[Biojava-l] BioJava-X parsing of RichSequences

[Ola Spjuth]

Thank you very much!
I shall update Bioclipse to use this for the next release (>0.9.0).

Cheers,

   .../Ola


On Thu, 2006-05-04 at 10:02 +0100, Richard Holland wrote:
> I have added the capability to guess the format of streams, and read
> directly from them. See RichSequence.IOTools.readStream() for details.
> 
> In CVS biojava-live now.
> 
> cheers,
> Richard
> 
> On Wed, 2006-05-03 at 19:54 +0200, Egon Willighagen wrote:
> > On Wednesday 03 May 2006 18:50, Francois Pepin wrote:
> > > How much of the file is generally being read before the guess is made?
> > > I'm thinking very little is needed, especially compared to how much
> > > memory Java usually takes.
> > 
> > Generally not much. Jmol uses 16384 bytes.
> > 
> > > It would not be very difficult to save that first part of the stream and
> > > then play it back once the guess is made.
> > 
> > See how Jmol does it:
> > 
> > http://svn.sourceforge.net/viewcvs.cgi/jmol/trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java?view=markup
> > 
> > > I kind of like the idea of using streams, in cases where you are not
> > > reading from a file. Having to write everything to a temporary file to
> > > satisfy the API isn't a very appealing solution, I think.
> > >
> > > I could code something up if people are interested.
> > 
> > An additional advantage is that you get .gz support in one go:
> > 
> >       BufferedInputStream bis = new BufferedInputStream((InputStream)t, 8192);
> >       InputStream is = bis;
> >       bis.mark(5);
> >       int countRead = 0;
> >       countRead = bis.read(abMagic, 0, 4);
> >       bis.reset();
> >       if (countRead == 4 &&
> >           abMagic[0] == (byte)0x1F && abMagic[1] == (byte)0x8B)
> >         is = new GZIPInputStream(bis);
> > 
> > where t is your InputStream, and is the stream to use after the gzip 
> > check/unzip. For the full working code, see again Jmol CVS:
> > 
> > http://svn.sourceforge.net/viewcvs.cgi/jmol/trunk/Jmol/src/org/jmol/viewer/FileManager.java?view=markup
> > 
> > Egon
> >