private static Trait GetSelectedPersonsTrait(Person selectedPerson, TraitRepository traitRepository, PersonRepository personRepository, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
var listOfSelectedPersonTraits = selectedPerson.Phenotype.Traits;
if (selectedPerson.Phenotype.Traits.Count == 0)
{
Console.Clear();
Console.WriteLine("This person does not have any Traits");
PersonScreen(traitRepository, selectedPerson, personRepository, genotypeRepository, rng, context);
PersonScreenMenu(traitRepository, personRepository, selectedPerson, genotypeRepository, rng, context);
}
int number = 1;
foreach (var trait in selectedPerson.Phenotype.Traits)
{
Console.WriteLine(number + ") " + trait.ToString());
number = number + 1;
}
try
{
Console.WriteLine("++++++++++++++++++++++++++++++++++++++++++++++++++++++");
Console.WriteLine("Please input the index of trait you want to select: ");
int index = Convert.ToInt32(Console.ReadLine());
Trait selectedPersonTrait = listOfSelectedPersonTraits[index - 1];
return(selectedPersonTrait);
}
catch (Exception)
{
Console.WriteLine("There is no Trait located at that index. Please try again");
return(GetSelectedPersonsTrait(selectedPerson, traitRepository, personRepository, genotypeRepository, rng, context));
}
}
private static void DeleteTrait(Person selectedPerson, TraitRepository traitRepository, PersonRepository personRepository, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
Trait traitToBeDeleted = GetSelectedPersonsTrait(selectedPerson, traitRepository, personRepository, genotypeRepository, rng, context);
selectedPerson.Phenotype.Traits.Remove(traitToBeDeleted);
context.SaveChanges();
}
private static void DeleteGenotype(Person SelectedPerson, TraitRepository traitRepository, PersonRepository personRepository, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
Genotype genotypeToBeDeleted = GetSelectedPersonsGenotype(SelectedPerson, traitRepository, personRepository, genotypeRepository, rng, context);
SelectedPerson.Phenotype.TraitGenotypes.Remove(genotypeToBeDeleted);
context.SaveChanges();
// context.Genotypes.Remove(); HOW TO REMOVE FROM THE DATABASE
}
private static void ChangeSex(TraitRepository traitRepository, Person SelectedPerson, PersonRepository personRepository, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
Console.WriteLine("Please input a new sex (Male, Female or Unknown)");
string inputtedSex = Console.ReadLine();
Sex newSex = (Sex)Enum.Parse(typeof(Sex), inputtedSex, true);
SelectedPerson.Sex = newSex;
context.SaveChanges();
PersonScreen(traitRepository, SelectedPerson, personRepository, genotypeRepository, rng, context); //returns user to last menu
}
public void SetUp()
{
GeneticCounsellorDbContext context = null;
using (context = new GeneticCounsellorDbContext("Jess1"))
{
var traitRepository = new TraitRepository(context);
var personRepository = new PersonRepository(context);
genotypeRepository = new GenotypeRepository(context);
rng = new RealRandomNumberGenerator();
}
}
private static void CalculateParentalGenotypes(Person selectedPerson, TraitRepository traitRepository, PersonRepository personRepository, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
Genotype genotypeToTrace = GetSelectedPersonsGenotype(selectedPerson, traitRepository, personRepository, genotypeRepository, rng, context);
List <Genotype> parentalGenotypes = genotypeToTrace.CalculateParentalGenotypes(genotypeRepository, rng);
Console.WriteLine("Here are the potential parental genotypes:");
Console.WriteLine("====================================================");
foreach (var genotype in parentalGenotypes)
{
Console.WriteLine(genotype);
}
}
private static void ChangeName(TraitRepository traitRepository, Person SelectedPerson, PersonRepository personRepository, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
Console.WriteLine("Please input a new full name");
string newName = Console.ReadLine();
if (newName == "")
{
Console.WriteLine("It is against the Geneva convention for a person to be denied a name");
}
SelectedPerson.Name = newName;
context.SaveChanges();
PersonScreen(traitRepository, SelectedPerson, personRepository, genotypeRepository, rng, context);//returns user to last menu
}
private static void ListAllTraitsChoice(TraitRepository traitRepository)
{
StringBuilder sb2 = new StringBuilder();
ListAllTraitsScreen(sb2, traitRepository);
string s2 = sb2.ToString();
Console.Write(s2);
Console.WriteLine("____________________________________________________");
Console.WriteLine("-----------------------------------------------------");
Console.WriteLine("1) Add a trait");
Console.WriteLine("2) Delete a trait");
Console.WriteLine("-----------------------------------------------------");
}
private static void changeLiving(TraitRepository traitRepository, Person SelectedPerson, PersonRepository personRepository, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
Console.WriteLine("Please input a new Living status (True, False)");
string acceptableTrueString = "true";
string acceptableFalseString = "False";
string inputtedLiving = Console.ReadLine();
if (inputtedLiving == acceptableTrueString || inputtedLiving == acceptableFalseString)
{
bool inputLiving = (bool)Convert.ToBoolean(inputtedLiving);
SelectedPerson.Living = inputLiving;
}
context.SaveChanges();
PersonScreen(traitRepository, SelectedPerson, personRepository, genotypeRepository, rng, context); //returns user to last menu
}
private static void GeneticCounsellor() //Reads in all database information into Repositoriesand context
{
GeneticCounsellorDbContext context = null;
using (context = new GeneticCounsellorDbContext("Jess1"))
{
var traitRepository = new TraitRepository(context);
var personRepository = new PersonRepository(context);
var genotypeRepository = new GenotypeRepository(context);
var rng = new RealRandomNumberGenerator();
string personFilename = @"C:\Users\potts\Desktop\PersonsSeedData.txt";
string traitFilename = @"C:\Users\potts\Desktop\TraitSeedData.txt";
geneticCounsellorScreen(genotypeRepository, traitRepository, personRepository, personFilename, traitFilename, rng, context);
}
}
private static void PersonScreen(TraitRepository traitRepository, Person SelectedPerson, PersonRepository personRepository, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
Console.Clear();
Console.WriteLine("Name: " + SelectedPerson.Name);
Console.WriteLine("Sex: " + SelectedPerson.Sex);
Console.WriteLine("Living Status:" + SelectedPerson.Living);
string traitOutput = "";
foreach (var traits in SelectedPerson.Phenotype.Traits)
{
traitOutput = traitOutput + traits.ToString() + ",";
}
Console.WriteLine("Traits: " + traitOutput);
string outputGenotypes = "";
foreach (var genotype in SelectedPerson.Phenotype.TraitGenotypes)
{
outputGenotypes = outputGenotypes + genotype.ToString() + ',';
}
Console.WriteLine("Genotypes: " + outputGenotypes);
try
{
UpdatePhenotype(SelectedPerson);
}
catch (Exception)
{
Console.WriteLine("Phenotype: N/A");
}
try
{
Console.WriteLine("Mother: " + SelectedPerson.Mother.Name); //recursive viewing of the whole family
Console.WriteLine("Father: " + SelectedPerson.Father.Name);
}
catch (Exception)
{
Console.WriteLine("Incomplete parents inputted.");
}
PersonScreenMenu(traitRepository, personRepository, SelectedPerson, genotypeRepository, rng, context);
}
private static void AddExsistingGenotype(TraitRepository traitRepository, Person SelectedPerson, GenotypeRepository genotypeRepository, PersonRepository personRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
Console.Clear();
Console.WriteLine("Already exsisting Genotypes:");
int num = 0;
foreach (var g in genotypeRepository.ListGenotypes())
{
Console.WriteLine(num + ") " + g);
num++;
}
Console.WriteLine("Select a genotype from list:");
int genotypeIndex = Convert.ToInt32(Console.ReadLine());
var Allgenotypes = genotypeRepository.ListGenotypes();
SelectedPerson.AddGenotypeToPerson(Allgenotypes[genotypeIndex]);
context.SaveChanges();
PersonScreen(traitRepository, SelectedPerson, personRepository, genotypeRepository, rng, context); //returns user to last menu
}
private static void ListAllTraitsScreen(StringBuilder sb2, TraitRepository traitRepository)
{
Console.Clear();
var ListOfTraits = traitRepository.ListTraits();
int i = 0;
if (ListOfTraits.Count == 0)
{
sb2.AppendLine("There are no Traits in this system, please add one.");
sb2.AppendLine("____________________________________________________");
}
else
{
foreach (var t in ListOfTraits)
{
i++;
sb2.AppendLine(i + ") " + t.ToString());
}
}
}
private static Trait FindTraitByIndex(TraitRepository traitRepository) //Ru-used in multiple aspects of the code: very important
{
Console.WriteLine("_________________________________________________");
Console.Write("Enter a Trait Index No. :");
try
{
var ListOftraits = traitRepository.ListTraits();
int index = Convert.ToInt32(Console.ReadLine());
Trait SelectedTrait = ListOftraits[index - 1];
return(SelectedTrait);
}
catch (IndexOutOfRangeException)
{
Console.WriteLine("Not a valid index");
return(null);
}
catch (FormatException)
{
Console.WriteLine("Not a number");
return(null);
}
}
private static void PersonScreenMenu(TraitRepository traitRepository, PersonRepository personRepository, Person selectedPerson, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
Console.WriteLine("----------------------------------------------------------------------------------------------------------");
Console.WriteLine("1) Edit Person");
Console.WriteLine("2) Combine Genotype with other person");
Console.WriteLine("3) Update Phenotype");
Console.WriteLine("4) Calculate Parental Genotypes");
Console.WriteLine("----------------------------------------------------------------------------------------------------------");
int PersonMenuChoice = MenuUserInputInt(4);
switch (PersonMenuChoice)
{
case 0:
Console.Clear();
StringBuilder sb = new StringBuilder(); //return to last menu
ListAllPersonsScreen(sb, personRepository, genotypeRepository);
break;
case 1: //Edit Person
EditPersonScreen(traitRepository, personRepository, selectedPerson, genotypeRepository, rng, context);
break;
case 2: //Combine Genotypes
CombineGenotypesScreen(selectedPerson, personRepository, genotypeRepository, rng, traitRepository, context);
break;
case 3: //update Phenotype
UpdatePhenotype(selectedPerson);
break;
case 4:
CalculateParentalGenotypes(selectedPerson, traitRepository, personRepository, genotypeRepository, rng, context);
break;
default:
throw new Exception("Invalid Menu input");
}
}
private static void AddFather(TraitRepository traitRepository, Person selectedPerson, PersonRepository personRepository, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
StringBuilder sb = new StringBuilder();
ListAllPersonsScreen(sb, personRepository, genotypeRepository);
string s = sb.ToString();
Console.Write(s);
Person personToBeFather = FindPersonByIndex(personRepository);
bool can = selectedPerson.CanAddFather(personToBeFather);
if (can)
{
selectedPerson.AddFatherToPerson(personToBeFather);
context.SaveChanges();
PersonScreen(traitRepository, selectedPerson, personRepository, genotypeRepository, rng, context);
}
else
{
Console.WriteLine("Only biological males can be entered as biological fathers.");
Console.ReadLine();
}
}
private static void AddExsistingTrait(Person selectedPerson, TraitRepository traitRepository, PersonRepository personRepository, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
Console.Clear();
Console.WriteLine("Already exsisting Traits:");
int num = 0;
foreach (var t in traitRepository.ListTraits())
{
Console.WriteLine(num + ") " + t);
num++;
}
Console.WriteLine("Select a trait from the list:");
int traitIndex = Convert.ToInt32(Console.ReadLine());
var allTraits = traitRepository.ListTraits();
Trait chosenTrait = allTraits[traitIndex];
selectedPerson.AddTraitToPerson(chosenTrait);
Console.WriteLine("Select which genotype to add to person:");
chosenTrait.GenerateGenotypesForATrait(genotypeRepository);
AddExsistingGenotype(traitRepository, selectedPerson, genotypeRepository, personRepository, rng, context);
context.SaveChanges();
PersonScreen(traitRepository, selectedPerson, personRepository, genotypeRepository, rng, context);
}
private static void CreateTraitScreen(TraitRepository traitRepository)
{
try
{
Console.Clear();
Console.WriteLine("Name of trait:"); // Colourblindness
string inputName = Console.ReadLine();
Console.WriteLine("Type of inheritance (currently Dominant or Recessive only)"); //Reccessive
Dominance inputInheritanceType = (Dominance)Enum.Parse(typeof(Dominance), Console.ReadLine(), true);
Console.WriteLine("What letter should represent it?"); // C
string inputAlelleName = Console.ReadLine();
traitRepository.AddTrait(inputName, inputAlelleName, inputInheritanceType);
Console.Clear();
StringBuilder sb2 = new StringBuilder();
ListAllTraitsScreen(sb2, traitRepository);
string s2 = sb2.ToString();
Console.Write(s2);
}
catch (Exception)
{
Console.WriteLine("Input not recognised- Please try again");
CreateTraitScreen(traitRepository);
}
}
private static void geneticCounsellorScreen(GenotypeRepository genotypeRepository, TraitRepository traitRepository, PersonRepository personRepository, string personFilename, string traitFilename, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
Console.Clear();
Console.WriteLine("____________________________________________________");
Console.WriteLine("1) Add Person");
Console.WriteLine("2) List all Persons");
Console.WriteLine("3) Create trait");
Console.WriteLine("4) List all traits");
Console.WriteLine("5) Create family tree");
Console.WriteLine("____________________________________________________");
int geneticCounsellorMenuOption = MenuUserInputInt(5);
switch (geneticCounsellorMenuOption)//Allows user to navigate menu using integer keyboard inputs
{
case 0:
Console.Clear();
MainMenuScreen();
break;
case 1:
AddPersonScreen(personRepository, genotypeRepository);
geneticCounsellorScreen(genotypeRepository, traitRepository, personRepository, personFilename, traitFilename, rng, context);
break;
case 2:
ListAllPersonsChoice(personRepository, genotypeRepository);
int ListAllPersonsScreenOption = MenuUserInputInt(3);
switch (ListAllPersonsScreenOption)
{
case 0:
geneticCounsellorScreen(genotypeRepository, traitRepository, personRepository, personFilename, traitFilename, rng, context);
break;
case 1:
Person selectedPerson = FindPersonByIndex(personRepository);
PersonScreen(traitRepository, selectedPerson, personRepository, genotypeRepository, rng, context); //SELECTS A PERSON
break;
case 2:
DeletePerson(personRepository, genotypeRepository);
break;
case 3:
AddPersonScreen(personRepository, genotypeRepository);
geneticCounsellorScreen(genotypeRepository, traitRepository, personRepository, personFilename, traitFilename, rng, context);
break;
default:
throw new Exception("Invalid Menu input");
}
break;
case 3:
CreateTraitScreen(traitRepository);
break;
case 4:
ListAllTraitsChoice(traitRepository);
int ListAllTraitsScreenOption = MenuUserInputInt(2);
switch (ListAllTraitsScreenOption)
{
case 0:
geneticCounsellorScreen(genotypeRepository, traitRepository, personRepository, personFilename, traitFilename, rng, context);
break;
case 1:
CreateTraitScreen(traitRepository);
break;
case 2:
Trait selectedTraitToDelete = FindTraitByIndex(traitRepository); //DELETES A TRAIT
traitRepository.DeleteTrait(selectedTraitToDelete);
Console.WriteLine("#######################");
Console.WriteLine("Trait has been deleted.");
Console.WriteLine("#######################");
break;
}
break;
case 5:
FamilyTreeScreen(personRepository, genotypeRepository);
break;
default:
throw new Exception("Invalid Menu input");
}
}
private static void EditPersonScreen(TraitRepository traitRepository, PersonRepository personRepository, Person selectedPerson, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, GeneticCounsellorDbContext context)
{
Console.WriteLine("1) Change Name");
Console.WriteLine("2) Change Sex");
Console.WriteLine("3) Change Living");
Console.WriteLine("4) Add an exsisting Genotype from database");
Console.WriteLine("5) Delete a Genotype from Person ");
Console.WriteLine("6) Add an exsisting Trait from database");
Console.WriteLine("7) Delete a Trait from person");
Console.WriteLine("8) Add Mother from exsisting list of Persons");
Console.WriteLine("9) Add Father from exsisting list of Persons");
Console.WriteLine("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~");
int EditPersonMenuChoice = MenuUserInputInt(9);
switch (EditPersonMenuChoice)
{
case 0:
PersonScreenMenu(traitRepository, personRepository, selectedPerson, genotypeRepository, rng, context);
break;
case 1:
ChangeName(traitRepository, selectedPerson, personRepository, genotypeRepository, rng, context);
break;
case 2:
ChangeSex(traitRepository, selectedPerson, personRepository, genotypeRepository, rng, context);
break;
case 3:
changeLiving(traitRepository, selectedPerson, personRepository, genotypeRepository, rng, context);
break;
case 4:
StringBuilder sb = new StringBuilder();
ListAllPersonsScreen(sb, personRepository, genotypeRepository);
string s = sb.ToString();
Console.Write(s);
AddExsistingGenotype(traitRepository, selectedPerson, genotypeRepository, personRepository, rng, context);
break;
case 5:
DeleteGenotype(selectedPerson, traitRepository, personRepository, genotypeRepository, rng, context);
break;
case 6:
AddExsistingTrait(selectedPerson, traitRepository, personRepository, genotypeRepository, rng, context);
break;
case 7:
DeleteTrait(selectedPerson, traitRepository, personRepository, genotypeRepository, rng, context);
break;
case 8:
AddMother(traitRepository, selectedPerson, personRepository, genotypeRepository, rng, context);
break;
case 9:
AddFather(traitRepository, selectedPerson, personRepository, genotypeRepository, rng, context);
break;
}
}
private static void CombineGenotypesScreen(Person selectedPerson, PersonRepository personRepository, GenotypeRepository genotypeRepository, RealRandomNumberGenerator rng, TraitRepository traitRepository, GeneticCounsellorDbContext context)//TO DO: Change Seed Data to be compatible with added Genotypes
{
Console.Clear();
Genotype firstSelectedPerson = GetSelectedPersonsGenotype(selectedPerson, traitRepository, personRepository, genotypeRepository, rng, context); //Selected Genotypes
//Ensure only males and females are compatible
StringBuilder sb = new StringBuilder();
ListAllPersonsScreen(sb, personRepository, genotypeRepository);
string s = sb.ToString();
Console.WriteLine("++++++++++++++++++++++++++++++++++++++++++++++++++");
Console.WriteLine("Please select a person to combine genotypes with:");
Console.WriteLine("++++++++++++++++++++++++++++++++++++++++++++++++++");
Console.Write(s);
Person otherPerson = FindPersonByIndex(personRepository);
Genotype otherSelectedPerson = GetSelectedPersonsGenotype(otherPerson, traitRepository, personRepository, genotypeRepository, rng, context);
Genotype resultingGenotype = firstSelectedPerson.MostLikelyGenotype(otherSelectedPerson, genotypeRepository, rng);
Console.WriteLine("______________________________________________________________________________________________________________");
Console.WriteLine(resultingGenotype.ToString() + " is the most likely genotype combination in offspring between these two persons");
Console.WriteLine("______________________________________________________________________________________________________________");
}