Java Program About Genome Analysis Project Given the starter code, and All the files required in the attachment. mainly about the inheitance. Martians have

Java Program About Genome Analysis Project Given the starter code, and All the files required in the attachment. mainly about the inheitance. Martians have come to earth and allowed us to study their genomes. It is discovered that their
DNA, like humans, consists of Adenine (A), Guanine (G), Cytosine (C) and Thymine (T) and can
be coded as sequences of these letters, e.g., GACCCATT
Your boss has provided you with the library class GenomeAnalyzer, which takes care of some
of the bookkeeping of analyzing genome strands. You cannot directly change the
GenomeAnalyzer class, but you’ll subclass it to add extensions to the code that is there.
GenomeAnalyzer already knows how to read from a file, check if the data in that file is valid (text
consisting only of ‘G’, ‘T’, ‘A’, and ‘C’) and it can detect some simple patterns in the DNA.
Part 1
Write a subclass of the given GenomeAnalyzer named MartianGenomeAnalyzer, and provide it
with the following methods:
•
•
•
•
int detectGenius() — a martian is a genius if it has the string, “GAGA” anywhere in its
genome. This method should call the superclass method findSimpleSequence to do its
job, and should return the index of the first “G” of the first instance of “GAGA” in the
genome, or -1 if not found.
int detectRepeater(letter) — a martian who tends to repeat his words can be detected if,
anywhere in his genome, the given letter is repeated five times. This method should call
the superclass method findSimpleSequence to do its job. It should return the index of the
match, or -1 if not found.
int detectGastroDisease() — a martian has gastro disease if it contains a string that
begins with G, followed by one or more Ts, followed by another G. So GTTTG and GTG
fit the pattern, but GTTTC does not. The method should return the index of the match, or
-1 if not found.
A main method that tests these methods with input files with both positive and negative
samples.
Part 2
Your boss wants you to test for various patterns in the DNA, as in the above task, but wants you
to refactor your code so that it is easy to run a series of detection tests (with a loop). You need a
list of detectors, each of a different subclass type, and you need to use polymorphism.
For this task, you’ll write a new subclass of GenomeAnalyzer, MartianGenomeSeriesAnalyzer,
which codes things in a more flexible manner than in the MartianGenomeAnalyzer (you are
replacing MartianGenomeAnalyzer).
Code an interface “PatternDetector” and a set of classes that implement that interface.
PatternDetector should provide the following methods:
int detect(GenomeAnalyzer analyzer); — detects if pattern exists in analyzer code
String labelString(); — a string describing the detector (for display)
String additionalInfo() — a string describing additional info about an analysis.
additionalInfo should have a default implementation that returns “”.
Provide three implementations for PatternDetector, one for each of the methods you wrote in
part 1. So you’ll have classes GeniusDetector, GastroDiseaseDetector, and RepeaterDetector,
all that implement PatternDetector and its methods.
MartianGenomeSeriesAnalyzer will have the following methods:
•
•
•
constructor
void addDetector(PatternDetector) — adds a detector to the series of tests to be run
void runAll — runs all the tests
Its main method should look something like:
public static void main(String args[]){
MartianGenomeSeriesAnalyzer seriesAnalyzer = new
MartianGenomeSeriesAnalyzer(“test.txt”);
seriesAnalyzer.addDetector(new GeniusDetector());
seriesAnalyzer.addDetector(new GastroDiseaseDetector());
// add more detectors
seriesAnalyzer.runAll();
}
Extra Credit
1. Recode the Detectors using Java’s pattern matching facility (or not using it if you did use it in
the original) 5 points
2. Detect multiple matches within the same sequence. Add the method “ArrayList
detect()” to the PattenDetector, and implement that method for each of PatternDetector
subclasses. The function will return a list of the starting indexes for the matches found, or null.
The new detect methods should call the original one multiple times to do its job
15 points
Reading
The following probably won’t help with the coding, but provide short introductions to DNA
sequencing terminology and computer science efforts in this area:
link on some of the CS questions involved (e.g. massive data). easy read

The Computer Science behind DNA Sequencing

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good definitions, e.g., 3 letter combos are the words,
http://www.brooklyn.cuny.edu/bc/ahp/BioInfo/GP/GeneticCode.html

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