public FKPM(double fkpm, double hi, double lo, BioSample samp)
{
Sample = samp;
FKPMCount = fkpm;
HI = hi;
LO = lo;
}
protected static void SendToStaticFKPM(PreSampleDefinition p, BioSample bios)
{
bios.HasExprs = true;
if (LatestFKPMColIndexed == null)
{
LatestFKPMColIndexed = new Dictionary <string, BioSample[]> ();
}
foreach (string st in p.FileNames)
{
if (!LatestFKPMColIndexed.ContainsKey(st))
{
LatestFKPMColIndexed.Add(st, new BioSample[p.TotalColumns]);
}
foreach (int ii in p.ColIDs)
{
int index = ii - 9;
if (index != 0)
{
index /= 4;
}
LatestFKPMColIndexed [st] [index] = bios;
}
}
hasFKPMSomethingToLoad = true;
}
public static void Assemble()
{
Genome = new Genome();
ProgramState.Init();
AppSettings.Assemble();
RankSplit.Assemble();
FPKMFileNames = new List <string> ();
BAMFileNames = new List <string> ();
VariantFileNames = new List <string> ();
TypeDict = new ElementTypeDictionary();
Samples = new Dictionary <string, BioSample> ();
BioSample.ResetStaticLoader();
GeneToScaffDict = new Dictionary <string, string> ();
RegionToScaffDict = new Dictionary <string, string> ();
RSPToMergeSeries = new List <Series> ();
StatsTester.Assemble();
}
private static void RunSampleAllocationLoading(object ob)
{
try
{
BioSample.ResetStaticLoader();
List <PreSampleDefinition> prel = (List <PreSampleDefinition>)ob;
foreach (PreSampleDefinition pre in prel)
{
if (!Samples.ContainsKey(pre.ID))
{
Samples.Add(pre.ID, new BioSample(pre.ID));
}
Samples [pre.ID].RecieveDefinition(pre);
}
BioSample.LoadAllStatic();
}
catch (Exception e) {
ShowMessageWindow(e.Message, true);
}
}
protected static void SendToStatic(PreSampleDefinition p, BioSample bios)
{
bios.HasVars = true;
if (LatestVarColIndexed == null)
{
LatestVarColIndexed = new Dictionary <string, BioSample[]> ();
}
if (IsGenotypedNames == null)
{
IsGenotypedNames = new Dictionary <string, bool> ();
}
if (p.IsGenotyped)
{
if (!LatestVarColIndexed.ContainsKey(p.FileNames [0]))
{
LatestVarColIndexed.Add(p.FileNames [0], new BioSample[p.TotalColumns]);
}
foreach (int ii in p.ColIDs)
{
LatestVarColIndexed [p.FileNames [0]] [ii - 9] = bios;
}
if (!IsGenotypedNames.ContainsKey(p.FileNames [0]))
{
IsGenotypedNames.Add(p.FileNames [0], p.IsGenotyped);
}
}
else
{
foreach (string s in p.FileNames)
{
if (!IsGenotypedNames.ContainsKey(s))
{
IsGenotypedNames.Add(s, p.IsGenotyped);
}
}
}
hasVarSomethingToLoad = true;
}
public NameRead(BioSample samp, int _start, int _end, string name)
: base(samp, _start, _end)
{
Name = name;
}
public NameRead(BioSample samp, string name) : base(samp)
{
Name = name;
}
public SeqRead(BioSample samp, int _start, int _end)
{
Sample = samp;
Start = _start;
End = _end;
}
public SeqRead(BioSample samp)
{
Sample = samp;
}
public SampleVariant(int ma, int alt, BioSample bio)
{
MajorInd = ma;
AltInd = alt;
BioS = bio;
}