/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.bio.program.fastq;

import java.net.URL;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;

import java.util.ArrayList;
import java.util.List;

/**
 * Abstract reader implementation for FASTQ formatted sequences.
 *
 * @since 1.7.1
 */
abstract class AbstractFastqReader
    implements FastqReader
{

    /** Parser state. */
    private static enum State
    {
        /** Description parser state. */
        DESCRIPTION,

        /** Sequence parser state. */
        SEQUENCE,

        /** Repeat description parser state. */
        REPEAT_DESCRIPTION,

        /** Quality score parser state. */
        QUALITY,

        /** Complete parser state. */
        COMPLETE;
    };

    /**
     * Return the FASTQ sequence format variant for this reader.
     *
     * @return the FASTQ sequence format variant for this reader
     */
    protected abstract FastqVariant getVariant();

    /**
     * Validate the specified description.
     *
     * @param builder FASTQ formatted sequence builder, will not be null
     * @param description description to validate, will not be null
     * @param lineNumber current line number in input stream
     * @throws IOException if the specified description is not valid
     */
    protected abstract void validateDescription(FastqBuilder builder, String description, int lineNumber)
        throws IOException;

    /**
     * Validate the specified sequence.
     *
     * @param builder FASTQ formatted sequence builder, will not be null
     * @param sequence sequence to validate, will not be null
     * @param lineNumber current line number in input stream
     * @throws IOException if the specified sequence is not valid
     */
    protected abstract void validateSequence(FastqBuilder builder, String sequence, int lineNumber)
        throws IOException;

    /**
     * Validate the specified repeat description.
     *
     * @param builder FASTQ formatted sequence builder, will not be null
     * @param repeatDescription repeat description to validate, will not be null
     * @param lineNumber current line number in input stream
     * @throws IOException if the specified repeat description is not valid
     */
    protected abstract void validateRepeatDescription(FastqBuilder builder, String repeatDescription, int lineNumber)
        throws IOException;

    /**
     * Validate the specified quality scores.
     *
     * @param builder FASTQ formatted sequence builder, will not be null
     * @param quality quality scores to validate, will not be null
     * @param lineNumber current line number in input stream
     * @throws IOException if the specified quality scores are not valid
     */
    protected abstract void validateQuality(FastqBuilder builder, String quality, int lineNumber)
        throws IOException;


    /** {@inheritDoc} */
    public final Iterable<Fastq> read(final File file) throws IOException
    {
        if (file == null)
        {
            throw new IllegalArgumentException("file must not be null");
        }
        InputStream inputStream = null;
        try
        {
            inputStream = new FileInputStream(file);
            return read(inputStream);
        }
        catch (IOException e)
        {
            throw e;
        }
        finally
        {
            if (inputStream != null)
            {
                try
                {
                    inputStream.close();
                }
                catch (IOException e)
                {
                    // ignore
                }
            }
        }
    }

    /** {@inheritDoc} */
    public final Iterable<Fastq> read(final URL url) throws IOException
    {
        if (url == null)
        {
            throw new IllegalArgumentException("url must not be null");
        }
        InputStream inputStream = null;
        try
        {
            inputStream = url.openStream();
            return read(inputStream);
        }
        catch (IOException e)
        {
            throw e;
        }
        finally
        {
            if (inputStream != null)
            {
                try
                {
                    inputStream.close();
                }
                catch (IOException e)
                {
                    // ignore
                }
            }
        }
    }

    /** {@inheritDoc} */
    public final Iterable<Fastq> read(final InputStream inputStream) throws IOException
    {
        if (inputStream == null)
        {
            throw new IllegalArgumentException ("inputStream must not be null");
        }
        int lineNumber = 0;
        State state = State.DESCRIPTION;
        List<Fastq> result = new ArrayList<Fastq>();
        FastqBuilder builder = new FastqBuilder().withVariant(getVariant());
        BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream));
        while (reader.ready())
        {
            String line = reader.readLine();
            switch (state)
            {
            case DESCRIPTION:
                validateDescription(builder, line, lineNumber);
                builder.withDescription(line.substring(1).trim());
                state = State.SEQUENCE;
                break;
            case SEQUENCE:
                validateSequence(builder, line, lineNumber);
                builder.withSequence(line.trim());
                state = State.REPEAT_DESCRIPTION;
                break;
            case REPEAT_DESCRIPTION:
                if (!line.startsWith("+"))
                {
                    builder.appendSequence(line.trim());
                }
                else
                {
                    validateRepeatDescription(builder, line, lineNumber);
                    state = State.QUALITY;
                }
                break;
            case QUALITY:
                validateQuality(builder, line, lineNumber);
                builder.withQuality(line.trim());
                state = State.COMPLETE;
                break;
            case COMPLETE:
                if (!builder.sequenceAndQualityLengthsMatch())
                {
                    builder.appendQuality(line.trim());
                }
                else
                {
                    try
                    {
                        result.add(builder.build());
                    }
                    catch (IllegalStateException e)
                    {
                        throw new IOException("caught an IllegalStateException at line " + lineNumber, e);
                    }
                    validateDescription(builder, line, lineNumber);
                    builder.withDescription(line.substring(1).trim());
                    state = State.SEQUENCE;
                }
                break;
            default:
                break;
            }
            lineNumber++;
        }
        if (state == State.COMPLETE)
        {
            try
            {
                result.add(builder.build());
                state = State.DESCRIPTION;
            }
            catch (IllegalStateException e)
            {
                throw new IOException("caught an IllegalStateException at line " + lineNumber, e);
            }
        }
        if (state != State.DESCRIPTION)
        {
            throw new IOException("truncated sequence at line " + lineNumber);
        }
        return result;
    }
}
@@ -7471,37 +7471,177 @@
 e %22 + lineNumber
-, e);
+ + %22 %22 + e.getMessage());%0D%0A                        //throw new IOException(%22caught an IllegalStateException at line %22 + lineNumber, e);  jdk 1.6+
 %0D%0A              
@@ -8316,21 +8316,153 @@
 neNumber
-, e);
+ + %22 %22 + e.getMessage());%0D%0A                //throw new IOException(%22caught an IllegalStateException at line %22 + lineNumber, e);  jdk 1.6+
 %0D%0A      

fix for IOException 1.6+ ctr use with jdk 1.5