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 void SendFKPM(FKPM fkp)
{
if (!FragPerKiloMil.ContainsKey(fkp.Sample.ID))
{
FragPerKiloMil.Add(fkp.Sample.ID, new List <FKPM> ());
}
FragPerKiloMil [fkp.Sample.ID].Add(fkp);
MainData.LoadedFKPM++;
}
public FKPMGene(string gen, FKPM fk)
{
fkpm = fk;
gene = gen;
}
protected static void LoadFKPMFile(string fName, BioSample[] samps)
{
if (!AppSettings.Loading.FKPM_USE_OTHER_THAN_DIFFOUT.Item)
{
using (StreamReader sr = new StreamReader(fName)) {
sr.ReadLine();
string line;
int idInd = AppSettings.Loading.FKPM_ID_COLUMN.Item;
while ((line = sr.ReadLine()) != null)
{
string[] spstr = line.Split('\t');
string gen = spstr [idInd];
for (int i = 9; (i + 3) < spstr.Length; i += 4)
{
bool parseSuccess = true;
double hi; double lo; double fkpm;
if (!double.TryParse(spstr [i], out fkpm))
{
parseSuccess = false;
}
if (!double.TryParse(spstr [i + 1], out hi))
{
parseSuccess = false;
}
if (!double.TryParse(spstr [i + 2], out lo))
{
parseSuccess = false;
}
if (!spstr [i + 3].Contains("OK"))
{
parseSuccess = false;
}
int sampInd = i - 9;
if (i > 0)
{
sampInd++;
sampInd /= 4;
}
if (parseSuccess)
{
FKPM fk = new FKPM(fkpm, hi, lo, samps [sampInd]);
FKPMGene fkg = new FKPMGene(gen, fk);
AllFKPMS.Add(fkg);
}
}
}
}
}
else
{
int colsPerItem = 1;
if (AppSettings.Loading.FKPM_FILE_HAS_HILO.Item)
{
colsPerItem += 2;
}
if (AppSettings.Loading.FKPM_FILE_HAS_TESTOK.Item)
{
colsPerItem += 1;
}
char[] spch = AppSettings.Loading.FKPM_FILE_DELIM.Item;
int firstScore = AppSettings.Loading.FKPM_SCORE_COLUMN.Item;
int idInd = AppSettings.Loading.FKPM_ID_COLUMN.Item;
using (StreamReader sr = new StreamReader(fName)) {
sr.ReadLine();
string line;
while ((line = sr.ReadLine()) != null)
{
string[] spstr = line.Split(spch);
string gen = spstr [idInd];
for (int i = firstScore; (i + colsPerItem - 1) < spstr.Length; i += colsPerItem)
{
bool parseSuccess = true;
double hi = 0; double lo = 0; double fkpm;
if (!double.TryParse(spstr [i], out fkpm))
{
parseSuccess = false;
}
if (AppSettings.Loading.FKPM_FILE_HAS_HILO.Item)
{
int loIn = AppSettings.Loading.FKPM_TESTLO_COLUMN.Item;
int hiIn = AppSettings.Loading.FKPM_TESTHI_COLUMN.Item;
loIn = i + loIn - firstScore;
hiIn = i + hiIn - firstScore;
if (!double.TryParse(spstr [hiIn], out hi))
{
parseSuccess = false;
}
if (!double.TryParse(spstr [loIn], out lo))
{
parseSuccess = false;
}
}
if (AppSettings.Loading.FKPM_FILE_HAS_TESTOK.Item)
{
int textIn = AppSettings.Loading.FKPM_TESTOK_COLUMN.Item;
textIn = i + textIn - firstScore;
if (!spstr [textIn].Contains(AppSettings.Loading.FKPM_TESTOK_TEXT.Item))
{
parseSuccess = false;
}
}
int sampInd = i - 9;
if (i > 0)
{
sampInd++;
sampInd /= 4;
}
if (parseSuccess)
{
FKPM fk = new FKPM(fkpm, hi, lo, samps [sampInd]);
FKPMGene fkg = new FKPMGene(gen, fk);
AllFKPMS.Add(fkg);
}
}
}
}
}
}