public void GETEditHappyTest()
{
int?id = 12;
var expected = new CrossType
{
Id = 12,
Name = "bananas"
};
var mockRepo = new Mock <IPlantBreedingRepo>();
mockRepo.Setup(r => r.GetCrossType(id.Value)).Returns(expected);
var controller = new CrossTypesController(mockRepo.Object);
var response = controller.Edit(id) as ViewResult;
Assert.IsNotNull(response);
Assert.IsNotNull(response.Model);
Assert.IsNotNull(response.Model as CrossType);
var actual = response.Model as CrossType;
Assert.AreEqual(expected, actual);
}
public void CrossoverWeights(double[] parent1, double[] parent2,
out double[] child1, out double[] child2, CrossType type)
{
int size = parent1.Length;
child1 = new double[size];
child2 = new double[size];
switch (type)
{
case CrossType.ARYTM:
arytmCrossover(parent1, parent2, child1, child2);
break;
case CrossType.ONE_POINT:
onePointCrossover(parent1, parent2, child1, child2);
break;
case CrossType.REGULAR:
regularCrossover(parent1, parent2, child1, child2);
break;
default:
break;
}
}
static void Run(int ind, int ind_max, int ind_inc, int total_it, int stringlenbegin, BreedType breed, CrossType cross, string filename)
{
using (System.IO.StreamWriter file = new System.IO.StreamWriter(filename, true))
{
GenControl cont = new GenControl(breed,cross);
cont.setFile(filename);
float average;
for (int j = ind; j <= ind_max; j += ind_inc)
{
average = 0;
Console.WriteLine("String Length: " + j);
for (int i = 0; i < total_it; i++)
{
var gener = cont.defaultInitString(j, stringlenbegin, stringlenbegin*2);
average += gener;
Console.Write(gener + " ");
}
average /= ((float)total_it);
file.WriteLine(j + "," + average);
Console.WriteLine();
Console.WriteLine("Average: " + average);
Console.WriteLine();
Console.WriteLine();
}
}
}
public ActionResult Create([Bind(Include = "Id,Name,Value,GenusId")] CrossType crossType)
{
if (ModelState.IsValid)
{
m_repo.SaveCrossType(crossType);
return(RedirectToAction("IndexByGenus", new { id = crossType.GenusId }));
}
return(View(crossType));
}
/// <summary>
/// genetic Average value
/// </summary>
/// <param name="gen">another genetic</param>
private static Genetic[] Cross(int[,] Gen, int[,] gen)
{
int pos = rand.Next(0, Width) + rand.Next(0, Height) * Width;
Genetic[] result = new Genetic[2]
{
new Genetic(),
new Genetic()
};
CrossType t = Global.CrossType;
if (Global.CrossType == CrossType.Random)
{
if (rand.NextDouble() > 0.5)
{
t = CrossType.Vertical;
}
else
{
t = CrossType.Horizontal;
}
}
for (int h = 0; h < Height; h++)
{
for (int w = 0; w < Width; w++)
{
int a = h, b = w;
if (t == CrossType.Vertical)
{
a = w;
b = h;
}
if (h * Width + w < pos)
{
result[0].Gen[a, b] = Gen[a, b];
result[1].Gen[a, b] = gen[a, b];
}
else
{
result[1].Gen[a, b] = Gen[a, b];
result[0].Gen[a, b] = gen[a, b];
}
}
}
return(result);
}
// GET: CrossTypes/Details/5
public ActionResult Details(int?id)
{
if (!id.HasValue)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
CrossType crossType = m_repo.GetCrossType(id.Value);
if (crossType == null)
{
return(HttpNotFound());
}
return(View(crossType));
}
public void GETDeleteNullTest()
{
int? id = 12;
CrossType expected = null;
var mockRepo = new Mock <IPlantBreedingRepo>();
mockRepo.Setup(r => r.GetCrossType(id.Value)).Returns(expected);
var controller = new CrossTypesController(mockRepo.Object);
var response = controller.Retire(null, null) as HttpStatusCodeResult;
Assert.IsNotNull(response);
Assert.IsTrue(response.StatusCode == 400);
}
public void POSTEditHappyTest()
{
var crossType = new CrossType()
{
Id = 12, Name = "Banana"
};
var mockRepo = new Mock <IPlantBreedingRepo>();
var controller = new CrossTypesController(mockRepo.Object);
var response = controller.Edit(crossType) as RedirectToRouteResult;
Assert.IsNotNull(response);
Assert.IsNotNull(response.RouteValues);
Assert.AreEqual("IndexByGenus", response.RouteValues["action"]);
}
public void DetailsNullTest()
{
int? id = 12;
CrossType expected = null;
var mockRepo = new Mock <IPlantBreedingRepo>();
mockRepo.Setup(r => r.GetCrossType(id.Value)).Returns(expected);
var controller = new CrossTypesController(mockRepo.Object);
var response = controller.Details(id) as HttpNotFoundResult;
Assert.IsNotNull(response);
Assert.IsTrue(response.StatusCode == 404);
}
public ActionResult Retire(int?id, int?genus)
{
if (!id.HasValue)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
CrossType crossType = m_repo.GetCrossType(id.Value);
if (crossType == null)
{
return(HttpNotFound());
}
crossType.Retired = !crossType.Retired;
m_repo.SaveCrossType(crossType);
return(RedirectToAction("IndexByGenus", new { id = genus }));
}
public void GETDeleteHappyTest()
{
var expected = new CrossType()
{
Id = 12, Name = "Banana"
};
var mockRepo = new Mock <IPlantBreedingRepo>();
var controller = new CrossTypesController(mockRepo.Object);
var response1 = controller.Create(expected) as RedirectToRouteResult;
controller.Retire(expected.Id, expected.Id);
var response2 = controller.Details(expected.Id) as HttpNotFoundResult;
Assert.IsNotNull(response1);
Assert.IsNotNull(response1.RouteValues);
Assert.AreEqual("IndexByGenus", response1.RouteValues["action"]);
Assert.IsTrue(response2.StatusCode == 404);
}
public void POSTEditWithBadSessionTest()
{
var crossType = new CrossType()
{
Id = 12, Name = "Banana"
};
var mockRepo = new Mock <IPlantBreedingRepo>();
var controller = new CrossTypesController(mockRepo.Object);
controller.ModelState.AddModelError("test", "play them off, keyboard cat");
var response = controller.Edit(crossType) as ViewResult;
Assert.IsNotNull(response);
Assert.IsNotNull(response.Model);
Assert.IsNotNull(response.Model as CrossType);
var actual = response.Model as CrossType;
Assert.AreEqual(crossType, actual);
}
public void POSTDeleteHappyCase()
{
int?id = 12;
var crossType = new CrossType
{
Id = 12,
Name = "bananas"
};
var genus = new List <Genus>
{
new Genus
{
Id = 3,
Name = "Rubus",
DefaultPlantsInRep = 3,
VirusLabel1 = "RBDV",
VirusLabel2 = "ToRSV",
VirusLabel3 = "SNSV",
Retired = false,
ExternalId = null,
VirusLabel4 = "BCRV"
}
};
var mockRepo = new Mock <IPlantBreedingRepo>();
mockRepo.Setup(r => r.GetCrossType(id.Value)).Returns(crossType);
mockRepo.Setup(r => r.GetAllGenera()).Returns(genus);
var controller = new CrossTypesController(mockRepo.Object);
var response = controller.Retire(id, 3) as RedirectToRouteResult;
Assert.IsNotNull(response);
Assert.IsNotNull(response.RouteValues);
Assert.AreEqual("IndexByGenus", response.RouteValues["action"]);
}
public GenControl(BreedType _breed, CrossType _cross)
{
breed = _breed;
cross = _cross;
targetString = Encoding.ASCII.GetBytes("THE_STRING_MATCH");
}
public void SetCrossType(CrossType cross)
{
switch (cross)
{
case CrossType.OnePoint:
crossPoints = 1;
break;
case CrossType.TwoPoint:
crossPoints = 2;
break;
case CrossType.Uniform:
crossPoints = 5;
break;
}
}
public override string ToString()
{
string position = "";
switch (CrossType)
{
case PsmCrossType.Single:
break;
case PsmCrossType.Loop:
position = "(" + LinkPositions[0].ToString() + "-" + LinkPositions[1].ToString() + ")";
break;
default:
position = "(" + LinkPositions[0].ToString() + ")";
break;
}
var sb = new StringBuilder();
sb.Append(FullFilePath + "\t");
sb.Append(ScanNumber + "\t");
sb.Append(PrecursorScanNumber + "\t");
sb.Append(ScanPrecursorMonoisotopicPeakMz + "\t");
sb.Append(ScanPrecursorCharge + "\t");
sb.Append(ScanPrecursorMass + "\t");
sb.Append(CrossType.ToString() + "\t");
if (LinkPositions != null)
{
if (CrossType == PsmCrossType.Loop)
{
sb.Append(BaseSequence[LinkPositions[0] - 1] + ";" + BaseSequence[LinkPositions[1] - 1] + "\t");
}
else if (CrossType == PsmCrossType.Inter || CrossType == PsmCrossType.Intra)
{
sb.Append(BaseSequence[LinkPositions[0] - 1] + ";" + BetaPeptide.BaseSequence[BetaPeptide.LinkPositions[0] - 1] + "\t");
}
else
{
// deadend
sb.Append(BaseSequence[LinkPositions[0] - 1] + "\t");
}
}
else
{
sb.Append("\t");
}
sb.Append("\t");
List <PeptideWithSetModifications> pepsWithMods = BestMatchingPeptides.Select(p => p.Peptide).ToList();
var proteinAccessionString = ProteinAccession != null ? ProteinAccession : PsmTsvWriter.Resolve(pepsWithMods.Select(b => b.Protein.Accession), FullSequence).ResolvedString;
sb.Append(proteinAccessionString + "\t");
sb.Append(XlProteinPos + (XlProteinPosLoop.HasValue? "~" + XlProteinPosLoop.Value : null) + "\t");
sb.Append(BaseSequence + "\t");
sb.Append(FullSequence + position + "\t");
sb.Append((PeptideMonisotopicMass.HasValue ? PeptideMonisotopicMass.Value.ToString() : "---")); sb.Append("\t");
sb.Append(Score + "\t");
sb.Append(XlRank[0] + "\t");
if (ChildMatchedFragmentIons == null)
{
foreach (var mid in MatchedIonDataDictionary(this.MatchedFragmentIons))
{
sb.Append(mid.Value);
sb.Append("\t");
}
}
else
{
StringBuilder[] scanFragmentStringbuilder = new StringBuilder[6];
int i = 0;
foreach (var mid in MatchedIonDataDictionary(this.MatchedFragmentIons))
{
scanFragmentStringbuilder[i] = new StringBuilder();
scanFragmentStringbuilder[i].Append("{" + ScanNumber + "@" + mid.Value + "}");
i++;
}
foreach (var childScan in ChildMatchedFragmentIons)
{
int j = 0;
int oneBasedScan = childScan.Key;
foreach (var mid in MatchedIonDataDictionary(childScan.Value))
{
scanFragmentStringbuilder[j].Append("{" + oneBasedScan + "@" + mid.Value + "}");
j++;
}
}
foreach (var s in scanFragmentStringbuilder)
{
sb.Append(s.ToString() + "\t");
}
}
if (BetaPeptide != null)
{
sb.Append("\t");
List <PeptideWithSetModifications> betaPepsWithMods = BetaPeptide.BestMatchingPeptides.Select(p => p.Peptide).ToList();
var betaProteinAccessionString = BetaPeptide.ProteinAccession != null ? BetaPeptide.ProteinAccession : PsmTsvWriter.Resolve(betaPepsWithMods.Select(b => b.Protein.Accession), FullSequence).ResolvedString;
sb.Append(betaProteinAccessionString + "\t");
sb.Append(BetaPeptide.XlProteinPos + "\t");
sb.Append(BetaPeptide.BaseSequence + "\t");
sb.Append(BetaPeptide.FullSequence + "(" + BetaPeptide.LinkPositions[0].ToString() + ")" + "\t");
sb.Append(BetaPeptide.PeptideMonisotopicMass.ToString() + "\t");
sb.Append(BetaPeptide.Score + "\t");
sb.Append(XlRank[1] + "\t");
if (BetaPeptide.ChildMatchedFragmentIons == null)
{
foreach (var betamid in MatchedIonDataDictionary(this.BetaPeptide.MatchedFragmentIons))
{
sb.Append(betamid.Value);
sb.Append("\t");
}
}
else
{
StringBuilder[] scanFragmentStringbuilder = new StringBuilder[6];
int i = 0;
foreach (var betamid in MatchedIonDataDictionary(this.BetaPeptide.MatchedFragmentIons))
{
scanFragmentStringbuilder[i] = new StringBuilder();
scanFragmentStringbuilder[i].Append("{" + ScanNumber + "@" + betamid.Value + "}");
i++;
}
foreach (var betaChildScan in BetaPeptide.ChildMatchedFragmentIons)
{
int j = 0;
int betaOneBasedScan = betaChildScan.Key;
foreach (var betamid in MatchedIonDataDictionary(betaChildScan.Value))
{
scanFragmentStringbuilder[j].Append("{" + betaOneBasedScan + "@" + betamid.Value + "}");
j++;
}
}
foreach (var s in scanFragmentStringbuilder)
{
sb.Append(s.ToString() + "\t");
}
}
sb.Append("\t");
sb.Append(XLTotalScore + "\t");
// mass of crosslinker
sb.Append(((PeptideMonisotopicMass.HasValue) ? (ScanPrecursorMass - BetaPeptide.PeptideMonisotopicMass - PeptideMonisotopicMass.Value).ToString() : "---")); sb.Append("\t");
int alphaNumParentIons = MatchedFragmentIons.Count(p => p.NeutralTheoreticalProduct.ProductType == ProductType.M);
int betaNumParentIons = BetaPeptide.MatchedFragmentIons.Count(p => p.NeutralTheoreticalProduct.ProductType == ProductType.M);
sb.Append(alphaNumParentIons + ";" + betaNumParentIons + "\t");
sb.Append(alphaNumParentIons + betaNumParentIons + "\t");
sb.Append(((ParentIonMaxIntensityRanks != null) && (ParentIonMaxIntensityRanks.Any()) ? ParentIonMaxIntensityRanks.Min().ToString() : "-")); sb.Append("\t");
}
if (BetaPeptide == null)
{
sb.Append((IsDecoy) ? "D" : (IsContaminant) ? "C" : "T");
sb.Append("\t");
}
else
{
sb.Append((IsDecoy || BetaPeptide.IsDecoy) ? "D" : (IsContaminant || BetaPeptide.IsContaminant) ? "C" : "T");
sb.Append("\t");
}
sb.Append(FdrInfo.QValue.ToString());
sb.Append("\t");
return(sb.ToString());
}
public void CrossoverCars(CarSimpleData p1, CarSimpleData p2, out CarSimpleData c1, out CarSimpleData c2, CrossType type)
{
c1 = new CarSimpleData();
c2 = new CarSimpleData();
double [] c1w;
double [] c2w;
CrossoverWeights(p1.Weights, p2.Weights, out c1w, out c2w, type);
c1.Weights = c1w;
c2.Weights = c2w;
float newSensorLength = CrossoverFloats(p1.SensorsLength, (float)p1.Fitness, p2.SensorsLength, (float)p2.Fitness);
float newAngleBetweenSensors = CrossoverFloats(p1.AngleBetweenSensors, (float)p1.Fitness, p2.AngleBetweenSensors, (float)p2.Fitness);
c1.SensorsLength = newSensorLength;
c2.SensorsLength = newSensorLength;
c1.AngleBetweenSensors = newAngleBetweenSensors;
c2.AngleBetweenSensors = newAngleBetweenSensors;
}
public override string ToString()
{
string position = "";
switch (CrossType)
{
case PsmCrossType.Single:
break;
case PsmCrossType.Loop:
position = "(" + LinkPositions[0].ToString() + "-" + LinkPositions[1].ToString() + ")";
break;
default:
position = "(" + LinkPositions[0].ToString() + ")";
break;
}
var sb = new StringBuilder();
sb.Append(FullFilePath + "\t");
sb.Append(ScanNumber + "\t");
sb.Append(PrecursorScanNumber + "\t");
sb.Append(ScanPrecursorMonoisotopicPeakMz + "\t");
sb.Append(ScanPrecursorCharge + "\t");
sb.Append(ScanPrecursorMass + "\t");
sb.Append(CrossType.ToString() + "\t");
if (LinkPositions != null)
{
if (CrossType == PsmCrossType.Loop)
{
sb.Append(BaseSequence[LinkPositions[0] - 1] + ";" + BaseSequence[LinkPositions[1] - 1] + "\t");
}
else if (CrossType == PsmCrossType.Inter || CrossType == PsmCrossType.Intra)
{
sb.Append(BaseSequence[LinkPositions[0] - 1] + ";" + BetaPeptide.BaseSequence[BetaPeptide.LinkPositions[0] - 1] + "\t");
}
else
{
// deadend
sb.Append(BaseSequence[LinkPositions[0] - 1] + "\t");
}
}
else
{
sb.Append("\t");
}
sb.Append("\t");
sb.Append(ProteinAccession + "\t");
sb.Append(XlProteinPos + "\t");
sb.Append(BaseSequence + "\t");
sb.Append(FullSequence + position + "\t");
sb.Append((PeptideMonisotopicMass.HasValue ? PeptideMonisotopicMass.Value.ToString() : "---")); sb.Append("\t");
sb.Append(Score + "\t");
sb.Append(XlRank[0] + "\t");
foreach (var mid in MatchedIonDataDictionary(this.MatchedFragmentIons))
{
sb.Append(mid.Value);
sb.Append("\t");
}
StringBuilder childScanFragmentStringbuilder = new StringBuilder();
if (ChildMatchedFragmentIons != null)
{
foreach (var childScan in ChildMatchedFragmentIons)
{
int oneBasedScan = childScan.Key;
var matchedIonsDict = MatchedIonDataDictionary(childScan.Value);
childScanFragmentStringbuilder.Append("{" + oneBasedScan + "|" + matchedIonsDict[PsmTsvHeader.MatchedIonMzRatios] + "}");
}
}
sb.Append(childScanFragmentStringbuilder.ToString() + "\t");
if (BetaPeptide != null)
{
sb.Append("\t");
sb.Append(BetaPeptide.ProteinAccession + "\t");
sb.Append(BetaPeptide.XlProteinPos + "\t");
sb.Append(BetaPeptide.BaseSequence + "\t");
sb.Append(BetaPeptide.FullSequence + "(" + BetaPeptide.LinkPositions[0].ToString() + ")" + "\t");
sb.Append(BetaPeptide.PeptideMonisotopicMass.ToString() + "\t");
sb.Append(BetaPeptide.Score + "\t");
sb.Append(XlRank[1] + "\t");
foreach (var betamid in MatchedIonDataDictionary(this.BetaPeptide.MatchedFragmentIons))
{
sb.Append(betamid.Value);
sb.Append("\t");
}
StringBuilder childScanFragmentStringbuilderBeta = new StringBuilder();
if (BetaPeptide.ChildMatchedFragmentIons != null)
{
foreach (var childScan in BetaPeptide.ChildMatchedFragmentIons)
{
int oneBasedScan = childScan.Key;
var matchedIonsDict = MatchedIonDataDictionary(childScan.Value);
childScanFragmentStringbuilderBeta.Append("{" + oneBasedScan + "|" + matchedIonsDict[PsmTsvHeader.MatchedIonMzRatios] + "}");
}
}
sb.Append(childScanFragmentStringbuilderBeta.ToString() + "\t");
sb.Append("\t");
sb.Append(XLTotalScore + "\t");
// mass of crosslinker
sb.Append(((PeptideMonisotopicMass.HasValue) ? (ScanPrecursorMass - BetaPeptide.PeptideMonisotopicMass - PeptideMonisotopicMass.Value).ToString() : "---")); sb.Append("\t");
int alphaNumParentIons = MatchedFragmentIons.Count(p => p.NeutralTheoreticalProduct.ProductType == ProductType.M);
int betaNumParentIons = BetaPeptide.MatchedFragmentIons.Count(p => p.NeutralTheoreticalProduct.ProductType == ProductType.M);
sb.Append(alphaNumParentIons + ";" + betaNumParentIons + "\t");
sb.Append(alphaNumParentIons + betaNumParentIons + "\t");
sb.Append(((ParentIonMaxIntensityRanks != null) && (ParentIonMaxIntensityRanks.Any()) ? ParentIonMaxIntensityRanks.Min().ToString() : "-")); sb.Append("\t");
}
if (BetaPeptide == null)
{
sb.Append((IsDecoy) ? "D" : (IsContaminant) ? "C" : "T");
sb.Append("\t");
}
else
{
sb.Append((IsDecoy || BetaPeptide.IsDecoy) ? "D" : (IsContaminant || BetaPeptide.IsContaminant) ? "C" : "T");
sb.Append("\t");
}
sb.Append(FdrInfo.QValue.ToString());
sb.Append("\t");
return(sb.ToString());
}
