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; }