[Biojava-l] SCF file wont load from URL

[Andy Yates]

That sounds like http proxy problems in my book.

Try looking at this page: http://mindprod.com/jgloss/proxy.html

The main thing to take home is try setting the system properties:

proxySet=true
http.proxyHost=proxyHostName
http.proxyPort=proxyHostPort

You can do this programatically using the System.setProperty() method or 
with -DpropertyName=propertyValue from the command line.

Hope that helps,

Andy Yates

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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> 
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