a sequence is now the raw allelic representation of a chromosome. A chromosome is a single sequence. A genome may contain multiple sets of a chromosomes. This is referred to as the ploidy. A locus is a specific location on a chromosome. A genotype represents the allelic value of all copies of a chromosome at a specific locus. A Trait is a characteristic which is defined by a set of loci. A phenotype is the value associated with a trait. An individiaul has a genome that is genotypeable and phenotypeable.
Fixed compilation errors and created implementations for several templated objects
Added basic tests for genome factory and sequences
Renamed template header files to hpp; added default chromosome length to be 100
Changed memory organization of Sequence pointers in Individuals and chromosome pointers in GenomeFactory.
Modified genome to not consider ploidy.
Added test to verify genomefactory size changes with chromosomes
Added chromosome copy constructor
Merge branch 'add_sex_chromosomes' into revision_0
Added new the concept of a tuple of chromosomes. Conceptually, an individual has multiple copies of a chromosome. These copies are logically orderable.
Merge branch 'revision_0'

Modified revision_0