improving Interfaces: Shotgun
We don't want to use a String to represent a DNA strand/sequence Probably not efficient for merging two strands Strands can't have annotations: names, features,.. Doesn't mirror what's done in BioJava library We want to use a class to represent a sequence, but we don't want to force client code into using a specific class Doesn't allow for future improvements Doesn't allow for idiosyncratic coding requirements Doesn't adhere to good engineering principles What are our options?
10.1
Genome Revolution: COMPSCI 006G
Whats a class? State and behavior
What behavior does a Strand have? Construct from As far as shotgun goes, what are operations on strand? In addition to shotgun, what might we do with strands? List constructors, methods,
What state does a strand need to accomplish this behavior? Postpone this decision as long as possible Once we decide, how can we allow for future changes? Refactoring? Private state and behavior
10.2
Genome public Revolution: COMPSCI 006G
Starting design/implementation
Start with something simple we can test Develop a plan for adding behavior Add behavior and test incrementally Design and implement tests with outside classes or methods internal to the class were building Advantages and disadvantages? White box/Clear box and black box testing Black box means we cant see inside what were testing Advantages and disadvantages? Other approaches?
Genome Revolution: COMPSCI 006G
10.3
Example: Rectangle
We want to implement a Rectangle class. Why? Co...