static void Main()
{
//Problem 1. Point3D
Console.WriteLine("Problem 1. Point3D");
Console.WriteLine("--------------------");
Point p1 = new Point(1, 2, 3);
Point p2 = new Point(3.4, 4.66, 5.55);
Console.WriteLine(p1);
Console.WriteLine(p2);
Console.WriteLine(Point.StartPoint);
Console.WriteLine();
//Problem 2. Distance Calculator
Console.WriteLine("Problem 2. Distance Calculator");
Console.WriteLine("-------------------------------");
double distance = DistanceCalculator.CalculateDistance(p1, p2);
Console.WriteLine(distance);
Console.WriteLine();
//Problem 3. Paths
Console.WriteLine("Problem 3. Paths");
Console.WriteLine("-------------------------------");
Path path = new Path(p1, p2, Point.StartPoint);
Console.WriteLine("Save path: {0}", path);
Storage.SavePathInFile("path.txt", path);
Path loadPath = Storage.LoadPathOfFile("path.txt");
Console.WriteLine("Load path: {0}", loadPath);
}
static void Main()
{
Point3D firstPoint = new Point3D("First Point", -7, -4, 3);
Point3D secondPoint = new Point3D("Second Point", 17, 6, 2.5);
Console.WriteLine("The distance between the two points is : {0}", DistanceCalculator.CalculateDistance(firstPoint, secondPoint));
}
static void Main()
{
Point3D a = new Point3D(-7, -4, 3);
Point3D b = new Point3D(17, 6, 2.5);
Console.WriteLine(DistanceCalculator.CalculateDistance(a, b));
}
public static void Main(string[] args)
{
Console.WriteLine("Hello World!");
// generateLocations();
// generateRelations();
var pointRelationships = JsonSerializer.Deserialize <IReadOnlyList <PointRelationship> >(File.ReadAllText(pointRelationshipPath));
var nodeConnector = new NodeConnector();
var sw = new Stopwatch();
Console.WriteLine("connect start");
sw.Start();
var pointNodes = nodeConnector.Connect(pointRelationships);
sw.Stop();
Console.WriteLine($"connect stop: {sw.ElapsedMilliseconds}");
var distanceCalculator = new DistanceCalculator();
string source = "1520000";
string target = "2610012";
Console.WriteLine("calculate start");
sw.Reset();
sw.Start();
Console.WriteLine($"{source}~{target}: {distanceCalculator.CalculateDistance(pointNodes, source, target)}m");
sw.Stop();
Console.WriteLine($"calculate stop: {sw.ElapsedMilliseconds}");
}
private static void Main()
{
Console.WriteLine("Problem 1. Point3D");
Point3D p1 = new Point3D(1, 2, 3);
Point3D p2 = new Point3D(3.4, 4.66, 5.55);
Console.WriteLine(p1);
Console.WriteLine(p2);
Console.WriteLine(Point3D.StartPoint);
Console.WriteLine();
Console.WriteLine("Problem 2. Distance Calculator");
double distance = DistanceCalculator.CalculateDistance(p1, p2);
Console.WriteLine(distance);
Console.WriteLine();
Console.WriteLine("Problem 3. Paths3D");
Path3D path = new Path3D(p1, p2, Point3D.StartPoint);
Console.WriteLine("Save path: {0}", path);
Storage.SavePathInFile("path.txt", path);
Path3D loadPath = Storage.LoadPathOfFile("path.txt");
Console.WriteLine("Load path: {0}", loadPath);
}
public void DistanceCalculationwithTwoContigs()
{
const int KmerLength = 6;
IList <ISequence> sequences = new List <ISequence>()
{
new Sequence(Alphabets.DNA, "GATCTGATAA")
{
ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor substrate 1 (IRS1) on chromosome 2.X1:0.5K"
},
new Sequence(Alphabets.DNA, "ATCTGATAAG")
{
ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor on chromosome 2.F:0.5K"
},
new Sequence(Alphabets.DNA, "TCTGATAAGG")
{
ID = ">gi|263191773|ref | H**o sapiens ........insulin receptor on chromosome 2.2:0.5K"
},
new Sequence(Alphabets.DNA, "TTTTTGATGG")
{
ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor substrate 1 (IRS1) on chromosome 2.Y1:0.5K"
},
new Sequence(Alphabets.DNA, "TTTTGATGGC")
{
ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor on chromosome 2.R:0.5K"
},
new Sequence(Alphabets.DNA, "TTTGATGGCA")
{
ID = ">gi|263191773|ref | H**o sapiens ........insulin receptor on chromosome 2.1:0.5K"
}
};
IList <ISequence> contigs = new List <ISequence> {
new Sequence(Alphabets.DNA, "GATCTGATAAGG"),
new Sequence(Alphabets.DNA, "TTTTTGATGGCA")
};
ReadContigMapper mapper = new ReadContigMapper();
ReadContigMap maps = mapper.Map(contigs, sequences, KmerLength);
MatePairMapper mapPairedReads = new MatePairMapper();
ContigMatePairs pairs = mapPairedReads.MapContigToMatePairs(sequences, maps);
OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter();
ContigMatePairs contigpairedReads = filter.FilterPairedReads(pairs);
DistanceCalculator calc = new DistanceCalculator(contigpairedReads);
contigpairedReads = calc.CalculateDistance();
Assert.AreEqual(contigpairedReads.Values.Count, 1);
Assert.IsTrue(contigpairedReads.ContainsKey(contigs[0]));
Dictionary <ISequence, IList <ValidMatePair> > map = contigpairedReads[contigs[0]];
Assert.IsTrue(map.ContainsKey(contigs[1]));
IList <ValidMatePair> valid = map[contigs[1]];
Assert.AreEqual(valid.First().DistanceBetweenContigs[0], (float)478.000031);
Assert.AreEqual(valid.First().DistanceBetweenContigs[1], (float)477.0);
Assert.AreEqual(valid.First().StandardDeviation[0], (float)14.1421356);
Assert.AreEqual(valid.First().StandardDeviation[1], (float)14.1421356);
Assert.AreEqual(valid.First().Weight, 2);
}
public void DistanceCalculationwithTwoContigsWeightedMean()
{
const int KmerLength = 6;
List <ISequence> sequences = new List <ISequence>();
Sequence seq = new Sequence(Alphabets.DNA, "GATCTGATAA".Select(a => (byte)a).ToArray());
seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor"
+ "substrate 1 (IRS1) on chromosome 2.x1:2K";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "ATCTGATAAG".Select(a => (byte)a).ToArray());
seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor"
+ "on chromosome 2.f:0.5K";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "TCTGATAAGG".Select(a => (byte)a).ToArray());
seq.ID = ">gi|263191773|ref | H**o sapiens ........insulin receptor"
+ "on chromosome 2.2:0.5K";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "TTTTTGATGG".Select(a => (byte)a).ToArray());
seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor"
+ "substrate 1 (IRS1) on chromosome 2.y1:2K";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "TTTTGATGGC".Select(a => (byte)a).ToArray());
seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor"
+ "on chromosome 2.r:0.5K";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "TTTGATGGCA".Select(a => (byte)a).ToArray());
seq.ID = ">gi|263191773|ref | H**o sapiens ........insulin receptor"
+ "on chromosome 2.1:0.5K";
sequences.Add(seq);
IList <ISequence> contigs = new List <ISequence> {
new Sequence(Alphabets.DNA, "GATCTGATAAGG".Select(a => (byte)a).ToArray()),
new Sequence(Alphabets.DNA, "TTTTTGATGGCA".Select(a => (byte)a).ToArray())
};
ReadContigMapper mapper = new ReadContigMapper();
ReadContigMap maps = mapper.Map(contigs, sequences, KmerLength);
MatePairMapper mapPairedReads = new MatePairMapper();
ContigMatePairs pairedReads = mapPairedReads.MapContigToMatePairs(sequences, maps);
OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter();
ContigMatePairs contigpairedReads = filter.FilterPairedReads(pairedReads);
DistanceCalculator calc = new DistanceCalculator(contigpairedReads);
contigpairedReads = calc.CalculateDistance();
Assert.AreEqual(contigpairedReads.Values.Count, 1);
Assert.IsTrue(contigpairedReads.ContainsKey(contigs[0]));
Dictionary <ISequence, IList <ValidMatePair> > map = contigpairedReads[contigs[0]];
Assert.IsTrue(map.ContainsKey(contigs[1]));
IList <ValidMatePair> valid = map[contigs[1]];
Assert.AreEqual(valid.First().DistanceBetweenContigs[0], (float)1228.0);
Assert.AreEqual(valid.First().DistanceBetweenContigs[1], (float)1227.0);
Assert.AreEqual(valid.First().StandardDeviation[0], (float)60);
Assert.AreEqual(valid.First().StandardDeviation[1], (float)60);
Assert.AreEqual(valid.First().Weight, 2);
}
public double CalculateDistance(List <Point3D> listOfPoints)
{
double result = 0;
for (int i = 0; i < listOfPoints.Count - 1; i++)
{
result += DistanceCalculator.CalculateDistance(listOfPoints[i], listOfPoints[i + 1]);
}
return(result);
}
public void CalculateDistanceTest()
{
DistanceCalculator target = new DistanceCalculator(); // TODO: Initialize to an appropriate value
double time = 5; // TODO: Initialize to an appropriate value
double speed = 6; // TODO: Initialize to an appropriate value
double expected = 30; // TODO: Initialize to an appropriate value
double actual;
actual = target.CalculateDistance(time, speed);
Assert.AreEqual(expected, actual);
//Assert.Inconclusive("Verify the correctness of this test method.");
}
public void CalculateDistanceForLeg()
{
var locations = new LocationRepository().GetAll();
var hookNorton = locations.First(l => l.Name.StartsWith("Hook Norton"));
var theBridge = locations.First(l => l.Name.StartsWith("The Bridge"));
var dist = DistanceCalculator.CalculateDistance(hookNorton, theBridge);
dist.Should().BeApproximately(144.738, 0.1);
}
public void CalculateDistanceTest()
{
DistanceCalculator target = new DistanceCalculator(); // TODO: Initialize to an appropriate value
double time = 5; // TODO: Initialize to an appropriate value
double speed = 6; // TODO: Initialize to an appropriate value
double expected = 30; // TODO: Initialize to an appropriate value
double actual;
actual = target.CalculateDistance(time, speed);
Assert.AreEqual(expected, actual);
//Assert.Inconclusive("Verify the correctness of this test method.");
}
static void Main()
{
Console.WriteLine(Point3D.StartingPoint);
Console.WriteLine();
var point_1 = new Point3D(2, 4, 6);
var point_2 = new Point3D(1, 6, 4);
double distace = DistanceCalculator.CalculateDistance(point_1, point_2);
Console.WriteLine(distace);
}
public void Should_Correctly_Generate_Distance()
{
// verified manually first using an online distance calculator -> https://www.vcalc.com/wiki/vCalc/Haversine+-+Distance
var latFrom = 53.339428;
var longFrom = -6.257664;
Assert.Equal(42, DistanceCalculator.CalculateDistance(latFrom, longFrom, 52.986375, -6.043701));
Assert.Equal(313, DistanceCalculator.CalculateDistance(latFrom, longFrom, 51.92893, -10.27699));
Assert.Equal(302, DistanceCalculator.CalculateDistance(latFrom, longFrom, 52.3191841, -10.4240951));
Assert.Equal(222, DistanceCalculator.CalculateDistance(latFrom, longFrom, 51.8856167, -8.5072391));
Assert.Equal(109, DistanceCalculator.CalculateDistance(latFrom, longFrom, 53.807778, -7.714444));
}
public void DistanceCalculation()
{
var termWeightRepresentation = new Mock<ITermWeightRepresentation>();
termWeightRepresentation.Setup(x => x.TermWeight(It.Is<string>(y => y == "bee"))).Returns(0.91629);
termWeightRepresentation.Setup(x => x.TermWeight(It.Is<string>(y => y == "wasp"))).Returns(0.91629);
termWeightRepresentation.Setup(x => x.TermWeight(It.Is<string>(y => y == "fly"))).Returns(0.22314);
var termsCollection = new TermsCollection(new[] {"bee", "wasp", "fly", "fruit", "like"});
var distanceCalculator = new DistanceCalculator();
double actualDistance = distanceCalculator.CalculateDistance(termWeightRepresentation.Object,
termsCollection);
Assert.AreEqual(1.314903211, actualDistance, 0.0001);
}
protected void btnCalculate_Click(object sender, EventArgs e)
{
try
{
DistanceCalculator distanceCalculator = new DistanceCalculator();
lblDistance.Text = distanceCalculator.CalculateDistance
(Convert.ToDouble(txtTime.Text),
Convert.ToDouble(txtSpeed.Text)).ToString();
}
catch (Exception ex)
{
lblDistance.Text = ex.Message;
}
}
private void GenerateRecsForNodeArray()
{
List <Node> nodes = new List <Node>();
MemoryTree.ToList(nodes);
nodes = nodes.Except(CurrentUser.NotShow).Except(CurrentUser.Favourite).ToList();
foreach (Node node in nodes)
{
node.Distance = 0.0;
foreach (Node n in CurrentUser.Favourite)
{
DistanceCalculator calculator = new DistanceCalculator(node, n);
node.Distance += calculator.CalculateDistance((MeasureType)MeasureTypeIndex);
}
node.Distance /= (double)CurrentUser.Favourite.Count();
}
nodes.Sort(delegate(Node node1, Node node2)
{
if (node1 == null && node2 == null)
{
return(0);
}
if (node1 == null)
{
return(-1);
}
if (node2 == null)
{
return(1);
}
if (node1.Distance == node2.Distance)
{
return(0);
}
if (node1.Distance > node2.Distance)
{
return(1);
}
return(-1);
});
Recommendations = new ObservableCollection <Node>(nodes.Take(UsersCount));
AddRecommendationsToItems();
}
protected void btnCalculate_Click(object sender, EventArgs e)
{
try
{
DistanceCalculator distanceCalculator = new DistanceCalculator();
lblDistance.Text = distanceCalculator.CalculateDistance
(Convert.ToDouble(txtTime.Text),
Convert.ToDouble(txtSpeed.Text)).ToString();
}
catch (Exception ex)
{
lblDistance.Text = ex.Message;
}
}
private IEnumerable <Node> GenerateRecsForNodeArray()
{
var nodes = new List <Node>();
MemoryTree.ToList(nodes);
nodes = nodes.Except(CurrentUser.NotShow).Except(CurrentUser.Favourite).ToList();
foreach (var node in nodes)
{
node.Distance = 0.0;
foreach (var n in CurrentUser.Favourite)
{
var calculator = new DistanceCalculator(node, n);
node.Distance += calculator.CalculateDistance((MeasureType)MeasureTypeIndex);
}
node.Distance /= (double)CurrentUser.Favourite.Count();
}
nodes.Sort(delegate(Node node1, Node node2)
{
if (node1 == null && node2 == null)
{
return(0);
}
if (node1 == null)
{
return(-1);
}
if (node2 == null)
{
return(1);
}
if (node1.Distance == node2.Distance)
{
return(0);
}
if (node1.Distance > node2.Distance)
{
return(1);
}
return(-1);
});
return(nodes);
}
static void Main(string[] args)
{
Console.WriteLine("Day1 Star1");
FuelRequirementsCalculator fuelRequirementsCalculator = new FuelRequirementsCalculator();
Console.WriteLine($"Result: {fuelRequirementsCalculator.CalculateTotalFuelRequirements(InputReader.InputReader.ReadDay1Input())}");
Console.WriteLine();
Console.WriteLine("Day1 Star2");
Day1.Star2.FuelRequirementsCalculator fuelRequirementsCalculator2 = new Day1.Star2.FuelRequirementsCalculator();
Console.WriteLine($"Result: {fuelRequirementsCalculator2.CalculateTotalFuelRequirements(InputReader.InputReader.ReadDay1Input())}");
Console.WriteLine();
Console.WriteLine("Day 2 Star1");
IntCodeComputer intCodeComputer = new IntCodeComputer();
Console.WriteLine($"Result {intCodeComputer.Process(InputReader.InputReader.ReadDay2Input())}");
Console.WriteLine();
Console.WriteLine("Day 2 Star2");
Day2.Star2.IntCodeComputer intCodeComputer2 = new Day2.Star2.IntCodeComputer();
Console.WriteLine($"Result: {intCodeComputer2.FindInputsToProduceValue(InputReader.InputReader.ReadDay2Input(), 19690720)}");
Console.WriteLine();
Console.WriteLine("Day3 Star1");
DistanceCalculator distanceCalculator = new DistanceCalculator();
Console.WriteLine($"Result {distanceCalculator.CalculateDistance(InputReader.InputReader.ReadDay3Input())}");
Console.WriteLine();
Console.WriteLine("Day3 Star2");
Day3.Star2.DistanceCalculator distanceCalculator2 = new Day3.Star2.DistanceCalculator();
Console.WriteLine($"Result {distanceCalculator2.CalculateDistance(InputReader.InputReader.ReadDay3SmallInput())}");
Console.WriteLine();
Console.WriteLine("Day4 Star1");
PasswordFinder passwordFinder = new PasswordFinder();
Console.WriteLine($"Result: {passwordFinder.FindPossiblePasswords(145852, 616942).Count()}");
Console.WriteLine();
Console.WriteLine("Day4 Star2");
Day4.Star2.PasswordFinder passwordFinder2 = new Day4.Star2.PasswordFinder();
Console.WriteLine($"Result {passwordFinder2.FindPossiblePasswords(145852, 616942).Count()}");
}
static void Main()
{
Console.WriteLine("Please enter coordinates of the first point separated by space:");
string coordinates = Console.ReadLine();
string[] tempString = coordinates.Split(' ');
double x1 = double.Parse(tempString[0]);
double y1 = double.Parse(tempString[1]);
double z1 = double.Parse(tempString[2]);
Console.WriteLine("Please enter coordinates of the second point separated by space:");
coordinates = Console.ReadLine();
tempString = coordinates.Split(' ');
double x2 = double.Parse(tempString[0]);
double y2 = double.Parse(tempString[1]);
double z2 = double.Parse(tempString[2]);
Console.WriteLine(DistanceCalculator.CalculateDistance(x1, y1, z1, x2, y2, z2));
}
private void GenerateRecsForSingleNode(Node node)
{
List <Node> nodes = new List <Node>();
MemoryTree.ToList(nodes);
nodes = nodes.Except(CurrentUser.NotShow).Except(new[] { node }).ToList();
foreach (Node n in nodes)
{
DistanceCalculator calculator = new DistanceCalculator(node, n);
n.Distance = calculator.CalculateDistance((MeasureType)MeasureTypeIndex);
}
nodes.Sort(delegate(Node node1, Node node2)
{
if (node1 == null && node2 == null)
{
return(0);
}
if (node1 == null)
{
return(-1);
}
if (node2 == null)
{
return(1);
}
if (node1.Distance == node2.Distance)
{
return(0);
}
if (node1.Distance > node2.Distance)
{
return(1);
}
return(-1);
});
Recommendations = new ObservableCollection <Node>(nodes.Take(RecsLength));
AddRecommendationsToItems();
}
private IEnumerable <Node> GenerateRecsForSingleNode(Node node)
{
var nodes = new List <Node>();
MemoryTree.ToList(nodes);
nodes = nodes.Except(CurrentUser.NotShow).Except(new[] { node }).ToList();
foreach (var n in nodes)
{
var calculator = new DistanceCalculator(node, n);
n.Distance = calculator.CalculateDistance((MeasureType)MeasureTypeIndex);
}
nodes.Sort(delegate(Node node1, Node node2)
{
if (node1 == null && node2 == null)
{
return(0);
}
if (node1 == null)
{
return(-1);
}
if (node2 == null)
{
return(1);
}
if (node1.Distance == node2.Distance)
{
return(0);
}
if (node1.Distance > node2.Distance)
{
return(1);
}
return(-1);
});
return(nodes);
}
public override void Train(TrainingParameters parameters)
{
SomTrainingParameters p = (SomTrainingParameters)parameters;
try
{
parameters.Validate();
}
catch (TrainingParametersException e)
{
throw new SomLogicalException($"Improper training parameters. {e.Message}");
}
var trainingData = p.TrainingData;
var iterations = p.NumberOfIterations;
var neighborhoodFunction = p.NeighbourhoodFunction;
var learningRate = p.LearningRate;
var tiredness = p.TirednessMechanism;
if (trainingData.First().Count != Dimensions)
{
throw new SomLogicalException("Training data points dimensions doesn't match som dimensions.");
}
tiredness?.Initialize(Neurons);
Observer?.SaveState(Neurons);
int numberOfShuffles = (iterations / trainingData.Count) + 1;
for (int j = 0; j < numberOfShuffles; j++)
{
var shuffled = trainingData.Shuffle();
for (int i = 0; i < shuffled.Count; i++)
{
if (j * shuffled.Count + i == iterations)
{
return;
}
Dictionary <Neuron, double> neuronsDistances = new Dictionary <Neuron, double>();
for (int k = 0; k < Neurons.Count; k++)
{
//store neurons with their distances
neuronsDistances.Add(Neurons[k],
DistanceCalculator.CalculateDistance(shuffled[i], Neurons[k].CurrentWeights));
}
var potentialWinners = tiredness == null ? Neurons : tiredness.SelectPotentialWinners(Neurons);
Neuron winner = neuronsDistances.Where(pair => potentialWinners.Contains(pair.Key))
.OrderBy(pair => pair.Value).First().Key;
tiredness?.Update(winner, Neurons);
var neuronsNeighbourhoodCoefficients =
neighborhoodFunction.CalculateNeighborhoodValues(winner, neuronsDistances, DistanceCalculator,
j * trainingData.Count + i);
foreach (var neuron in Neurons)
{
var diffVec = shuffled[i].Subtract(neuron.CurrentWeights);
var deltaWeight = diffVec.Multiply(learningRate.GetValue(j * trainingData.Count + i) *
neuronsNeighbourhoodCoefficients[neuron]);
neuron.CurrentWeights = neuron.CurrentWeights + deltaWeight;
}
Observer?.SaveState(Neurons);
}
}
}
public override void Train(TrainingParameters parameters)
{
KMeansTrainingParameters p = (KMeansTrainingParameters)parameters;
try
{
p.Validate();
}
catch (TrainingParametersException e)
{
throw new SomLogicalException($"Improper training parameters. {e.Message}");
}
var trainingData = parameters.TrainingData;
var epochs = p.Epochs;
if (trainingData.First().Count != Dimensions)
{
throw new SomLogicalException("Training data points dimensions doesn't match som dimensions.");
}
Observer?.SaveState(Neurons);
bool end = false;
for (int j = 0; j < epochs && !end; j++)
{
var shuffled = trainingData.Shuffle();
Dictionary <Neuron, List <Vector <double> > > neuronsZones = new Dictionary <Neuron, List <Vector <double> > >();
foreach (var neuron in Neurons)
{
neuronsZones.Add(neuron, new List <Vector <double> >());
}
for (int i = 0; i < shuffled.Count; i++)
{
Dictionary <Neuron, double> neuronsDistances = new Dictionary <Neuron, double>();
for (int k = 0; k < Neurons.Count; k++)
{
//store neurons with their distances
neuronsDistances.Add(Neurons[k],
DistanceCalculator.CalculateDistance(shuffled[i], Neurons[k].CurrentWeights));
}
Neuron winner = neuronsDistances.OrderBy(pair => pair.Value).First().Key;
neuronsZones[winner].Add(shuffled[i]);
}
var aggregate = Vector <double> .Build.DenseOfEnumerable(new List <double>(new double[Dimensions]));
end = true;
foreach (var pair in neuronsZones)
{
foreach (var vec in pair.Value)
{
aggregate = aggregate.Add(vec);
}
if (pair.Value.Count != 0)
{
aggregate = aggregate.Divide(pair.Value.Count);
var diff = aggregate.Subtract(pair.Key.CurrentWeights).Map(Math.Abs).Sum();
if (end && diff > 0.0001)
{
end = false;
}
pair.Key.CurrentWeights = aggregate;
}
}
Observer?.SaveState(Neurons);
}
}
public void CalculateDistance_CalculatingDistance_DistanceIsCorrect(double x1, double x2, double y1, double y2, double distance)
{
Assert.That(_uut.CalculateDistance(x1, x2, y1, y2), Is.EqualTo(distance).Within(0.5));
}
public void TracePathTestWithPalindromicContig()
{
const int kmerLength = 6;
const int dangleThreshold = 3;
const int redundantThreshold = 7;
List <ISequence> sequences = new List <ISequence>();
Sequence seq = new Sequence(Alphabets.DNA, "ATGCCTC");
seq.DisplayID = ">10.x1:abc";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "CCTCCTAT");
seq.DisplayID = "1";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "TCCTATC");
seq.DisplayID = "2";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "TGCCTCCT");
seq.DisplayID = "3";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "ATCTTAGC");
seq.DisplayID = "4";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "CTATCTTAG");
seq.DisplayID = "5";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "CTTAGCG");
seq.DisplayID = "6";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "GCCTCCTAT");
seq.DisplayID = ">8.x1:abc";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "TAGCGCGCTA");
seq.DisplayID = ">8.y1:abc";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "AGCGCGC");
seq.DisplayID = ">9.x1:abc";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "TTTTTT");
seq.DisplayID = "7";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "TTTTTAAA");
seq.DisplayID = "8";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "TAAAAA");
seq.DisplayID = "9";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "TTTTAG");
seq.DisplayID = "10";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "TTTAGC");
seq.DisplayID = "11";
sequences.Add(seq);
seq = new Sequence(Alphabets.DNA, "GCGCGCCGCGCG");
seq.DisplayID = "12";
sequences.Add(seq);
KmerLength = kmerLength;
SequenceReads.Clear();
AddSequenceReads(sequences);
CreateGraph();
DanglingLinksThreshold = dangleThreshold;
DanglingLinksPurger = new DanglingLinksPurger(dangleThreshold);
RedundantPathLengthThreshold = redundantThreshold;
RedundantPathsPurger = new RedundantPathsPurger(redundantThreshold);
UnDangleGraph();
RemoveRedundancy();
IList <ISequence> contigs = BuildContigs();
ReadContigMapper mapper = new ReadContigMapper();
ReadContigMap maps = mapper.Map(contigs, sequences, kmerLength);
MatePairMapper builder = new MatePairMapper();
CloneLibrary.Instance.AddLibrary("abc", (float)5, (float)15);
ContigMatePairs pairedReads = builder.MapContigToMatePairs(sequences, maps);
ContigMatePairs overlap;
OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter();
overlap = filter.FilterPairedReads(pairedReads, 0);
DistanceCalculator dist = new DistanceCalculator();
dist.CalculateDistance(overlap);
Graph.BuildContigGraph(contigs, this.KmerLength);
TracePath path = new TracePath();
IList <ScaffoldPath> paths = path.FindPaths(Graph, overlap, kmerLength, 3);
Assert.AreEqual(paths.Count, 3);
Assert.AreEqual(paths.First().Count, 3);
ScaffoldPath scaffold = paths.First();
DeBruijnGraph graph = Graph;
Assert.IsTrue(graph.GetNodeSequence(scaffold[0].Key).ToString().Equals("ATGCCTCCTATCTTAGC"));
Assert.IsTrue(graph.GetNodeSequence(scaffold[1].Key).ToString().Equals("TTAGCGCG"));
Assert.IsTrue(graph.GetNodeSequence(scaffold[2].Key).ToString().Equals("GCGCGC"));
}
//CALCULA LA DISTANCIA CON 6 PUNTOS DADOS PARA QUE COJA UN CAMINO CORRECTO ANTES DE IR HACIA CASA DE ROSITA
void CalculateDistance()
{
dateRositaRoutine = distanceCalculatorScript.CalculateDistance(auxiliarPoints);
specialRoutines[0] = dateRositaRoutine;
}
public void TracePathTestWithPalindromicContig()
{
const int kmerLengthConst = 5;
const int dangleThreshold = 3;
const int redundantThreshold = 6;
var sequences = new List <ISequence>()
{
new Sequence(Alphabets.DNA, "ATGCCTC")
{
ID = "0"
},
new Sequence(Alphabets.DNA, "CCTCCTAT")
{
ID = "1"
},
new Sequence(Alphabets.DNA, "TCCTATC")
{
ID = "2"
},
new Sequence(Alphabets.DNA, "TGCCTCCT")
{
ID = "3"
},
new Sequence(Alphabets.DNA, "ATCTTAGC")
{
ID = "4"
},
new Sequence(Alphabets.DNA, "CTATCTTAG")
{
ID = "5"
},
new Sequence(Alphabets.DNA, "CTTAGCG")
{
ID = "6"
},
new Sequence(Alphabets.DNA, "GCCTCCTAT")
{
ID = "7"
},
new Sequence(Alphabets.DNA, "TAGCGCGCTA")
{
ID = "8"
},
new Sequence(Alphabets.DNA, "AGCGCGC")
{
ID = "9"
},
new Sequence(Alphabets.DNA, "TTTTTT")
{
ID = "10"
},
new Sequence(Alphabets.DNA, "TTTTTAAA")
{
ID = "11"
},
new Sequence(Alphabets.DNA, "TAAAAA")
{
ID = "12"
},
new Sequence(Alphabets.DNA, "TTTTAG")
{
ID = "13"
},
new Sequence(Alphabets.DNA, "TTTAGC")
{
ID = "14"
},
new Sequence(Alphabets.DNA, "GCGCGCCGCGCG")
{
ID = "15"
},
};
KmerLength = kmerLengthConst;
SequenceReads.Clear();
SetSequenceReads(sequences);
CreateGraph();
DanglingLinksThreshold = dangleThreshold;
DanglingLinksPurger = new DanglingLinksPurger(dangleThreshold);
RedundantPathLengthThreshold = redundantThreshold;
RedundantPathsPurger = new RedundantPathsPurger(redundantThreshold);
UnDangleGraph();
RemoveRedundancy();
IList <ISequence> contigs = BuildContigs().ToList();
ReadContigMapper mapper = new ReadContigMapper();
ReadContigMap maps = mapper.Map(contigs, sequences, kmerLengthConst);
MatePairMapper builder = new MatePairMapper();
CloneLibrary.Instance.AddLibrary("abc", 5, 15);
ContigMatePairs pairedReads = builder.MapContigToMatePairs(sequences, maps);
OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter();
ContigMatePairs overlap = filter.FilterPairedReads(pairedReads, 0);
DistanceCalculator dist = new DistanceCalculator(overlap);
overlap = dist.CalculateDistance();
ContigGraph graph = new ContigGraph();
graph.BuildContigGraph(contigs, this.KmerLength);
TracePath path = new TracePath();
IList <ScaffoldPath> paths = path.FindPaths(graph, overlap, kmerLengthConst, 3);
Assert.AreEqual(paths.Count, 3);
Assert.AreEqual(paths.First().Count, 3);
ScaffoldPath scaffold = paths.First();
Assert.AreEqual("ATGCCTCCTATCTTAGC", graph.GetNodeSequence(scaffold[0].Key).ConvertToString());
Assert.AreEqual("TTAGCGCG", graph.GetNodeSequence(scaffold[1].Key).ConvertToString());
Assert.AreEqual("GCGCGC", graph.GetNodeSequence(scaffold[2].Key).ConvertToString());
}