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

When we have completed our k-mer counting, we need to return the results. Since we will have multiple k-mer counters with several different data structures, we are provided with a common interface KMerResults.

public interface KMerResults {
	Iterable<byte[]> foundKMers();

	int getCount(byte[] kMer);
}

StringMapKMerResults

For this particular assignment we will be using instances of Map<String, Integer>, so the provided class StringMapKMerResults will serve well:

public final class StringMapKMerResults extends AbstractMapKMerResults<String> {
	public StringMapKMerResults(int k, Map<String, Integer> map) {
		super(k, map, StringKMerCodec.INSTANCE);
	}
}

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

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 Map: ConcurrentHashMap. Like before, you will be need to complete the parse method but this time in parallel.

Recall that the ConcurrentHashMap will NOT prevent data races. We need to use a method like compute instead of a get/modify/put pattern to prevent atomicity races.

Get then put is not atomic.

Call compute. Call compute.

Use ConcurrentHashMap. Use ConcurrentHashMap.

Or say shoot. Or say shoot.

Videos

Video: ConcurrentHashMap compute

Video: StringHashMapKMerCounter

Video: StringConcurrentHashMapKMerCounter

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