src/org/gel/mauve/format/RawFastaBridgeFilterReader.java

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package org.gel.mauve.format;

import java.io.FilterReader;
import java.io.IOException;
import java.io.Reader;

public class RawFastaBridgeFilterReader extends FilterReader {
        private final static String HEADER = ">raw\n";

        private int remainingHeader = HEADER.length ();

        protected RawFastaBridgeFilterReader (Reader in) {
                super (in);
        }

        /*
         * (non-Javadoc)
         * 
         * @see java.io.Reader#read()
         */
        public int read () throws IOException {
                if (remainingHeader > 0) {
                        char c = HEADER.charAt (HEADER.length () - remainingHeader);
                        remainingHeader--;
                        return c;
                } else {
                        return super.read ();
                }
        }

        /*
         * (non-Javadoc)
         * 
         * @see java.io.Reader#read(char[], int, int)
         */
        public int read (char [] cbuf, int off, int len) throws IOException {
                if (remainingHeader > 0) {
                        int counter = 0;

                        while (remainingHeader > 0) {
                                cbuf[off] = (char) read ();
                                off++;
                                len--;
                                counter++;
                        }
                        return counter + super.read (cbuf, off, len);
                } else {
                        return super.read (cbuf, off, len);
                }
        }

        /*
         * (non-Javadoc)
         * 
         * @see java.io.Reader#skip(long)
         */
        public long skip (long n) throws IOException {
                if (remainingHeader > 0) {
                        if (n <= remainingHeader) {
                                remainingHeader = remainingHeader - (int) n;
                                return n;
                        } else {
                                int oldRemaining = remainingHeader;
                                remainingHeader = 0;
                                n = n - oldRemaining;
                                return super.skip (n) + oldRemaining;
                        }

                } else {
                        return super.skip (n);
                }
        }

        /*
         * (non-Javadoc)
         * 
         * @see java.io.Reader#reset()
         */
        public void reset () throws IOException {
                throw new IOException ("Reset not supported.");
        }

        /*
         * (non-Javadoc)
         * 
         * @see java.io.Reader#mark(int)
         */
        public void mark (int readAheadLimit) throws IOException {
                throw new IOException ("Mark not supported");
        }

        /*
         * (non-Javadoc)
         * 
         * @see java.io.Reader#markSupported()
         */
        public boolean markSupported () {
                return false;
        }
}

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