[Biojava-l] SCF file wont load from URL

[K.R. Carter]

yes. here is the code snippet.

SCF scfFile = new SCF();

scfFile.load(new URL("
http://www.conifergdb.org/software/wtm0.6/process/guest@muohio.edu_060713_052442/chromat_dir/COLD1_16_H12.b1_A029").openStream(),
0);

I use this SCF class to open read files from the local machine and it works
perfectly fine. The hangup occurs when I try and open one from the URL.

i also put some system.out.println statements in the SCF class for debugging
purposes.

using v3 parser
begin parsing...
input stream not null
parsing samples...
reading samples into...
reading samples into...
reading samples into...
reading samples into...
parsing bases...

seems like once it reaches parsing bases, then the problem occurs. i placed
these println statments at the beginning of the methods. i put this:
System.out.println("file is parsed... ");
at the end of the parse() method:

public void parse() throws IOException,
                UnsupportedChromatogramFormatException {
            parsed = false;
            // sort the sections of the file by ascending offset
            Integer SAMPLES  = new Integer(0),
                    BASES    = new Integer(1),
                    COMMENTS = new Integer(2),
                    PRIVATE  = new Integer(3);
            TreeMap sectionOrder = new TreeMap();
            sectionOrder.put(new Long(header.samples_offset),  SAMPLES);
            sectionOrder.put(new Long(header.bases_offset),    BASES);
            sectionOrder.put(new Long(header.comments_offset), COMMENTS);
            sectionOrder.put(new Long(header.private_offset),  PRIVATE);

            for (Iterator it = sectionOrder.keySet().iterator() ;
            it.hasNext() ;) {
                Integer sect = (Integer) sectionOrder.get(it.next());
                if      (sect == SAMPLES)  parseSamples();
                else if (sect == BASES)    parseBases();
                else if (sect == COMMENTS) parseComments();
                else if (sect == PRIVATE)  parsePrivate();
            }
            parsed = true;
            System.out.println("file is parsed... "); <-- i added this
        }

That statement ("file is parsed") never gets printed. I believe the hangup
is at parseBases(). I'm unsure. I'm still trying to find out exactly where
it is.

Kiki

On 9/1/06, Andy Yates <ady at sanger.ac.uk> wrote:
>
> 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!
> >> > _______________________________________________
> >> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >> >
> >>
> >
>