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TASSEL 6 is a software package to evaluate traits association. Feature Tables are at the heart of the package where, a feature is a range of positions or a single position. Row in the that table are taxon.
/*
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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;
}
}