From k_stellar at msn.com  Fri Sep  1 11:11:13 2006
From: k_stellar at msn.com (K.R. Carter)
Date: Fri, 1 Sep 2006 11:11:13 -0400
Subject: [Biojava-l] SCF file wont load from URL
In-Reply-To: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
References: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
Message-ID: <5d9376b50609010811l749aa271q85547e0d60860a6c@mail.gmail.com>

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!
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>

From k_stellar at msn.com  Fri Sep  1 11:21:14 2006
From: k_stellar at msn.com (K.R. Carter)
Date: Fri, 1 Sep 2006 11:21:14 -0400
Subject: [Biojava-l] SCF file wont load from URL
In-Reply-To: <44F6A237.1060302@sanger.ac.uk>
References: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
	<44F6A237.1060302@sanger.ac.uk>
Message-ID: <5d9376b50609010821v6c34011v199f43096b93df0c@mail.gmail.com>

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
> >
>

From ady at sanger.ac.uk  Fri Sep  1 12:50:53 2006
From: ady at sanger.ac.uk (Andy Yates)
Date: Fri, 1 Sep 2006 17:50:53 +0100 (BST)
Subject: [Biojava-l] SCF file wont load from URL
In-Reply-To: <5d9376b50609010821v6c34011v199f43096b93df0c@mail.gmail.com>
References: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
	<44F6A237.1060302@sanger.ac.uk>
	<5d9376b50609010821v6c34011v199f43096b93df0c@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0609011750200.13288@deskpro12500.dynamic.sanger.ac.uk>

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
>> >
>> 
>

From k_stellar at msn.com  Fri Sep  1 13:14:49 2006
From: k_stellar at msn.com (K.R. Carter)
Date: Fri, 1 Sep 2006 13:14:49 -0400
Subject: [Biojava-l] SCF file wont load from URL
In-Reply-To: <Pine.LNX.4.64.0609011750200.13288@deskpro12500.dynamic.sanger.ac.uk>
References: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
	<44F6A237.1060302@sanger.ac.uk>
	<5d9376b50609010821v6c34011v199f43096b93df0c@mail.gmail.com>
	<Pine.LNX.4.64.0609011750200.13288@deskpro12500.dynamic.sanger.ac.uk>
Message-ID: <5d9376b50609011014y636ee5b0ge1f1c81303d42884@mail.gmail.com>

yes. here is the code snippet.

SCF scfFile = new SCF();

scfFile.load(new URL("
http://www.conifergdb.org/software/wtm0.6/process/guest at 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
> >> >
> >>
> >
>

From ady at sanger.ac.uk  Fri Sep  1 13:46:35 2006
From: ady at sanger.ac.uk (Andy Yates)
Date: Fri, 1 Sep 2006 18:46:35 +0100 (BST)
Subject: [Biojava-l] SCF file wont load from URL
In-Reply-To: <5d9376b50609011014y636ee5b0ge1f1c81303d42884@mail.gmail.com>
References: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
	<44F6A237.1060302@sanger.ac.uk>
	<5d9376b50609010821v6c34011v199f43096b93df0c@mail.gmail.com>
	<Pine.LNX.4.64.0609011750200.13288@deskpro12500.dynamic.sanger.ac.uk>
	<5d9376b50609011014y636ee5b0ge1f1c81303d42884@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0609011821120.13288@deskpro12500.dynamic.sanger.ac.uk>

The only things I can suggest is to make sure that you can parse the file 
from the URL when it's on your local machine.

I've knocked up some code which I think shoudl work which is very similar 
to yours in principle the only major difference is that I've wrapped the 
InputStream in a BufferedInputStream which if anything will improve 
performance.

//-------
SCF scfFile = new SCF();
BufferedInputStream bis = null;
try {
 	bis = new BufferedInputStream(new 
URL("http://yoururl").openStream());
 	scfFile.load(bis);
}
catch(MalformedURLException e) {
 	System.err.println("Malformed URL");
 	e.printStackTrace();
}
catch(IOException e) {
 	System.err.println("Reading problem");
 	e.printStackTrace();
}
finally {
 	try {
 		bis.close();
 	}
 	catch(IOException e) {
 		System.err.println("Arrgh");
 		e.printStackTrace();
 	}
}
//-------

I know that this URL definatly works if nothing else does.

http://trace.ensembl.org/tmp/ml1B-a1798c05.q1c.scf.gz

To parse this file you'll have to pass wrap it all up in a GZIPInputStream 
such as:

BufferedInputStream bis = new BufferedInputStream(new 
GZIPInputStream(url.openStream()));

Hope that helps otherwise it seems like there might be quite an incidious 
problem in the code somewhere. In defence of the libraries my current 
group parses something like 30 traces per second at maximum input from a 
variety of resources including file based and URL based and we haven't 
encountered any problems. Normally if there is a problem with the parsing 
it is usually because the trace file is badly formed.

If you need to check this out try http://staden.sourceforge.net/ and 
staden io_lib which comes with the scf_dump program and trev which is a 
trace viewer.

Tell us how you get on

Andy

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

> yes. here is the code snippet.
>
> SCF scfFile = new SCF();
>
> scfFile.load(new URL("
> http://www.conifergdb.org/software/wtm0.6/process/guest at 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
>> >> >
>> >>
>> >
>> 
>

From k_stellar at msn.com  Fri Sep  1 14:03:19 2006
From: k_stellar at msn.com (K.R. Carter)
Date: Fri, 1 Sep 2006 14:03:19 -0400
Subject: [Biojava-l] SCF file wont load from URL
In-Reply-To: <Pine.LNX.4.64.0609011821120.13288@deskpro12500.dynamic.sanger.ac.uk>
References: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
	<44F6A237.1060302@sanger.ac.uk>
	<5d9376b50609010821v6c34011v199f43096b93df0c@mail.gmail.com>
	<Pine.LNX.4.64.0609011750200.13288@deskpro12500.dynamic.sanger.ac.uk>
	<5d9376b50609011014y636ee5b0ge1f1c81303d42884@mail.gmail.com>
	<Pine.LNX.4.64.0609011821120.13288@deskpro12500.dynamic.sanger.ac.uk>
Message-ID: <5d9376b50609011103h18aecfc8v9ab7723a86f1aee@mail.gmail.com>

OK. I think the trace may be badly formed. I say this because it worked with
no hangup after commenting out one line below:
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();  <-- i
commented this out
                else if (sect == PRIVATE)  parsePrivate();
            }

I believe that there is some problem with the comments section in my file.
Therefore I've simply commented out the line of code that parses the
comments until I can figure out what is wrong with my file. Another reason
I've come to think that it is the file is because all of my probabilities
are 0. I'm going to check out the staden web page to see if that can help me
determine what is wrong with my trace files. Thanks for all help. I'll let
you know when I find the exact problem.

Kiki

On 9/1/06, Andy Yates <ady at sanger.ac.uk> wrote:
>
> The only things I can suggest is to make sure that you can parse the file
> from the URL when it's on your local machine.
>
> I've knocked up some code which I think shoudl work which is very similar
> to yours in principle the only major difference is that I've wrapped the
> InputStream in a BufferedInputStream which if anything will improve
> performance.
>
> //-------
> SCF scfFile = new SCF();
> BufferedInputStream bis = null;
> try {
>         bis = new BufferedInputStream(new
> URL("http://yoururl").openStream());
>         scfFile.load(bis);
> }
> catch(MalformedURLException e) {
>         System.err.println("Malformed URL");
>         e.printStackTrace();
> }
> catch(IOException e) {
>         System.err.println("Reading problem");
>         e.printStackTrace();
> }
> finally {
>         try {
>                 bis.close();
>         }
>         catch(IOException e) {
>                 System.err.println("Arrgh");
>                 e.printStackTrace();
>         }
> }
> //-------
>
> I know that this URL definatly works if nothing else does.
>
> http://trace.ensembl.org/tmp/ml1B-a1798c05.q1c.scf.gz
>
> To parse this file you'll have to pass wrap it all up in a GZIPInputStream
> such as:
>
> BufferedInputStream bis = new BufferedInputStream(new
> GZIPInputStream(url.openStream()));
>
> Hope that helps otherwise it seems like there might be quite an incidious
> problem in the code somewhere. In defence of the libraries my current
> group parses something like 30 traces per second at maximum input from a
> variety of resources including file based and URL based and we haven't
> encountered any problems. Normally if there is a problem with the parsing
> it is usually because the trace file is badly formed.
>
> If you need to check this out try http://staden.sourceforge.net/ and
> staden io_lib which comes with the scf_dump program and trev which is a
> trace viewer.
>
> Tell us how you get on
>
> Andy
>
> On Fri, 1 Sep 2006, K.R. Carter wrote:
>
> > yes. here is the code snippet.
> >
> > SCF scfFile = new SCF();
> >
> > scfFile.load(new URL("
> >
> http://www.conifergdb.org/software/wtm0.6/process/guest at 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
> >> >> >
> >> >>
> >> >
> >>
> >
>

From ckol at iti.gr  Tue Sep  5 10:12:19 2006
From: ckol at iti.gr (Chrysa Collyda)
Date: Tue, 5 Sep 2006 17:12:19 +0300
Subject: [Biojava-l] Multiple Sequence Alignment with Profile HMMs
Message-ID: <004d01c6d0f5$4c94e870$3f55cf9b@CHRSOT>

Hello all,

I would like to pose again a question regarding multiple sequence alignment with profile HMMs. Any help would be deeply appreciated. 

i created a profile hmm from a set of unaligned homologues sequences then
i aligned some sequences to the model.i noticed that every sequence has
its own length for the alignment.is there any method by which i can create
a multiple sequence alignment between these sequences?


        thanks in advance,
        ckol



From christoph.gille at charite.de  Tue Sep  5 14:52:25 2006
From: christoph.gille at charite.de (Dr. Christoph Gille)
Date: Tue, 5 Sep 2006 20:52:25 +0200 (CEST)
Subject: [Biojava-l] EBI axis
Message-ID: <61674.84.190.59.28.1157482345.squirrel@webmail.charite.de>

Does somebody know whether the current biojava is using the
EBI SOAP Web services ?  EBI provides an API axis.jar.
I am just testing it.  Has somebody experiences with this API ?



From mark.schreiber at novartis.com  Tue Sep  5 20:55:19 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Wed, 6 Sep 2006 08:55:19 +0800
Subject: [Biojava-l] EBI axis
Message-ID: <OFF6DC25B7.5D5C6B4C-ON482571E1.000508A1-482571E1.00051091@ah.novartis.com>

Currently not but it would be a nice addition.

- Mark





"Dr. Christoph Gille" <christoph.gille at charite.de>
Sent by: biojava-l-bounces at lists.open-bio.org
09/06/2006 02:52 AM

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] EBI axis


Does somebody know whether the current biojava is using the
EBI SOAP Web services ?  EBI provides an API axis.jar.
I am just testing it.  Has somebody experiences with this API ?


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l




From mark.schreiber at novartis.com  Tue Sep  5 20:54:28 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Wed, 6 Sep 2006 08:54:28 +0800
Subject: [Biojava-l] Multiple Sequence Alignment with Profile HMMs
Message-ID: <OF163A4028.E0288473-ON482571E1.0004D23C-482571E1.0004FCBA@ah.novartis.com>

Hi -

At the moment the biojava HMMs can only do pairwise alignments. Your only 
options would be to do multiple pairwise alignments (following the 
principles of ClustalW) or align everything to a profile.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





"Chrysa Collyda" <ckol at iti.gr>
Sent by: biojava-l-bounces at lists.open-bio.org
09/05/2006 10:12 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Multiple Sequence Alignment with Profile HMMs


Hello all,

I would like to pose again a question regarding multiple sequence 
alignment with profile HMMs. Any help would be deeply appreciated. 

i created a profile hmm from a set of unaligned homologues sequences then
i aligned some sequences to the model.i noticed that every sequence has
its own length for the alignment.is there any method by which i can create
a multiple sequence alignment between these sequences?


        thanks in advance,
        ckol


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l




From tmo at ebi.ac.uk  Wed Sep  6 03:05:09 2006
From: tmo at ebi.ac.uk (Tom Oinn)
Date: Wed, 06 Sep 2006 08:05:09 +0100
Subject: [Biojava-l] EBI axis
In-Reply-To: <OFF6DC25B7.5D5C6B4C-ON482571E1.000508A1-482571E1.00051091@ah.novartis.com>
References: <OFF6DC25B7.5D5C6B4C-ON482571E1.000508A1-482571E1.00051091@ah.novartis.com>
Message-ID: <44FE7325.6000509@ebi.ac.uk>

mark.schreiber at novartis.com wrote:
> Currently not but it would be a nice addition.

For biojava I'd avoid using the jar file the EBI distributes - the 
services all have a common usage pattern so there might well be some 
mileage in creating a general invoker for services with this pattern.

Tom

> - Mark
> 
> 
> 
> 
> 
> "Dr. Christoph Gille" <christoph.gille at charite.de>
> Sent by: biojava-l-bounces at lists.open-bio.org
> 09/06/2006 02:52 AM
> 
>  
>         To:     biojava-l at biojava.org
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [Biojava-l] EBI axis
> 
> 
> Does somebody know whether the current biojava is using the
> EBI SOAP Web services ?  EBI provides an API axis.jar.
> I am just testing it.  Has somebody experiences with this API ?
> 
> 
> _______________________________________________
> 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


From mark.schreiber at novartis.com  Fri Sep  8 01:58:39 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 8 Sep 2006 13:58:39 +0800
Subject: [Biojava-l] biojava 1.5 beta release
Message-ID: <OF0E0180BE.ADF5BB96-ON482571E3.001DA974-482571E3.0020D63F@ah.novartis.com>

Dear All -

I have prepared a beta distribution of the much awaited biojava 1.5. The 
source, binaries and docs for the release can be obtained from the biojava 
site at http://biojava.org/wiki/BioJava:Download

The API docs are also available on line at 
http://www.biojava.org/docs/api15b/index.html

There are significant new features in this release:

* biojavax, the biojavax packages are extensions to the basic biojava. 
They give access to more detailed objects with better functionality. Most 
useful to the average user will be the new file parsers (see 
RichSequence.IOTools) and the RichSequence object. See the biojavax docs 
for more detail (http://biojava.org/wiki/BioJava:BioJavaXDocs).

* Hibernate interaction with BioSQL. The prefered method of interaction 
with BioSQL is now via Hibernate. RichSequence and it's associated objects 
have hibernate mappings to biosql databases. This provides a number of the 
benefits of Hibernates ORM to biojava, especially control over 
transactions and the removal of JDBC code. See 
http://biojava.org/wiki/BioJava:BioJavaXDocs#BioSQL_and_Hibernate. for 
details.

* Genetic Algorithms. A very flexible genetic algorithm library is 
available in the biojavax packages. Simple examples are at 
http://biojava.org/wiki/BioJava:BioJavaXDocs#Genetic_Algorithms. but much 
more powerful things are possible.

* Several new features are available in the Structure package that allow 
manipulation of 3D structure files and objects.

* Non HMM Implementations of the NW and SW alignment algorithms are now 
available in the alignment package.

* A new package for handling external processes 
(org.biojava.utils.process).

* Dozens of bug fixes.

Please take it out for a spin this weekend and let us know how it works. 
You will probably find it more reliable than biojava-1.4 even though this 
is technically a beta.

Many thanks to all the volunteers who have contributed to biojava!

Best regards,

- Mark



Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910


From stefang at fis.upv.es  Fri Sep  8 06:28:31 2006
From: stefang at fis.upv.es (Stefan Goetz)
Date: Fri, 8 Sep 2006 12:28:31 +0200
Subject: [Biojava-l] EBI axis
In-Reply-To: <61674.84.190.59.28.1157482345.squirrel@webmail.charite.de>
Message-ID: <001501c6d331$893de130$71a72a9e@stefang>

Yes, we use it in our application called Blast2GO to call the
WS_InterPro_Scan. 
It works really fine for us so far and was quite easy to integrate.
Cheers, Stefan G?tz

 ------------------------------------------------------------
 | Stefan G?tz - stefang(at)fis.upv.es                      |
 | IBM - Biomedical Informatics, Bioinformatics Area        |
 | BET - Bioengineering, Electronics and Telemedicine Group |
 | UPV - Politechnical University of Valencia - Spain       |
 ------------------------------------------------------------ 

> -----Original Message-----
> From: biojava-l-bounces at lists.open-bio.org 
> [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of 
> Dr. Christoph Gille
> Sent: Tuesday, September 05, 2006 8:52 PM
> To: biojava-l at biojava.org
> Subject: [Biojava-l] EBI axis
> 
> 
> Does somebody know whether the current biojava is using the
> EBI SOAP Web services ?  EBI provides an API axis.jar.
> I am just testing it.  Has somebody experiences with this API ?
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 



From srinandakumar at yahoo.com  Sat Sep  9 02:56:36 2006
From: srinandakumar at yahoo.com (srinandakumar at yahoo.com)
Date: Fri,  8 Sep 2006 23:56:36 -0700 (PDT)
Subject: [Biojava-l] I'm inviting you
Message-ID: <72625537.1157784996608.JavaMail.root@goodtree2.goodtree.com>

------=_Part_6685_72784630.1157784996607
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: 7bit


------=_Part_6685_72784630.1157784996607
Content-Type: text/html; charset=utf-8
Content-Transfer-Encoding: 7bit

<a href="http://www.goodtree.com/fr.html?i=373516x100000&f=biojava&iEv=ci2&l=&homeEmail=biojava-l at biojava.org">Accept my invitation</a><BR>It gives money to charity when you click on it.
It's invitation only.
------=_Part_6685_72784630.1157784996607--


From rajeee_sss at yahoo.com  Mon Sep 18 07:53:58 2006
From: rajeee_sss at yahoo.com (Rajeswari)
Date: Mon, 18 Sep 2006 04:53:58 -0700 (PDT)
Subject: [Biojava-l] (no subject)
Message-ID: <20060918115358.98507.qmail@web30010.mail.mud.yahoo.com>

Hi 
   
  How to read  FASTA,GENBANK,SWISSPORT and EMBL file using biojava coding.
   
  I download the programms from the biojava.org. but they compiled but not showme the result.
   
  how can i  break the crossproducts?
   
   
  Is there any reference book available for bio java?
   
   
  expecting the reply quickly.
   
  regards,
  s.rajee
   
   

 				
---------------------------------
Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business.

From sdavis2 at mail.nih.gov  Mon Sep 18 08:20:53 2006
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Mon, 18 Sep 2006 08:20:53 -0400
Subject: [Biojava-l] (no subject)
In-Reply-To: <20060918115358.98507.qmail@web30010.mail.mud.yahoo.com>
References: <20060918115358.98507.qmail@web30010.mail.mud.yahoo.com>
Message-ID: <200609180820.53883.sdavis2@mail.nih.gov>

On Monday 18 September 2006 07:53, Rajeswari wrote:
> Hi
>
>   How to read  FASTA,GENBANK,SWISSPORT and EMBL file using biojava coding.
>
>   I download the programms from the biojava.org. but they compiled but not
> showme the result.
>
>   how can i  break the crossproducts?
>
>
>   Is there any reference book available for bio java?
>
>
>   expecting the reply quickly.

You will probably need to read the documentation.

http://biojava.org/wiki/BioJava:CookBook
http://biojava.org/wiki/BioJava:Tutorial
http://www.biojava.org/docs/api14/index.html

Sean

From sdavis2 at mail.nih.gov  Mon Sep 18 08:20:53 2006
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Mon, 18 Sep 2006 08:20:53 -0400
Subject: [Biojava-l] (no subject)
In-Reply-To: <20060918115358.98507.qmail@web30010.mail.mud.yahoo.com>
References: <20060918115358.98507.qmail@web30010.mail.mud.yahoo.com>
Message-ID: <200609180820.53883.sdavis2@mail.nih.gov>

On Monday 18 September 2006 07:53, Rajeswari wrote:
> Hi
>
>   How to read  FASTA,GENBANK,SWISSPORT and EMBL file using biojava coding.
>
>   I download the programms from the biojava.org. but they compiled but not
> showme the result.
>
>   how can i  break the crossproducts?
>
>
>   Is there any reference book available for bio java?
>
>
>   expecting the reply quickly.

You will probably need to read the documentation.

http://biojava.org/wiki/BioJava:CookBook
http://biojava.org/wiki/BioJava:Tutorial
http://www.biojava.org/docs/api14/index.html

Sean

From jolyon.holdstock at ogt.co.uk  Wed Sep 20 11:35:11 2006
From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock)
Date: Wed, 20 Sep 2006 16:35:11 +0100
Subject: [Biojava-l] LabelledSequenceRenderer
Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F0100ABD7@EUCLID.internal.ogtip.com>

Hi,

 

I'm trying to use a LabelledSequenceRenderer with a
TranslatedSequencePanel.

It doesn't render properly - the sequence is curtailed and there is a
blank where the label should be.

I've seen messages in the archive that have commented on this but no
solution.

 

Can anyone help? Or is there an alternative strategy for labelling a
track?

 

Thanks,

 

Jolyon

 

 

Jolyon Holdstock Ph.D.

Senior Computational Biologist,

Oxford Gene Technology (Ops) Ltd.

Begbroke Business and Science Park

Sandy Lane, Yarnton

Oxford, OX5 1PF

 

Tel: 01865 309699

Fax: 01865 842116

 

Confidentiality Notice:

The contents of this email from the Oxford Gene Technology Group of
Companies are confidential and intended solely for the person to whom it
is addressed. It may contain privileged and confidential information. If
you are not the intended recipient you must not read, copy, distribute,
discuss or take any action in reliance on it.

 

 



From cezard at nokad-technology.com  Wed Sep 20 06:18:06 2006
From: cezard at nokad-technology.com (Titi)
Date: Wed, 20 Sep 2006 03:18:06 -0700 (PDT)
Subject: [Biojava-l] use NCBISequenceDB without gi AC
Message-ID: <6405091.post@talk.nabble.com>


Hello,

I'm quite new with biojava and need to retrieve Sequence from NCBI.
I've got Blast result containing accession number but this are from their
original database.
for example
dbj|BAC25242.1
gb|AAQ88642.1
emb|CAC08176.1

Is their any solution to transforme this accession number into gi ones so I
could use NCBISequenceDB.
Or any solution to access a single database with all kind of accession
number.

any answers are welcome.

Thanks

Tim

-- 
View this message in context: http://www.nabble.com/use-NCBISequenceDB-without-gi-AC-tf2304387.html#a6405091
Sent from the BioJava mailing list archive at Nabble.com.


From cezard at nokad-technology.com  Fri Sep 22 09:10:55 2006
From: cezard at nokad-technology.com (=?iso-8859-1?Q?CEZARD_Timoth=E9e?=)
Date: Fri, 22 Sep 2006 15:10:55 +0200
Subject: [Biojava-l] use NCBISequenceDB without gi AC
In-Reply-To: <4513A1A1.2000001@ebi.ac.uk>
Message-ID: <20060922131059.5C1CA443CF@smtp3-g19.free.fr>

Thank you for your answer.

I'm just too lazy I haven't read all the blast documentation.
If so, I may have found that set the -I option as true show the GI accession
number in the blast output.

Sorry for that.

Tim
-----Message d'origine-----
De?: Richard Holland [mailto:holland at ebi.ac.uk] 
Envoy??: vendredi 22 septembre 2006 10:41
??: Titi
Cc?: biojava-l at lists.open-bio.org
Objet?: Re: [Biojava-l] use NCBISequenceDB without gi AC

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

The answer is no, unfortunately. There is no way of automatically
mapping an accession from one database to another unless the source
database provider can give you access to a lookup table containing
equivalent pairs of accessions. Whether such things exist, I don't know!
It's best if you ask the database providers directly for advice.

You should also check your source sequence files that you used to run
the blast. You may find that the GI numbers are in the header lines of
the FASTA format, in which case you could parse the sequence files to
retrieve this information and build your own lookup table.

cheers,
Richard


Titi wrote:
> Hello,
> 
> I'm quite new with biojava and need to retrieve Sequence from NCBI.
> I've got Blast result containing accession number but this are from their
> original database.
> for example
> dbj|BAC25242.1
> gb|AAQ88642.1
> emb|CAC08176.1
> 
> Is their any solution to transforme this accession number into gi ones so
I
> could use NCBISequenceDB.
> Or any solution to access a single database with all kind of accession
> number.
> 
> any answers are welcome.
> 
> Thanks
> 
> Tim
> 
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.2.2 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFFE6Gh4C5LeMEKA/QRAl66AJsH7MzF6+4x7jY3795pFu295mQ4TgCbB5qf
ipqnv/Q8vVYYJmuTSC08HlE=
=Rsgd
-----END PGP SIGNATURE-----



From ks_moses at yahoo.com  Mon Sep 25 03:32:06 2006
From: ks_moses at yahoo.com (Simon Moses)
Date: Mon, 25 Sep 2006 00:32:06 -0700 (PDT)
Subject: [Biojava-l] biojava documentation download
Message-ID: <20060925073206.7702.qmail@web31814.mail.mud.yahoo.com>

dear sir,
   
  i want to maintain a local copy of biojava documentation(http://biojava.org/wiki/BioJava:CookBook, http://biojava.org/wiki/BioJava:Tutorial) in my system for reference. is that possible? if possible how can i download?
   
  regards,
  Simon Moses.


**************************
Visit My Home Page
http://www.geocities.com/ks_moses
updated: 28 Sep 2004.
Simon Moses
**************************
 		
---------------------------------
Do you Yahoo!?
 Get on board. You're invited to try the new Yahoo! Mail.

From rajeee_sss at yahoo.com  Mon Sep 25 05:08:06 2006
From: rajeee_sss at yahoo.com (Rajeswari)
Date: Mon, 25 Sep 2006 02:08:06 -0700 (PDT)
Subject: [Biojava-l] about reading files
Message-ID: <20060925090806.63969.qmail@web30001.mail.mud.yahoo.com>

Hi,
  How can I read a GenBank, Swissprot, And an Embl File through Bio-JAva?
   
  The programm given by biojave-org-Biojava- in anger shows error:
   
  ArrayIndexOutOf bounds Exception.
   
   
  Anybody plz offer me the correct programm or tell me the reason of this type of error
  and how can i recitify?
   
   
   
  cheers,
  s.rajee
   

 		
---------------------------------
Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls.  Great rates starting at 1?/min.

From jolyon.holdstock at ogt.co.uk  Mon Sep 25 09:10:18 2006
From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock)
Date: Mon, 25 Sep 2006 14:10:18 +0100
Subject: [Biojava-l] about reading files[Scanned]
Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F0100AE6D@EUCLID.internal.ogtip.com>

Have you tried passing a file to the program?
It expects one

For example:
>java ReadGB <genbank file>

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Rajeswari
Sent: 25 September 2006 10:08
To: Biojava-l at lists.open-bio.org
Subject: [Biojava-l] about reading files[Scanned]

Hi,
  How can I read a GenBank, Swissprot, And an Embl File through Bio-JAva?
   
  The programm given by biojave-org-Biojava- in anger shows error:
   
  ArrayIndexOutOf bounds Exception.
   
   
  Anybody plz offer me the correct programm or tell me the reason of this type of error
  and how can i recitify?
   
   
   
  cheers,
  s.rajee
   

 		
---------------------------------
Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls.  Great rates starting at 1?/min.
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l











This email has been scanned by Oxford Gene Technology Security Systems.



From gwu at molbio.mgh.harvard.edu  Mon Sep 25 12:44:25 2006
From: gwu at molbio.mgh.harvard.edu (gang wu)
Date: Mon, 25 Sep 2006 12:44:25 -0400
Subject: [Biojava-l] biojava documentation download
In-Reply-To: <20060925073206.7702.qmail@web31814.mail.mud.yahoo.com>
References: <20060925073206.7702.qmail@web31814.mail.mud.yahoo.com>
Message-ID: <45180769.1010700@molbio.mgh.harvard.edu>

Did you try wget?

wget -r -l0 http://biojava.org/wiki/BioJava:CookBook
wget -r -l0 http://biojava.org/wiki/BioJava:Tutorial

Gang



Simon Moses wrote:
> dear sir,
>    
>   i want to maintain a local copy of biojava documentation(http://biojava.org/wiki/BioJava:CookBook, http://biojava.org/wiki/BioJava:Tutorial) in my system for reference. is that possible? if possible how can i download?
>    
>   regards,
>   Simon Moses.
>
>
> **************************
> Visit My Home Page
> http://www.geocities.com/ks_moses
> updated: 28 Sep 2004.
> Simon Moses
> **************************
>  		
> ---------------------------------
> Do you Yahoo!?
>  Get on board. You're invited to try the new Yahoo! Mail.
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>   


From gwu at molbio.mgh.harvard.edu  Tue Sep 26 17:26:45 2006
From: gwu at molbio.mgh.harvard.edu (gang wu)
Date: Tue, 26 Sep 2006 17:26:45 -0400
Subject: [Biojava-l] how to get specific data from biosql database
In-Reply-To: <20060925090806.63969.qmail@web30001.mail.mud.yahoo.com>
References: <20060925090806.63969.qmail@web30001.mail.mud.yahoo.com>
Message-ID: <45199B15.5040809@molbio.mgh.harvard.edu>

Hi Everyone,

I finally finished loading some Genbank genome sequences(Arabidopsis 
thaliana and C. elegans) into my MySQL(5.0.19 on Redhad AS 4) BioSQL 
database though the load_seqdatabase.pl works extremely slow(If turning 
on -debug, a lot of messages about not able to find adaptor class for 
Bio::Annotation::TypeManager, is this about the dynamic library loading 
issue mention in one of Hilmar's message?).

Now I'm writing views and stored procedures so other projects can easily 
retrieve specific information. It's quite easy to write views like  
showing all organisms, showing all version information etc. But so far I 
have not figured out how to write a SQL statement to list all genes 
corresponding to the genbank files. Can anyone show me how to get the 
information or let me know where to find related guide? Thanks in advance.

Gang

From smh1008 at cam.ac.uk  Tue Sep 26 17:38:41 2006
From: smh1008 at cam.ac.uk (David Huen)
Date: 26 Sep 2006 22:38:41 +0100
Subject: [Biojava-l] how to get specific data from biosql database
In-Reply-To: <45199B15.5040809@molbio.mgh.harvard.edu>
References: <20060925090806.63969.qmail@web30001.mail.mud.yahoo.com>
	<45199B15.5040809@molbio.mgh.harvard.edu>
Message-ID: <Prayer.1.0.18.0609262238410.17909@hermes-2.csi.cam.ac.uk>

On Sep 26 2006, gang wu wrote:

Have you mailed the wrong list inadvertently? It would seem to be intended 
for Bioperl-l.

Best wishes,
David Huen

>Hi Everyone,
>
>I finally finished loading some Genbank genome sequences(Arabidopsis 
>thaliana and C. elegans) into my MySQL(5.0.19 on Redhad AS 4) BioSQL 
>database though the load_seqdatabase.pl works extremely slow(If turning 
>on -debug, a lot of messages about not able to find adaptor class for 
>Bio::Annotation::TypeManager, is this about the dynamic library loading 
>issue mention in one of Hilmar's message?).
>
>Now I'm writing views and stored procedures so other projects can easily 
>retrieve specific information. It's quite easy to write views like  
>showing all organisms, showing all version information etc. But so far I 
>have not figured out how to write a SQL statement to list all genes 
>corresponding to the genbank files. Can anyone show me how to get the 
>information or let me know where to find related guide? Thanks in advance.
>


From gwu at molbio.mgh.harvard.edu  Tue Sep 26 21:29:59 2006
From: gwu at molbio.mgh.harvard.edu (gang wu)
Date: Tue, 26 Sep 2006 21:29:59 -0400
Subject: [Biojava-l] how to get specific data from biosql database
In-Reply-To: <Prayer.1.0.18.0609262238410.17909@hermes-2.csi.cam.ac.uk>
References: <20060925090806.63969.qmail@web30001.mail.mud.yahoo.com>
	<45199B15.5040809@molbio.mgh.harvard.edu>
	<Prayer.1.0.18.0609262238410.17909@hermes-2.csi.cam.ac.uk>
Message-ID: <4519D417.9010609@molbio.mgh.harvard.edu>

Sorry for posting to the wrong list.Seems my mail client(Thunderbird) 
filters has a little problem and some BioJava list mails are saved in my 
BioSQL list folder. And I happened to pick one from BioJava and posed to 
the list address. I'll double check the list address in the future. Thanks.

Gang

David Huen wrote:
> On Sep 26 2006, gang wu wrote:
>
> Have you mailed the wrong list inadvertently? It would seem to be 
> intended for Bioperl-l.
>
> Best wishes,
> David Huen
>
>> Hi Everyone,
>>
>> I finally finished loading some Genbank genome sequences(Arabidopsis 
>> thaliana and C. elegans) into my MySQL(5.0.19 on Redhad AS 4) BioSQL 
>> database though the load_seqdatabase.pl works extremely slow(If 
>> turning on -debug, a lot of messages about not able to find adaptor 
>> class for Bio::Annotation::TypeManager, is this about the dynamic 
>> library loading issue mention in one of Hilmar's message?).
>>
>> Now I'm writing views and stored procedures so other projects can 
>> easily retrieve specific information. It's quite easy to write views 
>> like  showing all organisms, showing all version information etc. But 
>> so far I have not figured out how to write a SQL statement to list 
>> all genes corresponding to the genbank files. Can anyone show me how 
>> to get the information or let me know where to find related guide? 
>> Thanks in advance.
>>
>


From gautam.thakur at gmail.com  Fri Sep 29 03:37:51 2006
From: gautam.thakur at gmail.com (Gautam S. Thakur)
Date: Fri, 29 Sep 2006 03:37:51 -0400
Subject: [Biojava-l] getting protein id
Message-ID: <305798d50609290037l14a25d60u3509f2a55aae1c32@mail.gmail.com>

Hi,

As you know that every protein sequence has some unique header defined like
the below one

>gi|16127996|ref|NP_414543.1|bifunctional aspartokinase I/homeserine
dehydrogenase I [Escherichia coli K12]


I'm using biojava 1.5 API to read and extract the protein information.
However, I am not able to  get the Sequence ID (16127996) of the protein
that is after the "gi" string in above. Can anybody tell me how to get that?
Following code is correct and working but not giving the id as output, even
after checking all the related member function.

--------------------------------------------------------------------
try{
           BufferedReader br = new BufferedReader(
                   new FileReader("datafile"));
           //Getting the protein alphabet
           //Alphabet protein = AlphabetManager.alphabetForName("PROTEIN");
           org.biojavax.bio.seq.RichSequenceIterator richStream =
org.biojavax.bio.seq.RichSequence.IOTools.readFastaProtein(br, null);
//SeqIOTools.readFastaProtein(br);
           while(richStream.hasNext()){
               org.biojavax.bio.seq.RichSequence richSeq =
richStream.nextRichSequence();
               System.out.println(richSeq.getAccession());
               System.out.println(richSeq.getAlphabet());
               System.out.println(richSeq.getAnnotation());
               System.out.println(richSeq.getName());
               System.out.println(richSeq.getDescription());
               System.out.println(richSeq.getIdentifier());
               System.out.println(richSeq.seqString());
}                  }catch(Exception e) {
           //do nothing
       }
--------------------------------------------------------------------

Can any one help me out as to how to get the protein id?

Thanks and Regards,

-Gautam

-- 
"Destiny is no matter of chance.
It is a matter of choice.
It is not a thing to be waited for,
it is a thing to be achieved"

From markjschreiber at gmail.com  Fri Sep 29 04:33:17 2006
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 29 Sep 2006 16:33:17 +0800
Subject: [Biojava-l] getting protein id
In-Reply-To: <305798d50609290037l14a25d60u3509f2a55aae1c32@mail.gmail.com>
References: <305798d50609290037l14a25d60u3509f2a55aae1c32@mail.gmail.com>
Message-ID: <93b45ca50609290133q276fe319pffd34767e5758f34@mail.gmail.com>

Hi -

The GI should be returned by the getIdentifier() method. Is that not the case?

- Mark

On 9/29/06, Gautam S. Thakur <gautam.thakur at gmail.com> wrote:
> Hi,
>
> As you know that every protein sequence has some unique header defined like
> the below one
>
> >gi|16127996|ref|NP_414543.1|bifunctional aspartokinase I/homeserine
> dehydrogenase I [Escherichia coli K12]
>
>
> I'm using biojava 1.5 API to read and extract the protein information.
> However, I am not able to  get the Sequence ID (16127996) of the protein
> that is after the "gi" string in above. Can anybody tell me how to get that?
> Following code is correct and working but not giving the id as output, even
> after checking all the related member function.
>
> --------------------------------------------------------------------
> try{
>            BufferedReader br = new BufferedReader(
>                    new FileReader("datafile"));
>            //Getting the protein alphabet
>            //Alphabet protein = AlphabetManager.alphabetForName("PROTEIN");
>            org.biojavax.bio.seq.RichSequenceIterator richStream =
> org.biojavax.bio.seq.RichSequence.IOTools.readFastaProtein(br, null);
> //SeqIOTools.readFastaProtein(br);
>            while(richStream.hasNext()){
>                org.biojavax.bio.seq.RichSequence richSeq =
> richStream.nextRichSequence();
>                System.out.println(richSeq.getAccession());
>                System.out.println(richSeq.getAlphabet());
>                System.out.println(richSeq.getAnnotation());
>                System.out.println(richSeq.getName());
>                System.out.println(richSeq.getDescription());
>                System.out.println(richSeq.getIdentifier());
>                System.out.println(richSeq.seqString());
> }                  }catch(Exception e) {
>            //do nothing
>        }
> --------------------------------------------------------------------
>
> Can any one help me out as to how to get the protein id?
>
> Thanks and Regards,
>
> -Gautam
>
> --
> "Destiny is no matter of chance.
> It is a matter of choice.
> It is not a thing to be waited for,
> it is a thing to be achieved"
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From k_stellar at msn.com  Fri Sep  1 15:11:13 2006
From: k_stellar at msn.com (K.R. Carter)
Date: Fri, 1 Sep 2006 11:11:13 -0400
Subject: [Biojava-l] SCF file wont load from URL
In-Reply-To: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
References: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
Message-ID: <5d9376b50609010811l749aa271q85547e0d60860a6c@mail.gmail.com>

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!
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>


From k_stellar at msn.com  Fri Sep  1 15:21:14 2006
From: k_stellar at msn.com (K.R. Carter)
Date: Fri, 1 Sep 2006 11:21:14 -0400
Subject: [Biojava-l] SCF file wont load from URL
In-Reply-To: <44F6A237.1060302@sanger.ac.uk>
References: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
	<44F6A237.1060302@sanger.ac.uk>
Message-ID: <5d9376b50609010821v6c34011v199f43096b93df0c@mail.gmail.com>

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
> >
>


From ady at sanger.ac.uk  Fri Sep  1 16:50:53 2006
From: ady at sanger.ac.uk (Andy Yates)
Date: Fri, 1 Sep 2006 17:50:53 +0100 (BST)
Subject: [Biojava-l] SCF file wont load from URL
In-Reply-To: <5d9376b50609010821v6c34011v199f43096b93df0c@mail.gmail.com>
References: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
	<44F6A237.1060302@sanger.ac.uk>
	<5d9376b50609010821v6c34011v199f43096b93df0c@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0609011750200.13288@deskpro12500.dynamic.sanger.ac.uk>

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
>> >
>> 
>


From k_stellar at msn.com  Fri Sep  1 17:14:49 2006
From: k_stellar at msn.com (K.R. Carter)
Date: Fri, 1 Sep 2006 13:14:49 -0400
Subject: [Biojava-l] SCF file wont load from URL
In-Reply-To: <Pine.LNX.4.64.0609011750200.13288@deskpro12500.dynamic.sanger.ac.uk>
References: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
	<44F6A237.1060302@sanger.ac.uk>
	<5d9376b50609010821v6c34011v199f43096b93df0c@mail.gmail.com>
	<Pine.LNX.4.64.0609011750200.13288@deskpro12500.dynamic.sanger.ac.uk>
Message-ID: <5d9376b50609011014y636ee5b0ge1f1c81303d42884@mail.gmail.com>

yes. here is the code snippet.

SCF scfFile = new SCF();

scfFile.load(new URL("
http://www.conifergdb.org/software/wtm0.6/process/guest at 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
> >> >
> >>
> >
>


From ady at sanger.ac.uk  Fri Sep  1 17:46:35 2006
From: ady at sanger.ac.uk (Andy Yates)
Date: Fri, 1 Sep 2006 18:46:35 +0100 (BST)
Subject: [Biojava-l] SCF file wont load from URL
In-Reply-To: <5d9376b50609011014y636ee5b0ge1f1c81303d42884@mail.gmail.com>
References: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
	<44F6A237.1060302@sanger.ac.uk>
	<5d9376b50609010821v6c34011v199f43096b93df0c@mail.gmail.com>
	<Pine.LNX.4.64.0609011750200.13288@deskpro12500.dynamic.sanger.ac.uk>
	<5d9376b50609011014y636ee5b0ge1f1c81303d42884@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0609011821120.13288@deskpro12500.dynamic.sanger.ac.uk>

The only things I can suggest is to make sure that you can parse the file 
from the URL when it's on your local machine.

I've knocked up some code which I think shoudl work which is very similar 
to yours in principle the only major difference is that I've wrapped the 
InputStream in a BufferedInputStream which if anything will improve 
performance.

//-------
SCF scfFile = new SCF();
BufferedInputStream bis = null;
try {
 	bis = new BufferedInputStream(new 
URL("http://yoururl").openStream());
 	scfFile.load(bis);
}
catch(MalformedURLException e) {
 	System.err.println("Malformed URL");
 	e.printStackTrace();
}
catch(IOException e) {
 	System.err.println("Reading problem");
 	e.printStackTrace();
}
finally {
 	try {
 		bis.close();
 	}
 	catch(IOException e) {
 		System.err.println("Arrgh");
 		e.printStackTrace();
 	}
}
//-------

I know that this URL definatly works if nothing else does.

http://trace.ensembl.org/tmp/ml1B-a1798c05.q1c.scf.gz

To parse this file you'll have to pass wrap it all up in a GZIPInputStream 
such as:

BufferedInputStream bis = new BufferedInputStream(new 
GZIPInputStream(url.openStream()));

Hope that helps otherwise it seems like there might be quite an incidious 
problem in the code somewhere. In defence of the libraries my current 
group parses something like 30 traces per second at maximum input from a 
variety of resources including file based and URL based and we haven't 
encountered any problems. Normally if there is a problem with the parsing 
it is usually because the trace file is badly formed.

If you need to check this out try http://staden.sourceforge.net/ and 
staden io_lib which comes with the scf_dump program and trev which is a 
trace viewer.

Tell us how you get on

Andy

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

> yes. here is the code snippet.
>
> SCF scfFile = new SCF();
>
> scfFile.load(new URL("
> http://www.conifergdb.org/software/wtm0.6/process/guest at 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
>> >> >
>> >>
>> >
>> 
>


From k_stellar at msn.com  Fri Sep  1 18:03:19 2006
From: k_stellar at msn.com (K.R. Carter)
Date: Fri, 1 Sep 2006 14:03:19 -0400
Subject: [Biojava-l] SCF file wont load from URL
In-Reply-To: <Pine.LNX.4.64.0609011821120.13288@deskpro12500.dynamic.sanger.ac.uk>
References: <OF043651A4.CF475F6A-ON482571DB.002670F3-482571DB.002697C3@ah.novartis.com>
	<44F6A237.1060302@sanger.ac.uk>
	<5d9376b50609010821v6c34011v199f43096b93df0c@mail.gmail.com>
	<Pine.LNX.4.64.0609011750200.13288@deskpro12500.dynamic.sanger.ac.uk>
	<5d9376b50609011014y636ee5b0ge1f1c81303d42884@mail.gmail.com>
	<Pine.LNX.4.64.0609011821120.13288@deskpro12500.dynamic.sanger.ac.uk>
Message-ID: <5d9376b50609011103h18aecfc8v9ab7723a86f1aee@mail.gmail.com>

OK. I think the trace may be badly formed. I say this because it worked with
no hangup after commenting out one line below:
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();  <-- i
commented this out
                else if (sect == PRIVATE)  parsePrivate();
            }

I believe that there is some problem with the comments section in my file.
Therefore I've simply commented out the line of code that parses the
comments until I can figure out what is wrong with my file. Another reason
I've come to think that it is the file is because all of my probabilities
are 0. I'm going to check out the staden web page to see if that can help me
determine what is wrong with my trace files. Thanks for all help. I'll let
you know when I find the exact problem.

Kiki

On 9/1/06, Andy Yates <ady at sanger.ac.uk> wrote:
>
> The only things I can suggest is to make sure that you can parse the file
> from the URL when it's on your local machine.
>
> I've knocked up some code which I think shoudl work which is very similar
> to yours in principle the only major difference is that I've wrapped the
> InputStream in a BufferedInputStream which if anything will improve
> performance.
>
> //-------
> SCF scfFile = new SCF();
> BufferedInputStream bis = null;
> try {
>         bis = new BufferedInputStream(new
> URL("http://yoururl").openStream());
>         scfFile.load(bis);
> }
> catch(MalformedURLException e) {
>         System.err.println("Malformed URL");
>         e.printStackTrace();
> }
> catch(IOException e) {
>         System.err.println("Reading problem");
>         e.printStackTrace();
> }
> finally {
>         try {
>                 bis.close();
>         }
>         catch(IOException e) {
>                 System.err.println("Arrgh");
>                 e.printStackTrace();
>         }
> }
> //-------
>
> I know that this URL definatly works if nothing else does.
>
> http://trace.ensembl.org/tmp/ml1B-a1798c05.q1c.scf.gz
>
> To parse this file you'll have to pass wrap it all up in a GZIPInputStream
> such as:
>
> BufferedInputStream bis = new BufferedInputStream(new
> GZIPInputStream(url.openStream()));
>
> Hope that helps otherwise it seems like there might be quite an incidious
> problem in the code somewhere. In defence of the libraries my current
> group parses something like 30 traces per second at maximum input from a
> variety of resources including file based and URL based and we haven't
> encountered any problems. Normally if there is a problem with the parsing
> it is usually because the trace file is badly formed.
>
> If you need to check this out try http://staden.sourceforge.net/ and
> staden io_lib which comes with the scf_dump program and trev which is a
> trace viewer.
>
> Tell us how you get on
>
> Andy
>
> On Fri, 1 Sep 2006, K.R. Carter wrote:
>
> > yes. here is the code snippet.
> >
> > SCF scfFile = new SCF();
> >
> > scfFile.load(new URL("
> >
> http://www.conifergdb.org/software/wtm0.6/process/guest at 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
> >> >> >
> >> >>
> >> >
> >>
> >
>


From ckol at iti.gr  Tue Sep  5 14:12:19 2006
From: ckol at iti.gr (Chrysa Collyda)
Date: Tue, 5 Sep 2006 17:12:19 +0300
Subject: [Biojava-l] Multiple Sequence Alignment with Profile HMMs
Message-ID: <004d01c6d0f5$4c94e870$3f55cf9b@CHRSOT>

Hello all,

I would like to pose again a question regarding multiple sequence alignment with profile HMMs. Any help would be deeply appreciated. 

i created a profile hmm from a set of unaligned homologues sequences then
i aligned some sequences to the model.i noticed that every sequence has
its own length for the alignment.is there any method by which i can create
a multiple sequence alignment between these sequences?


        thanks in advance,
        ckol




From christoph.gille at charite.de  Tue Sep  5 18:52:25 2006
From: christoph.gille at charite.de (Dr. Christoph Gille)
Date: Tue, 5 Sep 2006 20:52:25 +0200 (CEST)
Subject: [Biojava-l] EBI axis
Message-ID: <61674.84.190.59.28.1157482345.squirrel@webmail.charite.de>

Does somebody know whether the current biojava is using the
EBI SOAP Web services ?  EBI provides an API axis.jar.
I am just testing it.  Has somebody experiences with this API ?




From mark.schreiber at novartis.com  Wed Sep  6 00:55:19 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Wed, 6 Sep 2006 08:55:19 +0800
Subject: [Biojava-l] EBI axis
Message-ID: <OFF6DC25B7.5D5C6B4C-ON482571E1.000508A1-482571E1.00051091@ah.novartis.com>

Currently not but it would be a nice addition.

- Mark





"Dr. Christoph Gille" <christoph.gille at charite.de>
Sent by: biojava-l-bounces at lists.open-bio.org
09/06/2006 02:52 AM

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] EBI axis


Does somebody know whether the current biojava is using the
EBI SOAP Web services ?  EBI provides an API axis.jar.
I am just testing it.  Has somebody experiences with this API ?


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l





From mark.schreiber at novartis.com  Wed Sep  6 00:54:28 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Wed, 6 Sep 2006 08:54:28 +0800
Subject: [Biojava-l] Multiple Sequence Alignment with Profile HMMs
Message-ID: <OF163A4028.E0288473-ON482571E1.0004D23C-482571E1.0004FCBA@ah.novartis.com>

Hi -

At the moment the biojava HMMs can only do pairwise alignments. Your only 
options would be to do multiple pairwise alignments (following the 
principles of ClustalW) or align everything to a profile.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





"Chrysa Collyda" <ckol at iti.gr>
Sent by: biojava-l-bounces at lists.open-bio.org
09/05/2006 10:12 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Multiple Sequence Alignment with Profile HMMs


Hello all,

I would like to pose again a question regarding multiple sequence 
alignment with profile HMMs. Any help would be deeply appreciated. 

i created a profile hmm from a set of unaligned homologues sequences then
i aligned some sequences to the model.i noticed that every sequence has
its own length for the alignment.is there any method by which i can create
a multiple sequence alignment between these sequences?


        thanks in advance,
        ckol


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l





From tmo at ebi.ac.uk  Wed Sep  6 07:05:09 2006
From: tmo at ebi.ac.uk (Tom Oinn)
Date: Wed, 06 Sep 2006 08:05:09 +0100
Subject: [Biojava-l] EBI axis
In-Reply-To: <OFF6DC25B7.5D5C6B4C-ON482571E1.000508A1-482571E1.00051091@ah.novartis.com>
References: <OFF6DC25B7.5D5C6B4C-ON482571E1.000508A1-482571E1.00051091@ah.novartis.com>
Message-ID: <44FE7325.6000509@ebi.ac.uk>

mark.schreiber at novartis.com wrote:
> Currently not but it would be a nice addition.

For biojava I'd avoid using the jar file the EBI distributes - the 
services all have a common usage pattern so there might well be some 
mileage in creating a general invoker for services with this pattern.

Tom

> - Mark
> 
> 
> 
> 
> 
> "Dr. Christoph Gille" <christoph.gille at charite.de>
> Sent by: biojava-l-bounces at lists.open-bio.org
> 09/06/2006 02:52 AM
> 
>  
>         To:     biojava-l at biojava.org
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [Biojava-l] EBI axis
> 
> 
> Does somebody know whether the current biojava is using the
> EBI SOAP Web services ?  EBI provides an API axis.jar.
> I am just testing it.  Has somebody experiences with this API ?
> 
> 
> _______________________________________________
> 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



From mark.schreiber at novartis.com  Fri Sep  8 05:58:39 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 8 Sep 2006 13:58:39 +0800
Subject: [Biojava-l] biojava 1.5 beta release
Message-ID: <OF0E0180BE.ADF5BB96-ON482571E3.001DA974-482571E3.0020D63F@ah.novartis.com>

Dear All -

I have prepared a beta distribution of the much awaited biojava 1.5. The 
source, binaries and docs for the release can be obtained from the biojava 
site at http://biojava.org/wiki/BioJava:Download

The API docs are also available on line at 
http://www.biojava.org/docs/api15b/index.html

There are significant new features in this release:

* biojavax, the biojavax packages are extensions to the basic biojava. 
They give access to more detailed objects with better functionality. Most 
useful to the average user will be the new file parsers (see 
RichSequence.IOTools) and the RichSequence object. See the biojavax docs 
for more detail (http://biojava.org/wiki/BioJava:BioJavaXDocs).

* Hibernate interaction with BioSQL. The prefered method of interaction 
with BioSQL is now via Hibernate. RichSequence and it's associated objects 
have hibernate mappings to biosql databases. This provides a number of the 
benefits of Hibernates ORM to biojava, especially control over 
transactions and the removal of JDBC code. See 
http://biojava.org/wiki/BioJava:BioJavaXDocs#BioSQL_and_Hibernate. for 
details.

* Genetic Algorithms. A very flexible genetic algorithm library is 
available in the biojavax packages. Simple examples are at 
http://biojava.org/wiki/BioJava:BioJavaXDocs#Genetic_Algorithms. but much 
more powerful things are possible.

* Several new features are available in the Structure package that allow 
manipulation of 3D structure files and objects.

* Non HMM Implementations of the NW and SW alignment algorithms are now 
available in the alignment package.

* A new package for handling external processes 
(org.biojava.utils.process).

* Dozens of bug fixes.

Please take it out for a spin this weekend and let us know how it works. 
You will probably find it more reliable than biojava-1.4 even though this 
is technically a beta.

Many thanks to all the volunteers who have contributed to biojava!

Best regards,

- Mark



Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910



From stefang at fis.upv.es  Fri Sep  8 10:28:31 2006
From: stefang at fis.upv.es (Stefan Goetz)
Date: Fri, 8 Sep 2006 12:28:31 +0200
Subject: [Biojava-l] EBI axis
In-Reply-To: <61674.84.190.59.28.1157482345.squirrel@webmail.charite.de>
Message-ID: <001501c6d331$893de130$71a72a9e@stefang>

Yes, we use it in our application called Blast2GO to call the
WS_InterPro_Scan. 
It works really fine for us so far and was quite easy to integrate.
Cheers, Stefan G?tz

 ------------------------------------------------------------
 | Stefan G?tz - stefang(at)fis.upv.es                      |
 | IBM - Biomedical Informatics, Bioinformatics Area        |
 | BET - Bioengineering, Electronics and Telemedicine Group |
 | UPV - Politechnical University of Valencia - Spain       |
 ------------------------------------------------------------ 

> -----Original Message-----
> From: biojava-l-bounces at lists.open-bio.org 
> [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of 
> Dr. Christoph Gille
> Sent: Tuesday, September 05, 2006 8:52 PM
> To: biojava-l at biojava.org
> Subject: [Biojava-l] EBI axis
> 
> 
> Does somebody know whether the current biojava is using the
> EBI SOAP Web services ?  EBI provides an API axis.jar.
> I am just testing it.  Has somebody experiences with this API ?
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 




From srinandakumar at yahoo.com  Sat Sep  9 06:56:36 2006
From: srinandakumar at yahoo.com (srinandakumar at yahoo.com)
Date: Fri,  8 Sep 2006 23:56:36 -0700 (PDT)
Subject: [Biojava-l] I'm inviting you
Message-ID: <72625537.1157784996608.JavaMail.root@goodtree2.goodtree.com>

------=_Part_6685_72784630.1157784996607
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: 7bit


------=_Part_6685_72784630.1157784996607
Content-Type: text/html; charset=utf-8
Content-Transfer-Encoding: 7bit

<a href="http://www.goodtree.com/fr.html?i=373516x100000&f=biojava&iEv=ci2&l=&homeEmail=biojava-l at biojava.org">Accept my invitation</a><BR>It gives money to charity when you click on it.
It's invitation only.
------=_Part_6685_72784630.1157784996607--



From rajeee_sss at yahoo.com  Mon Sep 18 11:53:58 2006
From: rajeee_sss at yahoo.com (Rajeswari)
Date: Mon, 18 Sep 2006 04:53:58 -0700 (PDT)
Subject: [Biojava-l] (no subject)
Message-ID: <20060918115358.98507.qmail@web30010.mail.mud.yahoo.com>

Hi 
   
  How to read  FASTA,GENBANK,SWISSPORT and EMBL file using biojava coding.
   
  I download the programms from the biojava.org. but they compiled but not showme the result.
   
  how can i  break the crossproducts?
   
   
  Is there any reference book available for bio java?
   
   
  expecting the reply quickly.
   
  regards,
  s.rajee
   
   

 				
---------------------------------
Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business.


From sdavis2 at mail.nih.gov  Mon Sep 18 12:20:53 2006
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Mon, 18 Sep 2006 08:20:53 -0400
Subject: [Biojava-l] (no subject)
In-Reply-To: <20060918115358.98507.qmail@web30010.mail.mud.yahoo.com>
References: <20060918115358.98507.qmail@web30010.mail.mud.yahoo.com>
Message-ID: <200609180820.53883.sdavis2@mail.nih.gov>

On Monday 18 September 2006 07:53, Rajeswari wrote:
> Hi
>
>   How to read  FASTA,GENBANK,SWISSPORT and EMBL file using biojava coding.
>
>   I download the programms from the biojava.org. but they compiled but not
> showme the result.
>
>   how can i  break the crossproducts?
>
>
>   Is there any reference book available for bio java?
>
>
>   expecting the reply quickly.

You will probably need to read the documentation.

http://biojava.org/wiki/BioJava:CookBook
http://biojava.org/wiki/BioJava:Tutorial
http://www.biojava.org/docs/api14/index.html

Sean


From sdavis2 at mail.nih.gov  Mon Sep 18 12:20:53 2006
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Mon, 18 Sep 2006 08:20:53 -0400
Subject: [Biojava-l] (no subject)
In-Reply-To: <20060918115358.98507.qmail@web30010.mail.mud.yahoo.com>
References: <20060918115358.98507.qmail@web30010.mail.mud.yahoo.com>
Message-ID: <200609180820.53883.sdavis2@mail.nih.gov>

On Monday 18 September 2006 07:53, Rajeswari wrote:
> Hi
>
>   How to read  FASTA,GENBANK,SWISSPORT and EMBL file using biojava coding.
>
>   I download the programms from the biojava.org. but they compiled but not
> showme the result.
>
>   how can i  break the crossproducts?
>
>
>   Is there any reference book available for bio java?
>
>
>   expecting the reply quickly.

You will probably need to read the documentation.

http://biojava.org/wiki/BioJava:CookBook
http://biojava.org/wiki/BioJava:Tutorial
http://www.biojava.org/docs/api14/index.html

Sean


From jolyon.holdstock at ogt.co.uk  Wed Sep 20 15:35:11 2006
From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock)
Date: Wed, 20 Sep 2006 16:35:11 +0100
Subject: [Biojava-l] LabelledSequenceRenderer
Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F0100ABD7@EUCLID.internal.ogtip.com>

Hi,

 

I'm trying to use a LabelledSequenceRenderer with a
TranslatedSequencePanel.

It doesn't render properly - the sequence is curtailed and there is a
blank where the label should be.

I've seen messages in the archive that have commented on this but no
solution.

 

Can anyone help? Or is there an alternative strategy for labelling a
track?

 

Thanks,

 

Jolyon

 

 

Jolyon Holdstock Ph.D.

Senior Computational Biologist,

Oxford Gene Technology (Ops) Ltd.

Begbroke Business and Science Park

Sandy Lane, Yarnton

Oxford, OX5 1PF

 

Tel: 01865 309699

Fax: 01865 842116

 

Confidentiality Notice:

The contents of this email from the Oxford Gene Technology Group of
Companies are confidential and intended solely for the person to whom it
is addressed. It may contain privileged and confidential information. If
you are not the intended recipient you must not read, copy, distribute,
discuss or take any action in reliance on it.

 

 




From cezard at nokad-technology.com  Wed Sep 20 10:18:06 2006
From: cezard at nokad-technology.com (Titi)
Date: Wed, 20 Sep 2006 03:18:06 -0700 (PDT)
Subject: [Biojava-l] use NCBISequenceDB without gi AC
Message-ID: <6405091.post@talk.nabble.com>


Hello,

I'm quite new with biojava and need to retrieve Sequence from NCBI.
I've got Blast result containing accession number but this are from their
original database.
for example
dbj|BAC25242.1
gb|AAQ88642.1
emb|CAC08176.1

Is their any solution to transforme this accession number into gi ones so I
could use NCBISequenceDB.
Or any solution to access a single database with all kind of accession
number.

any answers are welcome.

Thanks

Tim

-- 
View this message in context: http://www.nabble.com/use-NCBISequenceDB-without-gi-AC-tf2304387.html#a6405091
Sent from the BioJava mailing list archive at Nabble.com.



From cezard at nokad-technology.com  Fri Sep 22 13:10:55 2006
From: cezard at nokad-technology.com (=?iso-8859-1?Q?CEZARD_Timoth=E9e?=)
Date: Fri, 22 Sep 2006 15:10:55 +0200
Subject: [Biojava-l] use NCBISequenceDB without gi AC
In-Reply-To: <4513A1A1.2000001@ebi.ac.uk>
Message-ID: <20060922131059.5C1CA443CF@smtp3-g19.free.fr>

Thank you for your answer.

I'm just too lazy I haven't read all the blast documentation.
If so, I may have found that set the -I option as true show the GI accession
number in the blast output.

Sorry for that.

Tim
-----Message d'origine-----
De?: Richard Holland [mailto:holland at ebi.ac.uk] 
Envoy??: vendredi 22 septembre 2006 10:41
??: Titi
Cc?: biojava-l at lists.open-bio.org
Objet?: Re: [Biojava-l] use NCBISequenceDB without gi AC

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

The answer is no, unfortunately. There is no way of automatically
mapping an accession from one database to another unless the source
database provider can give you access to a lookup table containing
equivalent pairs of accessions. Whether such things exist, I don't know!
It's best if you ask the database providers directly for advice.

You should also check your source sequence files that you used to run
the blast. You may find that the GI numbers are in the header lines of
the FASTA format, in which case you could parse the sequence files to
retrieve this information and build your own lookup table.

cheers,
Richard


Titi wrote:
> Hello,
> 
> I'm quite new with biojava and need to retrieve Sequence from NCBI.
> I've got Blast result containing accession number but this are from their
> original database.
> for example
> dbj|BAC25242.1
> gb|AAQ88642.1
> emb|CAC08176.1
> 
> Is their any solution to transforme this accession number into gi ones so
I
> could use NCBISequenceDB.
> Or any solution to access a single database with all kind of accession
> number.
> 
> any answers are welcome.
> 
> Thanks
> 
> Tim
> 
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.2.2 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFFE6Gh4C5LeMEKA/QRAl66AJsH7MzF6+4x7jY3795pFu295mQ4TgCbB5qf
ipqnv/Q8vVYYJmuTSC08HlE=
=Rsgd
-----END PGP SIGNATURE-----




From ks_moses at yahoo.com  Mon Sep 25 07:32:06 2006
From: ks_moses at yahoo.com (Simon Moses)
Date: Mon, 25 Sep 2006 00:32:06 -0700 (PDT)
Subject: [Biojava-l] biojava documentation download
Message-ID: <20060925073206.7702.qmail@web31814.mail.mud.yahoo.com>

dear sir,
   
  i want to maintain a local copy of biojava documentation(http://biojava.org/wiki/BioJava:CookBook, http://biojava.org/wiki/BioJava:Tutorial) in my system for reference. is that possible? if possible how can i download?
   
  regards,
  Simon Moses.


**************************
Visit My Home Page
http://www.geocities.com/ks_moses
updated: 28 Sep 2004.
Simon Moses
**************************
 		
---------------------------------
Do you Yahoo!?
 Get on board. You're invited to try the new Yahoo! Mail.


From rajeee_sss at yahoo.com  Mon Sep 25 09:08:06 2006
From: rajeee_sss at yahoo.com (Rajeswari)
Date: Mon, 25 Sep 2006 02:08:06 -0700 (PDT)
Subject: [Biojava-l] about reading files
Message-ID: <20060925090806.63969.qmail@web30001.mail.mud.yahoo.com>

Hi,
  How can I read a GenBank, Swissprot, And an Embl File through Bio-JAva?
   
  The programm given by biojave-org-Biojava- in anger shows error:
   
  ArrayIndexOutOf bounds Exception.
   
   
  Anybody plz offer me the correct programm or tell me the reason of this type of error
  and how can i recitify?
   
   
   
  cheers,
  s.rajee
   

 		
---------------------------------
Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls.  Great rates starting at 1?/min.


From jolyon.holdstock at ogt.co.uk  Mon Sep 25 13:10:18 2006
From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock)
Date: Mon, 25 Sep 2006 14:10:18 +0100
Subject: [Biojava-l] about reading files[Scanned]
Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F0100AE6D@EUCLID.internal.ogtip.com>

Have you tried passing a file to the program?
It expects one

For example:
>java ReadGB <genbank file>

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Rajeswari
Sent: 25 September 2006 10:08
To: Biojava-l at lists.open-bio.org
Subject: [Biojava-l] about reading files[Scanned]

Hi,
  How can I read a GenBank, Swissprot, And an Embl File through Bio-JAva?
   
  The programm given by biojave-org-Biojava- in anger shows error:
   
  ArrayIndexOutOf bounds Exception.
   
   
  Anybody plz offer me the correct programm or tell me the reason of this type of error
  and how can i recitify?
   
   
   
  cheers,
  s.rajee
   

 		
---------------------------------
Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls.  Great rates starting at 1?/min.
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l











This email has been scanned by Oxford Gene Technology Security Systems.




From gwu at molbio.mgh.harvard.edu  Mon Sep 25 16:44:25 2006
From: gwu at molbio.mgh.harvard.edu (gang wu)
Date: Mon, 25 Sep 2006 12:44:25 -0400
Subject: [Biojava-l] biojava documentation download
In-Reply-To: <20060925073206.7702.qmail@web31814.mail.mud.yahoo.com>
References: <20060925073206.7702.qmail@web31814.mail.mud.yahoo.com>
Message-ID: <45180769.1010700@molbio.mgh.harvard.edu>

Did you try wget?

wget -r -l0 http://biojava.org/wiki/BioJava:CookBook
wget -r -l0 http://biojava.org/wiki/BioJava:Tutorial

Gang



Simon Moses wrote:
> dear sir,
>    
>   i want to maintain a local copy of biojava documentation(http://biojava.org/wiki/BioJava:CookBook, http://biojava.org/wiki/BioJava:Tutorial) in my system for reference. is that possible? if possible how can i download?
>    
>   regards,
>   Simon Moses.
>
>
> **************************
> Visit My Home Page
> http://www.geocities.com/ks_moses
> updated: 28 Sep 2004.
> Simon Moses
> **************************
>  		
> ---------------------------------
> Do you Yahoo!?
>  Get on board. You're invited to try the new Yahoo! Mail.
> _______________________________________________
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From gwu at molbio.mgh.harvard.edu  Tue Sep 26 21:26:45 2006
From: gwu at molbio.mgh.harvard.edu (gang wu)
Date: Tue, 26 Sep 2006 17:26:45 -0400
Subject: [Biojava-l] how to get specific data from biosql database
In-Reply-To: <20060925090806.63969.qmail@web30001.mail.mud.yahoo.com>
References: <20060925090806.63969.qmail@web30001.mail.mud.yahoo.com>
Message-ID: <45199B15.5040809@molbio.mgh.harvard.edu>

Hi Everyone,

I finally finished loading some Genbank genome sequences(Arabidopsis 
thaliana and C. elegans) into my MySQL(5.0.19 on Redhad AS 4) BioSQL 
database though the load_seqdatabase.pl works extremely slow(If turning 
on -debug, a lot of messages about not able to find adaptor class for 
Bio::Annotation::TypeManager, is this about the dynamic library loading 
issue mention in one of Hilmar's message?).

Now I'm writing views and stored procedures so other projects can easily 
retrieve specific information. It's quite easy to write views like  
showing all organisms, showing all version information etc. But so far I 
have not figured out how to write a SQL statement to list all genes 
corresponding to the genbank files. Can anyone show me how to get the 
information or let me know where to find related guide? Thanks in advance.

Gang


From smh1008 at cam.ac.uk  Tue Sep 26 21:38:41 2006
From: smh1008 at cam.ac.uk (David Huen)
Date: 26 Sep 2006 22:38:41 +0100
Subject: [Biojava-l] how to get specific data from biosql database
In-Reply-To: <45199B15.5040809@molbio.mgh.harvard.edu>
References: <20060925090806.63969.qmail@web30001.mail.mud.yahoo.com>
	<45199B15.5040809@molbio.mgh.harvard.edu>
Message-ID: <Prayer.1.0.18.0609262238410.17909@hermes-2.csi.cam.ac.uk>

On Sep 26 2006, gang wu wrote:

Have you mailed the wrong list inadvertently? It would seem to be intended 
for Bioperl-l.

Best wishes,
David Huen

>Hi Everyone,
>
>I finally finished loading some Genbank genome sequences(Arabidopsis 
>thaliana and C. elegans) into my MySQL(5.0.19 on Redhad AS 4) BioSQL 
>database though the load_seqdatabase.pl works extremely slow(If turning 
>on -debug, a lot of messages about not able to find adaptor class for 
>Bio::Annotation::TypeManager, is this about the dynamic library loading 
>issue mention in one of Hilmar's message?).
>
>Now I'm writing views and stored procedures so other projects can easily 
>retrieve specific information. It's quite easy to write views like  
>showing all organisms, showing all version information etc. But so far I 
>have not figured out how to write a SQL statement to list all genes 
>corresponding to the genbank files. Can anyone show me how to get the 
>information or let me know where to find related guide? Thanks in advance.
>



From gwu at molbio.mgh.harvard.edu  Wed Sep 27 01:29:59 2006
From: gwu at molbio.mgh.harvard.edu (gang wu)
Date: Tue, 26 Sep 2006 21:29:59 -0400
Subject: [Biojava-l] how to get specific data from biosql database
In-Reply-To: <Prayer.1.0.18.0609262238410.17909@hermes-2.csi.cam.ac.uk>
References: <20060925090806.63969.qmail@web30001.mail.mud.yahoo.com>
	<45199B15.5040809@molbio.mgh.harvard.edu>
	<Prayer.1.0.18.0609262238410.17909@hermes-2.csi.cam.ac.uk>
Message-ID: <4519D417.9010609@molbio.mgh.harvard.edu>

Sorry for posting to the wrong list.Seems my mail client(Thunderbird) 
filters has a little problem and some BioJava list mails are saved in my 
BioSQL list folder. And I happened to pick one from BioJava and posed to 
the list address. I'll double check the list address in the future. Thanks.

Gang

David Huen wrote:
> On Sep 26 2006, gang wu wrote:
>
> Have you mailed the wrong list inadvertently? It would seem to be 
> intended for Bioperl-l.
>
> Best wishes,
> David Huen
>
>> Hi Everyone,
>>
>> I finally finished loading some Genbank genome sequences(Arabidopsis 
>> thaliana and C. elegans) into my MySQL(5.0.19 on Redhad AS 4) BioSQL 
>> database though the load_seqdatabase.pl works extremely slow(If 
>> turning on -debug, a lot of messages about not able to find adaptor 
>> class for Bio::Annotation::TypeManager, is this about the dynamic 
>> library loading issue mention in one of Hilmar's message?).
>>
>> Now I'm writing views and stored procedures so other projects can 
>> easily retrieve specific information. It's quite easy to write views 
>> like  showing all organisms, showing all version information etc. But 
>> so far I have not figured out how to write a SQL statement to list 
>> all genes corresponding to the genbank files. Can anyone show me how 
>> to get the information or let me know where to find related guide? 
>> Thanks in advance.
>>
>



From gautam.thakur at gmail.com  Fri Sep 29 07:37:51 2006
From: gautam.thakur at gmail.com (Gautam S. Thakur)
Date: Fri, 29 Sep 2006 03:37:51 -0400
Subject: [Biojava-l] getting protein id
Message-ID: <305798d50609290037l14a25d60u3509f2a55aae1c32@mail.gmail.com>

Hi,

As you know that every protein sequence has some unique header defined like
the below one

>gi|16127996|ref|NP_414543.1|bifunctional aspartokinase I/homeserine
dehydrogenase I [Escherichia coli K12]


I'm using biojava 1.5 API to read and extract the protein information.
However, I am not able to  get the Sequence ID (16127996) of the protein
that is after the "gi" string in above. Can anybody tell me how to get that?
Following code is correct and working but not giving the id as output, even
after checking all the related member function.

--------------------------------------------------------------------
try{
           BufferedReader br = new BufferedReader(
                   new FileReader("datafile"));
           //Getting the protein alphabet
           //Alphabet protein = AlphabetManager.alphabetForName("PROTEIN");
           org.biojavax.bio.seq.RichSequenceIterator richStream =
org.biojavax.bio.seq.RichSequence.IOTools.readFastaProtein(br, null);
//SeqIOTools.readFastaProtein(br);
           while(richStream.hasNext()){
               org.biojavax.bio.seq.RichSequence richSeq =
richStream.nextRichSequence();
               System.out.println(richSeq.getAccession());
               System.out.println(richSeq.getAlphabet());
               System.out.println(richSeq.getAnnotation());
               System.out.println(richSeq.getName());
               System.out.println(richSeq.getDescription());
               System.out.println(richSeq.getIdentifier());
               System.out.println(richSeq.seqString());
}                  }catch(Exception e) {
           //do nothing
       }
--------------------------------------------------------------------

Can any one help me out as to how to get the protein id?

Thanks and Regards,

-Gautam

-- 
"Destiny is no matter of chance.
It is a matter of choice.
It is not a thing to be waited for,
it is a thing to be achieved"


From markjschreiber at gmail.com  Fri Sep 29 08:33:17 2006
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Fri, 29 Sep 2006 16:33:17 +0800
Subject: [Biojava-l] getting protein id
In-Reply-To: <305798d50609290037l14a25d60u3509f2a55aae1c32@mail.gmail.com>
References: <305798d50609290037l14a25d60u3509f2a55aae1c32@mail.gmail.com>
Message-ID: <93b45ca50609290133q276fe319pffd34767e5758f34@mail.gmail.com>

Hi -

The GI should be returned by the getIdentifier() method. Is that not the case?

- Mark

On 9/29/06, Gautam S. Thakur <gautam.thakur at gmail.com> wrote:
> Hi,
>
> As you know that every protein sequence has some unique header defined like
> the below one
>
> >gi|16127996|ref|NP_414543.1|bifunctional aspartokinase I/homeserine
> dehydrogenase I [Escherichia coli K12]
>
>
> I'm using biojava 1.5 API to read and extract the protein information.
> However, I am not able to  get the Sequence ID (16127996) of the protein
> that is after the "gi" string in above. Can anybody tell me how to get that?
> Following code is correct and working but not giving the id as output, even
> after checking all the related member function.
>
> --------------------------------------------------------------------
> try{
>            BufferedReader br = new BufferedReader(
>                    new FileReader("datafile"));
>            //Getting the protein alphabet
>            //Alphabet protein = AlphabetManager.alphabetForName("PROTEIN");
>            org.biojavax.bio.seq.RichSequenceIterator richStream =
> org.biojavax.bio.seq.RichSequence.IOTools.readFastaProtein(br, null);
> //SeqIOTools.readFastaProtein(br);
>            while(richStream.hasNext()){
>                org.biojavax.bio.seq.RichSequence richSeq =
> richStream.nextRichSequence();
>                System.out.println(richSeq.getAccession());
>                System.out.println(richSeq.getAlphabet());
>                System.out.println(richSeq.getAnnotation());
>                System.out.println(richSeq.getName());
>                System.out.println(richSeq.getDescription());
>                System.out.println(richSeq.getIdentifier());
>                System.out.println(richSeq.seqString());
> }                  }catch(Exception e) {
>            //do nothing
>        }
> --------------------------------------------------------------------
>
> Can any one help me out as to how to get the protein id?
>
> Thanks and Regards,
>
> -Gautam
>
> --
> "Destiny is no matter of chance.
> It is a matter of choice.
> It is not a thing to be waited for,
> it is a thing to be achieved"
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>