public Genome(
string workingDirectory,
string sectionTitle,
Memory memory,
HDDPerformance hddPerformance,
CacheOptions cacheOptions,
ISerializer <C> CSerializer,
IComparer <C> CComparer)
{
_memory = memory;
_hddPerformance = hddPerformance;
_CSerializer = CSerializer;
_CComparer = CComparer;
_sectionTitle = sectionTitle;
_cacheOptions = cacheOptions;
_stpWtch = new Stopwatch();
_config = ConfigurationManager.OpenExeConfiguration(ConfigurationUserLevel.None);
_settings = ConfigurationManager.OpenExeConfiguration(ConfigurationUserLevel.None).AppSettings.Settings;
if (_memory == Memory.RAM)
{
chrs = new Dictionary <string, Dictionary <char, Di4 <C, I, M> > >();
}
else if (_memory == Memory.HDD && _hddPerformance == HDDPerformance.Fastest)
{
chrs = new Dictionary <string, Dictionary <char, Di4 <C, I, M> > >();
_chrSection = (ChrSection)ConfigurationManager.GetSection(_sectionTitle);
if (_chrSection == null)
{
_chrSection = new ChrSection();
}
ConfigurationManager.RefreshSection(_sectionTitle);
foreach (ChrConfigElement element in _chrSection.genomeChrs)
{
if (!chrs.ContainsKey(element.chr))
{
chrs.Add(element.chr, new Dictionary <char, Di4 <C, I, M> >());
}
if (!chrs[element.chr].ContainsKey(element.strand))
{
chrs[element.chr].Add(element.strand, new Di4 <C, I, M>(GetDi4Options(element.index)));
}
}
}
}
internal ExecutionReport Add(
uint collectionID,
Dictionary <string, Dictionary <char, List <I> > > intervals,
char strand,
IndexingMode indexinMode,
MaxDegreeOfParallelism maxDegreeOfParallelism)
{
int totalIntervals = 0;
switch (_memory)
{
case Memory.HDD:
if (_chrSection == null)
{
_chrSection = new ChrSection();
}
ConfigurationManager.RefreshSection(_sectionTitle);
switch (_hddPerformance)
{
// TODO:
// This case is not complete, because other operations
// are not supporting this method.
case HDDPerformance.LeastMemory:
_stpWtch.Restart();
foreach (var chr in intervals)
{
foreach (var strandEntry in chr.Value)
{
using (var di4 = new Di4 <C, I, M>(GetDi4Options(GetDi4File(chr.Key, strand)))) // this might be wrong
{
di4.Add(strandEntry.Value, indexinMode, collectionID, maxDegreeOfParallelism.di4Degree);
totalIntervals += strandEntry.Value.Count;
}
}
}
_stpWtch.Stop();
break;
case HDDPerformance.Fastest:
/// Initialize by a sequential foreach loop.
foreach (var chr in intervals)
{
foreach (var strandEntry in chr.Value)
{
if (!chrs.ContainsKey(chr.Key))
{
chrs.Add(chr.Key, new Dictionary <char, Di4 <C, I, M> >());
}
if (!chrs[chr.Key].ContainsKey(strand))
{
chrs[chr.Key].Add(strand, new Di4 <C, I, M>(GetDi4Options(GetDi4File(chr.Key, strand))));
}
}
}
_stpWtch.Restart();
/// Populate inside a parallel foreach loop.
Parallel.ForEach(intervals,
new ParallelOptions {
MaxDegreeOfParallelism = maxDegreeOfParallelism.chrDegree
},
chr =>
{
foreach (var strandEntry in chr.Value)
{
chrs[chr.Key][strand].Add(strandEntry.Value, indexinMode, collectionID, maxDegreeOfParallelism.di4Degree);
//chrs[chr.Key][strand].Commit();
totalIntervals += strandEntry.Value.Count;
}
});
_stpWtch.Stop();
break;
}
if (_config.Sections[_sectionTitle] == null)
{
_config.Sections.Add(_sectionTitle, _chrSection);
}
_config.Save(ConfigurationSaveMode.Modified);
ConfigurationManager.RefreshSection(_sectionTitle);
break;
case Memory.RAM:
_stpWtch.Restart();
foreach (var chr in intervals)
{
foreach (var strandEntry in chr.Value)
{
if (!chrs.ContainsKey(chr.Key))
{
chrs.Add(chr.Key, new Dictionary <char, Di4 <C, I, M> >());
}
if (!chrs[chr.Key].ContainsKey(strand))
{
chrs[chr.Key].Add(strand, new Di4 <C, I, M>(GetDi4Options()));
}
chrs[chr.Key][strand].Add(strandEntry.Value, indexinMode, collectionID, maxDegreeOfParallelism.di4Degree);
totalIntervals += strandEntry.Value.Count;
}
}
_stpWtch.Stop();
break;
}
return(new ExecutionReport(totalIntervals, _stpWtch.Elapsed));
}
