net.maizegenetics.util.MultiMemberGZIPInputStream Maven / Gradle / Ivy

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TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
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/*
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package net.maizegenetics.util;

/**
 *
 * @author jcg233 
 * Code comes from one of the comments in: 
 * http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4691425
 * "GZIPInputStream fails to read concatenated .gz files"
 * 
 * So, the original author is anonymous.
 * 
 * Qi Sun first tested this.
 * 
 */
import java.io.InputStream;
import java.io.PushbackInputStream;
import java.util.zip.GZIPInputStream;
import java.io.IOException;

public
class MultiMemberGZIPInputStream extends GZIPInputStream {

    public MultiMemberGZIPInputStream(InputStream in, int size) throws IOException
    {
        // Wrap the stream in a PushbackInputStream...
        super(new PushbackInputStream(in, size), size);
        this.size=size;
    }

    public MultiMemberGZIPInputStream(InputStream in) throws IOException
    {
        // Wrap the stream in a PushbackInputStream...
        super(new PushbackInputStream(in, 1024));
        this.size=-1;
    }

    private MultiMemberGZIPInputStream(MultiMemberGZIPInputStream parent) throws IOException
    {
        super(parent.in);
        this.size=-1;
        this.parent=parent.parent==null ? parent : parent.parent;
        this.parent.child=this;
    }

    private MultiMemberGZIPInputStream(MultiMemberGZIPInputStream parent, int size) throws IOException
    {
        super(parent.in, size);
        this.size=size;
        this.parent=parent.parent==null ? parent : parent.parent;
        this.parent.child=this;
    }

    private MultiMemberGZIPInputStream parent;
    private MultiMemberGZIPInputStream child;
    private int size;
    private boolean eos;

    public int read(byte[] inputBuffer, int inputBufferOffset, int inputBufferLen) throws IOException {

        if (eos) { return -1;}
        if (this.child!=null)
            return this.child.read(inputBuffer, inputBufferOffset, inputBufferLen);

        int charsRead=super.read(inputBuffer, inputBufferOffset, inputBufferLen);
        if (charsRead==-1)
        {
            // Push any remaining buffered data back onto the stream
            // If the stream is then not empty, use it to construct
            // a new instance of this class and delegate this and any
            // future calls to it...
            int n = inf.getRemaining() - 8;
            if (n > 0)
            {
                // More than 8 bytes remaining in deflater
                // First 8 are gzip trailer. Add the rest to
                // any un-read data...
                ((PushbackInputStream)this.in).unread(buf, len-n, n);
            }
            else
            {
                // Nothing in the buffer. We need to know whether or not
                // there is unread data available in the underlying stream
                // since the base class will not handle an empty file.
                // Read a byte to see if there is data and if so,
                // push it back onto the stream...
                byte[] b=new byte[1];
                int ret=in.read(b,0,1);
                if (ret==-1)
                {
                    eos=true;
                    return -1;
                }
                else
                    ((PushbackInputStream)this.in).unread(b, 0, 1);
            }

            MultiMemberGZIPInputStream child;
            if (this.size==-1)
                child=new MultiMemberGZIPInputStream(this);
            else
                child=new MultiMemberGZIPInputStream(this, this.size);
            return child.read(inputBuffer, inputBufferOffset, inputBufferLen);
        }
        else
            return charsRead;
    }

}