String Map K Mer Assignment

Group Assignment

This is a group assignment.

Code To Investigate

Java Util Concurrent

ConcurrentHashMap

StringKMers

The following method should be useful as you build the assignment.

String toString(byte[] sequence, int offset, int kMerLength)

	/**
	 * Stores the information from the given sequence into a String. For example, if
	 * you had the sequence, "ACCTGTCAAAA" and you called this method with an offset
	 * of 1 and a k of 4, it would return "CCTG".
	 * 
	 * @param sequence the sequence of nucleobases to draw the bytes from
	 * @param offset   the offset for where to start looking for bytes
	 * @param k        the length of the k-mer to make a String for
	 * @return a String representation of the k-mer at the desired position
	 */
	public static String toString(byte[] sequence, int offset, int k) {
		return new String(sequence, offset, k, StandardCharsets.UTF_8);
	}

KMerResults

interface KMerResults

class StringMapKMerResults

Code To Implement

StringHashMapKMerCounter

class:	StringHashMapKMerCounter.java
methods:	parse
package:	kmer.group
source folder:	student/src/main/java

parse

method: public StringMapKMerResults parse(List<byte[]> sequences, int k) (sequential implementation only)

In this completely sequential implementation, you will have to write the parse method. The method takes in a list of arrays of bytes and a k-mer length. It should return an instance of StringMapKMerResults(which takes in a map), a class provided to you which does exactly what its name suggests.

parse should go through the amount of possible k-mers for every byte array in the list of sequences. As it goes through the bytes in the array, use the StringKMers.toString(sequence, offset, k) method to create a string to use as a key for the HashMap. The map should take in a String as the key and an Integer as the value. We recommend using the map.compute() method and reviewing how to use lambdas.

StringConcurrentHashMapKMerCounter

class:	StringConcurrentHashMapKMerCounter.java
methods:	constructor concurrentMapFactory createConcurrentMap parse
package:	kmer.group
source folder:	student/src/main/java

constructor and instance variable

Hang onto the concurrentMapFactory passed to the constructor in an instance variable so you can use it later.

public StringConcurrentMapUnbalancedKMerCounter(Supplier<ConcurrentMap<String, Integer>> concurrentMapFactory)

parse

method: public StringMapKMerResults parse(List<byte[]> sequences, int k) (parallel implementation required)

This implementation will make your sequential String HashMap implementation into a parallel one. To do so, you will be making use of Java’s thread-safe version of a HashMap: a ConcurrentHashMap. Like before, you will be need to complete the parse method but this time in parallel.

Testing Your Solution

class:	__StringKMerTestSuite.java
package:	kmer.group
source folder:	testing/src/test/java

sequential

class:	_StringSequentialKMerTestSuite.java
package:	kmer.group
source folder:	testing/src/test/java

concurrent

class:	_StringConcurrentKMerTestSuite.java
package:	kmer.group
source folder:	testing/src/test/java