Programming Assignment 1

Date Posted: September 10
Preliminary Class Diagram: September 19
Class Outline: September 26
Functionality Outline: October 3
Final Project Due: Tuesday, October 15
DDD: Tuesday, October 22

Programming Assignment 1

1. The simulation shall be able to define two "parent" organisms and their genotype for a test run. Data defining an organism shall consist of a name (given as a genus species, such as Pisum sativum), the number of genes in the genotype to be studied, and data defining each gene. All data defining the two organisms shall be read from a data file which will be provided. The format of the data file is given below. A parser class that can be used to read the data file will also be provided.
2. The simulation shall represent the genotype of an organism as a list of any number of genes. A Gene will contain, at a minimum, the following information.
   1. A brief description of the trait, e.g. "Plant stature".
   2. The specific phenotypes (displayed traits) represented by each allele of this gene, e.g. "tall" and "dwarf".
   3. An indicator as to which trait is the dominant trait.
   4. A character to represent each allele. Note: A capitol letter shall be used to represent a dominant trait and its' corresponding lower case letter to represent the recessive trait of the pair.
3. After reading all data defining two parent organisms the simulation shall then query the user for the number of offspring to generate. This can be in the range of 1 to 1000. A Mendelian cross between the two organisms shall then be performed and the results printed on the screen. The format of the output shall follow the outline given below.

<!-- Sample data file for use in the Mendelian Genetics Simulation Program 1      -->
<!-- Note: This file is not fully compatible with XML standards, but close enough -->
<!--        for the purposes of this project                                      -->

<MENDELIAN_GENETICS_SIM>
	<ORGANISM>
		<GENUS>
			Pisum
		</GENUS>
		<SPECIES>
			Sativum
		</SPECIES>
		<COMMON_NAME>
			Pea Plant
		<COMMON_NAME>
	</ORGANISM>
	<GENES>
		<GENE>
			<GENE_TRAIT>
				Plant Stature
			</GENE_TRAIT>
			<DOMINANT_ALLELE>
				Tall
			</DOMINANT_ALLELE>
			<DOMINANT_SYMBOL>
				T
			</DOMINANT_SYMBOL>
			<RECESSIVE_ALLELE>
				Dwarf
			</RECESSIVE_ALLELE>
			<RECESSIVE_SYMBOL>
				t
			</RECESSIVE_SYMBOL>
		</GENE>
		<GENE>
			<GENE_TRAIT>
				Seed Texture
			</GENE_TRAIT>
			<DOMINANT_ALLELE>
				Wrinkled
			</DOMINANT_ALLELE>
			<DOMINANT_SYMBOL>
				W
			</DOMINANT_SYMBOL>
			<RECESSIVE_ALLELE>
				Smooth
			</RECESSIVE_ALLELE>
			<RECESSIVE_SYMBOL>
				w
			</RECESSIVE_SYMBOL>
		</GENE>
		<GENE>
			<GENE_TRAIT>
				Seed Color
			</GENE_TRAIT>
			<DOMINANT_ALLELE>
				Green
			</DOMINANT_ALLELE>
			<DOMINANT_SYMBOL>
				S
			</DOMINANT_SYMBOL>
			<RECESSIVE_ALLELE>
				Yellow
			</RECESSIVE_ALLELE>
			<RECESSIVE_SYMBOL>
				s
			</RECESSIVE_SYMBOL>
		</GENE>
		<GENE>
			<GENE_TRAIT>
				Flower Color
			</GENE_TRAIT>
			<DOMINANT_ALLELE>
				Purple
			</DOMINANT_ALLELE>
			<DOMINANT_SYMBOL>
				C
			</DOMINANT_SYMBOL>
			<RECESSIVE_ALLELE>
				White
			</RECESSIVE_ALLELE>
			<RECESSIVE_SYMBOL>
				c
			</RECESSIVE_SYMBOL>
		</GENE>
	</GENES>
	<PARENTS>
		<PARENT>
			<GENOTYPE>
				Tt Ww Ss Cc
			</GENOTYPE>
		</PARENT>
		<PARENT>
			<GENOTYPE>
				Tt Ww Ss Cc
			</GENOTYPE>
		</PARENT>
	</PARENTS>
<MENDELIAN_GENETICS_SIM>

		

Master Genes:
        Trait Name: Plant Stature
                Dominant Name: Tall(T)
                Recessive Name: Dwarf(t)
        Trait Name: Seed Texture
                Dominant Name: Wrinkled(W)
                Recessive Name: Smooth(w)
        Trait Name: Seed Color
                Dominant Name: Green(S)
                Recessive Name: Yellow(s)
        Trait Name: Flower Color
                Dominant Name: Purple(C)
                Recessive Name: White(c)


Sim parent 1
	Organism genus-species: Pisum Sativum
	Common name: Pea Plant
	Genes:
		Gene type = Plant Stature
			Genotype = Tt
		Gene type = Seed Texture
			Genotype = Ww
		Gene type = Seed Color
			Genotype = Ss
		Gene type = Flower Color
			Genotype = Cc


Sim parent 2
	Organism genus-species: Pisum Sativum
	Common name: Pea Plant
	Genes:
		Gene type = Plant Stature
			Genotype = Tt
		Gene type = Seed Texture
			Genotype = Ww
		Gene type = Seed Color
			Genotype = Ss
		Gene type = Flower Color
			Genotype = Cc

How many offspring do you want to generate? (Type the number then press Enter)
==>1000


======================= Results of this Run =======================

Gene: Plant Stature
	251 homozygous dominant (Tall TT)
	498 heterozygous dominant (Tall Tt)
	251 homozygous recessive (Dwarf tt)

Gene: Seed Texture
	240 homozygous dominant (Wrinkled WW)
	498 heterozygous dominant (Wrinkled Ww)
	262 homozygous recessive (Smooth ww)

Gene: Seed Color
	242 homozygous dominant (Green SS)
	500 heterozygous dominant (Green Ss)
	258 homozygous recessive (Yellow ss)

Gene: Flower Color
	221 homozygous dominant (Purple CC)
	526 heterozygous dominant (Purple Cc)
	253 homozygous recessive (White cc)
		

All occurring genotypes with the count of each.

	Genotype = TT WW SS CC   Offspring count = 4
	Genotype = TT WW SS Cc   Offspring count = 9
	Genotype = TT WW Ss CC   Offspring count = 8
	Genotype = TT WW Ss Cc   Offspring count = 12
	Genotype = TT Ww SS CC   Offspring count = 2

        *** All other occurring genotypes are listed here but not 
		shown on this web page to save space.  See the demonstration
		of programming assignment 1.
        
	Genotype = tt ww Ss Cc   Offspring count = 16
	Genotype = tt ww SS cc   Offspring count = 2
	Genotype = tt ww Ss cc   Offspring count = 7
	Genotype = tt ww ss Cc   Offspring count = 8
	Genotype = tt ww ss cc   Offspring count = 2

			// Assume char line[32] holds a string of paired letters
			char *cptr;
			char ch1, ch2;  // Characters of a pair
			cptr = line;    // Set pointer to first letter in string
			while(*cptr != '\0') // while we have not reached the null terminator
			{
			    ch1 = *cptr;  // Read first character of a pair
			    cptr++;       // Increment to next letter
			    ch2 = *cptr;  // Read second character of a pair
			    cptr++;       // Increment to next space or null terminator
			    if(*cptr == ' ') // If it's a space...
			        cptr++;      // ...increment to next character
			    // Note: in the above if statement, if *cptr is not a space
			    //   then it must be the null terminator at the end of the
			    //   string so we don't want to increment past it or the while
			    //   loop will not terminate properly.

			    // Create a new gene for this pair of characters
			    Gene *g = new Gene();
			    if(ch1 < ch2) // If ch1 is a capital letter and ch2 is lower case
			    {             // Note: Capital letters have a lower ASCII value than lower case
			        g->setAllele1(ch1);  // If the gene pair is "Tt" we want 'T' in
			        g->setAllele2(ch2);  // the first allele and 't' in the second.
			    }
			    else // Either both are the same or ch2 is the capital 
			    {
			        g->setAllele1(ch2);
			        g->setAllele2(ch1);
			    }
			    // Call the appropriate function here to add the new gene
			    //  to the current parent organism
			}