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 void MergeSamp(PreSampleDefinition other)
{
FileNames.AddRange(other.FileNames);
FileNames.Add(other.singleFName);
ColIDs.Add(other.singleColIndex);
ColIDs.AddRange(other.ColIDs);
}
protected void OnFkpmLoad(object sender, EventArgs e)
{
if (MainData.FPKMFileNames.Count > 0)
{
List <PreSampleDefinition> prels = new List <PreSampleDefinition> ();
foreach (string st in MainData.FPKMFileNames)
{
List <string> cols = null;
FKPM.GetSampleNames(st, out cols);
int cnt = 0;
foreach (string ss in cols)
{
PreSampleDefinition pef = new PreSampleDefinition(SampleType.Expr);
pef.singleFName = st;
pef.singleColID = ss;
pef.singleColIndex = cnt + 9;
pef.IsGenotyped = false;
pef.TotalColumns = cols.Count;
prels.Add(pef);
cnt += 4;
}
}
SampleAllocationWindow swind = new SampleAllocationWindow(prels);
swind.ShowAll();
}
else
{
MainData.ShowMessageWindow("You need to add some files to load first!", false);
}
}
public PreSampleDefinition(PreSampleDefinition other, string _ID)
{
singleColIndex = other.singleColIndex;
singleColID = other.singleColID;
FileNames = other.FileNames;
FileNames.Add(other.singleFName);
ColIDs = other.ColIDs;
ColIDs.Add(other.singleColIndex);
IsGenotyped = other.IsGenotyped;
TotalColumns = other.TotalColumns;
SType = other.SType;
TotalColumns = other.TotalColumns;
ID = _ID;
}
public void RecieveDefinition(PreSampleDefinition pres)
{
if (pres.SType == SampleType.BAM)
{
SendBAMs(pres.FileNames);
}
else if (pres.SType == SampleType.Expr)
{
SendToStaticFKPM(pres, this);
}
else if (pres.SType == SampleType.Vcf)
{
SendToStatic(pres, this);
}
}
protected void OnVcfLoad(object sender, EventArgs e)
{
if (MainData.VariantFileNames.Count > 0)
{
List <PreSampleDefinition> prels = new List <PreSampleDefinition> ();
foreach (string st in MainData.VariantFileNames)
{
List <string> cols = null;
if (Variant.IsGenotyped(st, ref cols))
{
int cnt = 0;
foreach (string ss in cols)
{
PreSampleDefinition pef = new PreSampleDefinition(SampleType.Vcf);
pef.singleFName = st;
pef.singleColID = ss;
pef.singleColIndex = cnt + 9;
pef.IsGenotyped = true;
pef.TotalColumns = cols.Count;
prels.Add(pef);
cnt++;
}
}
else
{
PreSampleDefinition pef = new PreSampleDefinition(SampleType.Vcf);
pef.singleFName = st;
pef.IsGenotyped = false;
pef.TotalColumns = 0;
prels.Add(pef);
}
}
SampleAllocationWindow swind = new SampleAllocationWindow(prels);
swind.ShowAll();
}
else
{
MainData.ShowMessageWindow("You need to add some files to load first!", false);
}
}
protected void OnBamLoad(object sender, EventArgs e)
{
if (MainData.BAMFileNames.Count > 0)
{
List <PreSampleDefinition> prels = new List <PreSampleDefinition> ();
foreach (string st in MainData.BAMFileNames)
{
PreSampleDefinition pef = new PreSampleDefinition(SampleType.BAM);
pef.singleFName = st;
prels.Add(pef);
}
SampleAllocationWindow swind = new SampleAllocationWindow(prels);
swind.ShowAll();
}
else
{
MainData.ShowMessageWindow("You need to add some files to load first!", false);
}
}
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 EntryDefPair(Entry e, PreSampleDefinition p)
{
Ent = e;
Pres = p;
}