//
public bool Detailed_checkObjList(List <Object> listObjs)
{
int ntelends = 0;
foreach (Object o in listObjs)
{
foreach (Free_end fe in o.md.f_e)
{
if (fe.FE_type == MetaData.FreeEndType.telomeric)
{
ntelends++;
}
}
}
if (ntelends != IntactHumanGenome.nObjs * 2)
{
return(false);
}
foreach (Object o in listObjs)
{
if (o.Length <= 0)
{
return(false);
}
}
int itemp = 0;
foreach (Object o in listObjs)
{
itemp += o.Length;
}
if (itemp != IntactHumanGenome.WholeGenome())
{
return(false);
}
foreach (Object o in listObjs)
{
if (o.md.f_e.Count < 2 && o.md.O_type != MetaData.ObjectType.ring)
{
return(false);
}
}
foreach (Object o in listObjs)
{
foreach (Band b in o.md.chromo_bands)
{
if (b.Size == 0)
{
MessageBox.Show("Band Of 0-size. Do something!");
}
}
}
return(true);
}
public DSBs(string s)
{
Random random = new Random();
for (int i = 0; i < 20; i++)
{
P = DSBcomplP[1];
double R = 6.0;
double lattice_dim = 0.02;
int rnucleus = Convert.ToInt32(R / lattice_dim);
Location l;
while (true)
{
l.X = random.Next(0, 2 * rnucleus) - rnucleus;
l.Y = random.Next(0, 2 * rnucleus) - rnucleus;
l.Z = random.Next(0, 2 * rnucleus) - rnucleus;
double a = 1.0 / 2.0, b = 1.0 / 2.0, c = 4.0; // nucleus parameters for elliptic nucleus // zzz GUI input
if (a * (l.X - rnucleus) * (l.X - rnucleus) + b * (l.Y - rnucleus) * (l.Y - rnucleus) + c * (l.Z - rnucleus) * (l.Z - rnucleus) < rnucleus * rnucleus) // elliptic nucleus
{
break;
}
}
DSBstruct random_DSB = new DSBstruct()
{
ndsb = i,
random_time = 0.0, // SimpleRNG.GetUniform(), // hrs
position = random.Next(0, IntactHumanGenome.WholeGenome()),
L = l
};
listDSBs.Add(random_DSB);
}
}
//
public bool CheckObjList(List <Object> listObjs)
{
int ntelends = 0;
foreach (Object o in listObjs)
{
foreach (Free_end fe in o.md.f_e)
{
if (fe.FE_type == MetaData.FreeEndType.telomeric)
{
ntelends++;
}
}
}
if (ntelends != IntactHumanGenome.nObjs * 2)
{
return(false);
}
foreach (Object o in listObjs)
{
if (o.Length <= 0)
{
return(false);
}
foreach (Band b in o.md.chromo_bands)
{
if (b.Downstream_end_position >= b.Upstream_end_position)
{
return(false);
}
}
}
int itemp = 0;
foreach (Object o in listObjs)
{
itemp += o.Length;
}
if (itemp != IntactHumanGenome.WholeGenome())
{
return(false);
}
return(true);
}
public static void DoWork()
{
RandomWalk rw = new RandomWalk();
int nmonomers = IntactHumanGenome.WholeGenome();
rw.LL = new Location[nmonomers];
rw.nmonomer = new int[nmonomers];
Random random = new Random();
int rnucleus = Convert.ToInt32(R / lattice_dim);
int j = 0;
for (int chn = nThread * IntactHumanGenome.nObjs / nThreads; chn < (nThread + 1) * IntactHumanGenome.nObjs / nThreads; chn++)
{
while (true)
{
rw.LL[j].X = random.Next(0, 2 * rnucleus) - rnucleus; // RW random origin
rw.LL[j].Y = random.Next(0, 2 * rnucleus) - rnucleus;
rw.LL[j].Z = random.Next(0, 2 * rnucleus) - rnucleus;
if (InsideEllipsoid(rw.LL[j]))
{
break;
}
} // zzz666 these RWs don't have loops or domains yet
rw.nmonomer[j] = j;
j++;
for (int i = 0; i < Convert.ToInt32(IntactHumanGenome.NC[chn] / IntactHumanGenome.monomerSize) - 1; i++)
{
Location l_temp;
switch (random.Next(0, 3))
{
case 0:
{
l_temp.X = rw.LL[j - 1].X + (2 * random.Next(0, 2) - 1);
l_temp.Y = rw.LL[j - 1].Y;
l_temp.Z = rw.LL[j - 1].Z;
if (InsideEllipsoid(l_temp))
{
rw.LL[j] = l_temp;
}
}
break;
case 1:
{
l_temp.X = rw.LL[j - 1].X;
l_temp.Y = rw.LL[j - 1].Y + (2 * random.Next(0, 2) - 1);
l_temp.Z = rw.LL[j - 1].Z;
if (InsideEllipsoid(l_temp))
{
rw.LL[j] = l_temp;
}
}
break;
case 2:
{
l_temp.X = rw.LL[j - 1].X;
l_temp.Y = rw.LL[j - 1].Y;
l_temp.Z = rw.LL[j - 1].Z + (2 * random.Next(0, 2) - 1);
if (InsideEllipsoid(l_temp))
{
rw.LL[j] = l_temp;
}
}
break;
default:
break;
}
rw.nmonomer[j] = j;
j++;
}
}
ApplyRad2RWs(rs, rw, DSBdata); // collect all sets of DSBs and put them into a list
}
//
public bool PrepairDSBpositionsInGenome(RadiationSchema rs, DSBs DSBdata)
{
bool bParallel = false; // zzz666
try
{
RandomWalk rw = new RandomWalk();
int nmonomers = IntactHumanGenome.WholeGenome();
rw.LL = new Location[nmonomers];
rw.nmonomer = new int[nmonomers];
Random random = new Random();
int rnucleus = Convert.ToInt32(R / lattice_dim);
int j = 0;
if (!bParallel)
{
for (int chn = 0; chn < IntactHumanGenome.nObjs; chn++) // zzz666 split these into subtasks
{
while (true)
{
rw.LL[j].X = random.Next(0, 2 * rnucleus) - rnucleus; // RW random origin
rw.LL[j].Y = random.Next(0, 2 * rnucleus) - rnucleus;
rw.LL[j].Z = random.Next(0, 2 * rnucleus) - rnucleus;
if (InsideEllipsoid(rw.LL[j]))
{
break;
}
} // zzz666 these RWs don't have loops or domains yet
rw.nmonomer[j] = j;
j++;
for (int i = 0; i < Convert.ToInt32(IntactHumanGenome.NC[chn] / IntactHumanGenome.monomerSize) - 1; i++)
{
Location l_temp;
switch (random.Next(0, 3))
{
case 0:
{
l_temp.X = rw.LL[j - 1].X + (2 * random.Next(0, 2) - 1);
l_temp.Y = rw.LL[j - 1].Y;
l_temp.Z = rw.LL[j - 1].Z;
if (InsideEllipsoid(l_temp))
{
rw.LL[j] = l_temp;
}
}
break;
case 1:
{
l_temp.X = rw.LL[j - 1].X;
l_temp.Y = rw.LL[j - 1].Y + (2 * random.Next(0, 2) - 1);
l_temp.Z = rw.LL[j - 1].Z;
if (InsideEllipsoid(l_temp))
{
rw.LL[j] = l_temp;
}
}
break;
case 2:
{
l_temp.X = rw.LL[j - 1].X;
l_temp.Y = rw.LL[j - 1].Y;
l_temp.Z = rw.LL[j - 1].Z + (2 * random.Next(0, 2) - 1);
if (InsideEllipsoid(l_temp))
{
rw.LL[j] = l_temp;
}
}
break;
default:
break;
}
rw.nmonomer[j] = j;
j++;
}
}
if (ApplyRad2RWs(rs, rw, DSBdata)) // collect all sets of DSBs and put them into a list
{
return(true);
}
else
{
return(false);
}
}
else
{
//foreach (var item in new ManagementObjectSearcher("Select * from Win32_ComputerSystem").Get())
//{
// Console.WriteLine("Number Of Physical Processors: {0} ", item["NumberOfProcessors"]);
//}
int coreCount = 0;
foreach (var item in new ManagementObjectSearcher("Select * from Win32_Processor").Get())
{
coreCount += int.Parse(item["NumberOfCores"].ToString());
}
//Console.WriteLine("Number Of Cores: {0}", coreCount);
//Console.WriteLine("Number Of Logical Processors: {0}", Environment.ProcessorCount);
int processorCount = Environment.ProcessorCount;
int logicalprocessorCount = 0;
foreach (var item in new ManagementObjectSearcher("Select * from Win32_ComputerSystem").Get())
{
//Console.WriteLine("Number Of Logical Processors: {0}", item["NumberOfLogicalProcessors"]);
logicalprocessorCount += int.Parse(item["NumberOfLogicalProcessors"].ToString());
}
int nThreads = coreCount; // zzz ? or logicalprocessorCount?
Thread[] oThread = null;
for (thread = 0; thread < nThreads; thread++)
{
Work w = new Work(thread, nThreads, rs, DSBdata);
ThreadStart threadDelegate = new ThreadStart(Work.DoWork);
oThread[thread] = new Thread(threadDelegate);
oThread[thread].Start();
}
}
return(true);
// zzz666 run subtask all the way here, so that every CPU would produce DSBdata for each own RW, which has 46/nCPU chromosomes; meaure time with and w/o parallelization
}
catch { return(false); }
}
public Object(int chromonumber) // obj = intact chromo
{
try
{
Length = Convert.ToInt32(IntactHumanGenome.NC[chromonumber] / IntactHumanGenome.monomerSize);
md = new MetaData();
int itemp = Convert.ToInt32(IntactHumanGenome.CM[0] / IntactHumanGenome.monomerSize);
for (int i = 0; i < chromonumber; i++)
{
itemp += Convert.ToInt32(IntactHumanGenome.CM[chromonumber] / IntactHumanGenome.monomerSize);
}
md.c_l.Add(new Centromere()
{
Position = itemp, Relative_position = PositionWithRespectToReferencePoint.not_known
});
md.f_e.Add(new Free_end()
{
Position = Convert.ToInt32(IntactHumanGenome.DownstreamEndPosition(chromonumber) / IntactHumanGenome.monomerSize),
FE_type = MetaData.FreeEndType.telomeric,
Reacting = false,
Relative_position = PositionWithRespectToReferencePoint.not_known // TBD later
// relative_location has to be defined with respect to some point of reference, like a DSB; this var. will used later in the algo
});
md.f_e.Add(new Free_end()
{
Position = Convert.ToInt32(IntactHumanGenome.DownstreamEndPosition(chromonumber) / IntactHumanGenome.monomerSize) + Length,
FE_type = MetaData.FreeEndType.telomeric,
Reacting = false,
Relative_position = PositionWithRespectToReferencePoint.not_known
// relative_location has to be defined with respect to some point of reference, like a DSB, or a CM; this var. will used later in the algo
});
md.O_type = MetaData.ObjectType.intact_chromo;
md.chromo_bands.AddLast(new Band()
{
Size = Length,
Position_within_object = 0,
Chromo_num = chromonumber,
Downstream_end_position = md.f_e[0].Position,
Upstream_end_position = md.f_e[1].Position
});
NumberOfBands = md.chromo_bands.Count;
foreach (Band b in md.chromo_bands)
{
switch (chromonumber)
{
case (1 - 1):
case (2 - 1):
{
b.Color = System.Drawing.Color.Red;
}
break;
case (3 - 1):
case (4 - 1):
{
b.Color = System.Drawing.Color.Green;
}
break;
case (7 - 1):
case (8 - 1):
{
b.Color = System.Drawing.Color.Yellow;
}
break;
default:
{
b.Color = System.Drawing.Color.DarkBlue;
}
break;
}
}
}
catch
{
md = null; // if normal object definition is not possible, the MetaData are null
}
}
