Question
DNA sequences are often stored in a text file having a specific format called FASTA file. FASTA format is a text-based format for representing either
DNA sequences are often stored in a text file having a specific format called FASTA file. FASTA format is a text-based format for representing either nucleotide or amino acid sequences. The format allows for sequence names and comments to precede each sequence. Figure 2 shows a simple example of a fasta file.
>First sequence ACACAGGAA
>Second sequence
ACGTCAGGTC
sequence
TACTGACEC
Figure 2: Example of a FASTA file
Your program should be able to read all sequences from a FASTA file and compute the k-mer usage bias from all sequences in the file.
3 Requirements
In this phase, you are required to implement the following classes:
// This class represents a set of sequences. public class SequenceSet { // Constructor.
public SequenceSet ( ) ;
// Load sequences from FASTA file.
public static SequenceSet load (String fileName) ;
// Return the global usage over al L sequences in the set. The word Length is k and window step size is w. public Usage getUsage (int k, int w) ;
// Return al L sequences in the set in the same order they appear in the file. public LinkedList
// This class represents a single sequence. public class Sequence { // Constructor.
public Sequence (String header, String seq) ; // Return the header of the sequence. public String getHeader() ; public String getSeq() ;
// Return the usage for word Length k and window step size w. public Usage getUsage (int k, int w) ;
// This class represents usage data at the sequence or sequence set Level. public class Usage { // Constructor. public Usage ( ) ;
// Add a kmer with the corresponding number of occurrences. public add (String kmer, int count) ;
// Return the number of occurrences of kmer. public int getCount (String kmer) ; // Return al L kmers with their count.
public LinkedList
// This class represents a pair. This class must be used as it is without modifications .
public class Pair { public U first; public V second; public Pair (U first, V second) { this. first = first; this. second = second;
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