[Biojava-l] SCF file wont load from URL

[K.R. Carter]

Hello,

There is no stack trace. Here is the code that regenerates the problem.

SCF scfFile = new SCF();
scfFile.load(new URL("http://www.link.org/file.scf").getInputStream(), 0);

I've also tried without any shortcuts.

 One thing to also note is that I was able to open an SCF file from an
internet stream using a class written by ncbi...it's really odd.

-Kiki

On 8/31/06, mark.schreiber at novartis.com <mark.schreiber at novartis.com> wrote:
>
> Hi -
>
> This sounds very strange. Is there any stack trace? Could you possibly
> post the code that recreates the problem?
>
> - Mark
>
>
>
>
>
> "K.R. Carter" <k_stellar at msn.com>
> Sent by: biojava-l-bounces at lists.open-bio.org
> 08/31/2006 04:34 AM
> Please respond to kikia.reneese
>
>
>         To:     biojava-l at biojava.org
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [Biojava-l] SCF file wont load from URL
>
>
> Hello,
>
> I am trying to load an scf file by using the input stream from a url and
> it
> will not load. Does anyone know what might be happening? My program doesnt
> give an error, it just completely freezes.  I am using the latest ( i
> think)
> version of SCF class.
>
>
> /**
> * A {@link org.biojava.bio.chromatogram.Chromatogram} as loaded from an
> * SCF v2 or v3 file.  Also loads and exposes the SCF format's "private
> data"
> * and "comments" sections.  The quality values from the SCF are stored as
> * additional sequences on the base call alignment. The labels are the
> * <code>PROB_</code>* constants in this class.
> * The values are {@link
> org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol}
> * objects in the range 0 to 255.
> *
> *
> * @author Rhett Sutphin (<a href="http://genome.uiowa.edu/">UI CBCB</a>)
> */
>
> any help would be greatly appreciated.
>
> Thanks!
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>
>
>