FastaFile.java

package org.genedb.db.loading;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;

/**
 * Represents a FASTA file, and allows the records in the file to
 * be iterated over in order.
 *
 * @author rh11
 *
 */
public class FastaFile implements Iterable<FastaRecord> {
    private List<FastaRecord> records = new ArrayList<FastaRecord>();

    /**
     * Create a new FastaFile from the specified reader.
     * @param reader the reader to read from
     * @throws IOException
     */
    public FastaFile(Reader reader) throws IOException {
        int lineNumber = 1;
        int lineNumberOfHeader = 0;
        String id = null;
        String line;

        BufferedReader br = new BufferedReader(reader);
        StringBuilder sequence = new StringBuilder();
        while (null != (line = br.readLine())) {
            if (line.startsWith(">")) {
                if (id != null) {
                    records.add(new FastaRecord(id, sequence.toString(), lineNumberOfHeader));
                }
                lineNumberOfHeader = lineNumber;

                id = line.substring(1);
                int pipeIndex = line.indexOf("|");
                if (pipeIndex > -1) {
                    id = line.substring(1, pipeIndex);
                }
                sequence = new StringBuilder();
            } else {
                sequence.append(line.toLowerCase());
            }

            lineNumber++;
        }
        if (id != null) {
            records.add(new FastaRecord(id, sequence.toString(), lineNumberOfHeader));
        }
        br.close();
    }

    public Iterator<FastaRecord> iterator() {
        return records.iterator();
    }
}

class FastaRecord {
    private String id;
    private String sequence;
    private int lineNumber;

    FastaRecord(String id, String sequence, int lineNumber) {
        this.id = id;
        this.sequence = sequence;
        this.lineNumber = lineNumber;
    }

    public String getId() {
        return this.id;
    }

    public String getSequence() {
        return this.sequence;
    }

    public int getLineNumber() {
        return this.lineNumber;
    }

    // hashCode and equals methods generated by Eclipse.
    @Override
    public int hashCode() {
        final int prime = 31;
        int result = 1;
        result = prime * result + ((id == null) ? 0 : id.hashCode());
        result = prime * result + ((sequence == null) ? 0 : sequence.hashCode());
        return result;
    }

    @Override
    public boolean equals(Object obj) {
        if (this == obj)
            return true;
        if (obj == null)
            return false;
        if (getClass() != obj.getClass())
            return false;
        final FastaRecord other = (FastaRecord) obj;
        if (id == null) {
            if (other.id != null)
                return false;
        } else if (!id.equals(other.id))
            return false;
        if (sequence == null) {
            if (other.sequence != null)
                return false;
        } else if (!sequence.equals(other.sequence))
            return false;
        return true;
    }

}