[Biojava-l] SCF file wont load from URL

[Andy Yates]

Is it possible to send the snippit of code that you're running at all?

Andy

On Fri, 1 Sep 2006, K.R. Carter wrote:

> Thanks Andy,
>
> I programmatically set the proxy however, it still does not solve the
> problem.
>
> On 8/31/06, Andy Yates <ady at sanger.ac.uk> wrote:
>> 
>> 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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>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>> >
>> >
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>> >
>> 
>