Some refactorization of Chromosome class.
Renaming AnnotatedVariantFactory to AnnotationCollector.
Reformatting Annotation.java.
Reformatting AnnotationList.java
Refactoring BlockSubstitution.
Renaming BlockSubstitution => BlockSubstitutionAnnotationBuilder.
Refactoring DeletionAnnotation somewhat.
Renaming DeletionAnnotation to DeletionAnnotationBuilder.
Refactoring DuplicationAnnotation.
Renaming DuplicationAnnotation to DuplicationAnnotationBuilder.
Refactoring and reformatting InsertionAnnotation.
Renaming InsertionAnnotation to InsertionAnnotationBuilder.
Reformatting IntergenicAnnotation.
Renaming IntergenicAnnotation to IntergenicAnnotationBuilder.
Reformatting IntronicAnnotation.
Renaming IntronicAnnotation to IntronicAnnotationBuilder.
Updating variable names in NoncodingAnnotation, some reformatting.
Renaming NoncodingAnnotation to NoncodingAnnotationBuilder.
Refactoring SingleNucleotideSubstitution.
Renaming SingleNucleotideSubstitution to SingleNucleotideSubstitutionBuilder.