package edu.toronto.bb.core;

import java.io.IOException;
import java.io.OutputStream;
import java.util.Collection;
import java.util.List;

public class PhredWriter {

    OutputStream os;
    Collection<PhredScoreSequence> sequences;
    private int scoresPerLine = 60;
    byte[] lineSep = System.getProperty("line.separator").getBytes();
    String delimiter = " "; // single space to separate the socres

    public PhredWriter(OutputStream os, Collection<PhredScoreSequence> sequences) {
        this.os = os;
        this.sequences = sequences;
    }

    public void setScorePerLine(int scorePerLine) {
        this.scoresPerLine = scorePerLine; 
    }

    /**
     * Allow to overwrite the system's line separator
     * @param newLineSeparator
     */
    public void setLineSeparator(String newLineSeparator) {
        this.lineSep = newLineSeparator.getBytes();
    }


    /**
     * Write the sequence to the OutputStream os
     * @throws IOException 
     */
    public void process() throws IOException {				
        for (PhredScoreSequence sequence : sequences) {			
            buildHeader(sequence);
            buildSequenceContents(sequence);            
        }
    }

    private void buildHeader(PhredScoreSequence sequence) throws IOException {        
        os.write('>');
        os.write(sequence.getAccession().getID().getBytes());
        os.write(lineSep);
    }

    private void buildSequenceContents(PhredScoreSequence sequence) throws IOException {
        List<PhredScore> scores = sequence.getScores();
        int seqSize = scores.size();
        int scoresWrittenSoFar = 0;

        for (int i = 0; i < seqSize; i++) {
            scoresWrittenSoFar++;
            if (shouldWriteLineSep(scoresWrittenSoFar, seqSize)) {
                os.write(scores.get(i).toString().getBytes());
                os.write(lineSep);
            } else {
                os.write(scores.get(i).toString().getBytes());
                os.write(delimiter.getBytes());
            }
            
            

        }
        os.write(lineSep);  // end of the current sequence
    }
    
    private boolean shouldWriteLineSep(int scoresWrittenSoFar, int seqSize) {
        return scoresWrittenSoFar % scoresPerLine == 0 
                &&  scoresWrittenSoFar != seqSize;  // no need to write new line at the end of current sequence sample
    }





}

package edu.toronto.bb.core;

import java.io.IOException;
import java.io.OutputStream;
import java.util.Collection;
import java.util.List;

public class PhredWriter {

    OutputStream os;
    Collection<PhredScoreSequence> sequences;
    private int scoresPerLine = 60;
    byte[] lineSep = System.getProperty("line.separator").getBytes();
    String delimiter = " "; // single space to separate the socres

    public PhredWriter(OutputStream os, Collection<PhredScoreSequence> sequences) {
        this.os = os;
        this.sequences = sequences;
    }

    public void setScorePerLine(int scorePerLine) {
        this.scoresPerLine = scorePerLine; 
    }

    /**
     * Allow to overwrite the system's line separator
     * @param newLineSeparator
     */
    public void setLineSeparator(String newLineSeparator) {
        this.lineSep = newLineSeparator.getBytes();
    }

    /**
     * Write the sequence to the OutputStream os
     * @throws IOException 
     */
    public void process() throws IOException {				
        for (PhredScoreSequence sequence : sequences) {			
            buildHeader(sequence);
            buildSequenceContents(sequence);            
        }
    }

    private void buildHeader(PhredScoreSequence sequence) throws IOException {        
        os.write('>');
        os.write(sequence.getAccession().getID().getBytes());
        os.write(lineSep);
    }

    private void buildSequenceContents(PhredScoreSequence sequence) throws IOException {
        List<PhredScore> scores = sequence.getScores();
        int seqSize = scores.size();
        int scoresWrittenSoFar = 0;

        for (int i = 0; i < seqSize; i++) {
            scoresWrittenSoFar++;
            if (shouldWriteLineSep(scoresWrittenSoFar, seqSize)) {
                os.write(scores.get(i).toString().getBytes());
                os.write(lineSep);
            } else {
                os.write(scores.get(i).toString().getBytes());
                os.write(delimiter.getBytes());
            }                        
        }
        os.write(lineSep);  // end of the current sequence
    }
    
    private boolean shouldWriteLineSep(int scoresWrittenSoFar, int seqSize) {
        return scoresWrittenSoFar % scoresPerLine == 0 
                &&  scoresWrittenSoFar != seqSize;  // no need to write new line at the end of current sequence sample
    }





}

tidy up code