DataStructure

//All classes are written here and last class is Main


// This class represents a pair. This class must be used as it is without modifications.
public class Pair<U, V> {
	public U first;
	public V second;
	public Pair(U first, V second) {
		this.first = first;
		this.second = second;
	}
}

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public class Sequence {
	
	private String seq;
	private String header;
	
    	// Constructor.
	public Sequence(String header, String seq){
		this.header = header;
		this.seq = seq;
	}
	// Return the header of the sequence.
	public String getHeader(){
		return header;
	}
	public String getSeq(){
		return seq;
	}
//	// Return the usage for word length k and window step size w.
	public Usage getUsage(int k, int w){  
		/*
		 * 		for(int i=0;i<seq.length()-k+1;i+=w){
			String kmer = seq.substring(i, k+i);	
			us1.add(kmer, 1);
		} 
		
*/
		Usage us1 =new Usage();
		for(int i=0;i<seq.length()-k+1;i+=w){
			String kmer = seq.substring(i, k+i);	
			us1.add(kmer, 1);
		} 
		return us1;
	}
}
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import java.io.BufferedReader;
import java.io.Reader;
import java.io.FileReader;
import java.io.IOException;
import java.io.FileNotFoundException;

// This class represents a set of sequences.
public class SequenceSet {
	static LinkedList<Sequence> seqs;
	static LinkedList<Sequence> s;

	
	// Constructor.
	public SequenceSet(){
		seqs=new LinkedList<Sequence>();
		
	}

	// Load sequences from FASTA file.
	public static SequenceSet load(String fileName){
		SequenceSet objofseq =new SequenceSet();

		try {
/*
 * 			FileReader fileReader = new FileReader(fileName);
			BufferedReader reader = new BufferedReader(fileReader);
			String line = reader.readLine();
			String head,seqq;
			while(line != null){
*/
			FileReader fileReader = new FileReader(fileName);
			BufferedReader reader = new BufferedReader(fileReader);
			
			
			
			String line = reader.readLine();
			String head,seqq;
			while(line != null){

				if(line.startsWith(">")){
					head=line.substring(1);
					seqq = reader.readLine();
					objofseq.seqs.insert(new Sequence(head,seqq));
					}
				line = reader.readLine();
				}
			reader.close();
		}catch (Exception e) {
			System.out.println("error .....");		
		}
		
		return objofseq;
		
	}
	// Return the global usage over all sequences in the set. The word length is k and window step size is w.
	public Usage getUsage(int k, int w){
		
		Usage result=new Usage();
		seqs.findFirst();

		try{

		while(!seqs.last()){
			for(int i=0;i<seqs.retrieve().getSeq().length()-k+1;i=i+w){
				String kmer = seqs.retrieve().getSeq().substring(i, k+i);	
				result.add(kmer, 1);
			}
			seqs.findNext();
		}
		for(int i=0;i<seqs.retrieve().getSeq().length()-k+1;i=i+w){
			String kmer = seqs.retrieve().getSeq().substring(i, k+i);	
			result.add(kmer, 1);
		}

	}
	catch (Exception e) {
		System.out.println("NullPointerException");		
	}
	return result;
	
}

	

	
	
//	// Return all sequences in the set in the same order they appear in the file.
	public LinkedList<Sequence> getSequences(){
		return seqs;
	}
}

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// This class represents usage data at the sequence or sequence set level
public class Usage {
	
	LinkedList<Pair<String,Integer>> pairsList;
	// Constructor.
	public Usage(){
		pairsList = new LinkedList<Pair<String,Integer>>();
	}
	// Add a kmer with the corresponding number of occurrences.
	public void add(String kmer, int count){
		/*		Pair<String,Integer> p = new Pair<String,Integer>(kmer, count);*/
		Pair<String,Integer> p = new Pair<String,Integer>(kmer, count);
		int t=getCount(kmer);
		if(t==0){
			pairsList.insert(p);
		}
		else{
			pairsList.retrieve().second+=count;
		}
	}
	//Return the number of occurrences of kmer.
	public int getCount(String kmer){
		if(pairsList.empty())
			return 0;
		pairsList.findFirst();
		while(!pairsList.last()){
			//pairsList.retrieve().second
			if(pairsList.retrieve().first.equals(kmer))
				return pairsList.retrieve().second;
			pairsList.findNext();
		}
		
		if(pairsList.retrieve().first.equals(kmer))
			return pairsList.retrieve().second;

		return 0;
	}
	// Return all kmers with their count.
	public LinkedList<Pair<String, Integer>> getCounts(){
		return pairsList;
	}
}