize + transitionFlagsSize + headerScoreSize;
}
if (ChromatogramCache.FORMAT_VERSION_CACHE > ChromatogramCache.FORMAT_VERSION_CACHE_5)
{
// Cache version 6 adds status graph dimensions for every file
cacheSize += sizeof(float) * 2 * fileCachedCount;
}
if (ChromatogramCache.FORMAT_VERSION_CACHE > ChromatogramCache.FORMAT_VERSION_CACHE_6)
{
// Cache version 7 adds ion mobility information
cacheSize += sizeof(float) * 2 * tranCount;
}
if (ChromatogramCache.FORMAT_VERSION_CACHE > ChromatogramCache.FORMAT_VERSION_CACHE_8)
{
// Cache version 9 adds scan id values for every file
cacheSize += (sizeof(int) + sizeof(long)) * fileCachedCount;
// And scan ids location to global header
cacheSize += sizeof(long);
}
if (ChromatogramCache.FORMAT_VERSION_CACHE >= ChromatogramCache.FORMAT_VERSION_CACHE_11)
{
// Version 11 adds uncompressed buffer size for convenience, and some time span metadata
cacheSize += ChromGroupHeaderInfo.DeltaSize11 * groupCount;
}
if (ChromatogramCache.FORMAT_VERSION_CACHE >= CacheFormatVersion.Twelve)
{
cacheSize += peakCount * (ChromPeak.GetStructSize(CacheFormatVersion.Twelve) -
ChromPeak.GetStructSize(CacheFormatVersion.Eleven));
cacheSize += tranCount *
(ChromTransition.GetStructSize(CacheFormatVersion.Twelve) -
ChromTransition.GetStructSize(CacheFormatVersion.Eleven));
}
cacheSize += fileCachedCount *
(CachedFileHeaderStruct.GetStructSize(ChromatogramCache.FORMAT_VERSION_CACHE) -
CachedFileHeaderStruct.GetStructSize(CacheFormatVersion.Nine));
cacheSize += CacheHeaderStruct.GetStructSize(ChromatogramCache.FORMAT_VERSION_CACHE) -
CacheHeaderStruct.GetStructSize(ChromatogramCache.FORMAT_VERSION_CACHE_11);
return(cacheSize);
}
public unsafe void TestChromTransitionSize()
{
Assert.AreEqual(4, sizeof(ChromTransition4));
Assert.AreEqual(16, sizeof(ChromTransition5));
Assert.AreEqual(24, ChromTransition.GetStructSize(CacheFormatVersion.CURRENT));
}