From darin.london at duke.edu  Mon Jul  3 08:41:33 2006
From: darin.london at duke.edu (Darin London)
Date: Mon, 03 Jul 2006 08:41:33 -0400
Subject: [Biojava-dev] Call For Birds of a Feather Suggestions
Message-ID: <44A9107D.2050304@duke.edu>

The BOSC organizing comittee is currently seeking suggestions for Birds
of a Feather meeting ideas. Birds of a Feather meetings are one of the
more popular activities at BOSC, occurring at the end of each days
session. These are free-form meetings organized by the attendees
themselves to discuss one or a few topics of interest in greater detail.
BOF?s have been formed to allow developers and users of individual OBF
software to meet each other face-to-face to discuss the project, or to
discuss completely new ideas, and even start new software development
projects. These meetings offer a unique opportunity for individuals to
explore more about the activities of the various Open Source Projects,
and, in some cases, even take an active role influencing the future of
Open Source Software development. If you would like to create a BOF,
just sign up for a wiki account, login, and edit the <a
href="http://www.open-bio.org/wiki/BOSC_2006/Birds-of-a-Feather">BOSC
2006 Birds of a Feather page</a>.

From bubba.puryear at gmail.com  Mon Jul  3 11:40:40 2006
From: bubba.puryear at gmail.com (Bubba Puryear)
Date: Mon, 3 Jul 2006 11:40:40 -0400
Subject: [Biojava-dev] Accession defaults for GenbankFormat
Message-ID: <d2f7533b0607030840g53cb18eeif5e38e9efa9ce010@mail.gmail.com>

Hey all,

   I'm using biojava for an internal app for my client that has about 5000
internally developed genbank records. The majority of these records do not
have ACCESSION fields, since they didn't come from a public data source.
(Many of these were created using Invitrogen's Vector NTI and saved as
files)

  Because there is no accession number for these records, I get problems
when I try to use RichSequence and friends with this data. I've made a patch
for GenbankFormat.java that sets the accession to the locus name of the
record during parsing. If/When the accession field is parsed, this value is
over written, so I think it should be ok generally. I also have a test case
and test data file.

  The registration page thing discouraged attachments for this list -- how
should I provide these files? Thanks in advance,
Bubba

ps - The patch is small, I can inline it here:

Index: src/org/biojavax/bio/seq/io/GenbankFormat.java
===================================================================
RCS file:
/home/repository/biojava/biojava-live/src/org/biojavax/bio/seq/io/GenbankFormat.java,v
retrieving revision 1.63
diff -u -r1.63 GenbankFormat.java
--- src/org/biojavax/bio/seq/io/GenbankFormat.java    28 Jun 2006 17:02:47
-0000    1.63
+++ src/org/biojavax/bio/seq/io/GenbankFormat.java    1 Jul 2006 20:34:48
-0000
@@ -274,6 +274,9 @@
                 Matcher m = lp.matcher(loc);
                 if (m.matches()) {
                     rlistener.setName(m.group(1));
+                    // default accession to locus name for sources that do
not have accessions proper.
+                    accession = m.group(1);
+                    rlistener.setAccession(accession);
                     rlistener.setDivision(m.group(5));
                     rlistener.addSequenceProperty(Terms.getMolTypeTerm(),
m.group(3));
                     rlistener.addSequenceProperty(Terms.getDateUpdatedTerm
(),m.group(6));

From mark.schreiber at novartis.com  Mon Jul  3 22:19:21 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Tue, 4 Jul 2006 10:19:21 +0800
Subject: [Biojava-dev] Accession defaults for GenbankFormat
Message-ID: <OF4CDD72D6.AC92F35C-ON482571A1.000CAACF-482571A1.000CC21D@EU.novartis.net>

This seems reasonable. Can you forsee any problems Richard?

- 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





"Bubba Puryear" <bubba.puryear at gmail.com>
Sent by: biojava-dev-bounces at lists.open-bio.org
07/03/2006 11:40 PM

 
        To:     biojava-dev at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] Accession defaults for GenbankFormat


Hey all,

   I'm using biojava for an internal app for my client that has about 5000
internally developed genbank records. The majority of these records do not
have ACCESSION fields, since they didn't come from a public data source.
(Many of these were created using Invitrogen's Vector NTI and saved as
files)

  Because there is no accession number for these records, I get problems
when I try to use RichSequence and friends with this data. I've made a 
patch
for GenbankFormat.java that sets the accession to the locus name of the
record during parsing. If/When the accession field is parsed, this value 
is
over written, so I think it should be ok generally. I also have a test 
case
and test data file.

  The registration page thing discouraged attachments for this list -- how
should I provide these files? Thanks in advance,
Bubba

ps - The patch is small, I can inline it here:

Index: src/org/biojavax/bio/seq/io/GenbankFormat.java
===================================================================
RCS file:
/home/repository/biojava/biojava-live/src/org/biojavax/bio/seq/io/GenbankFormat.java,v
retrieving revision 1.63
diff -u -r1.63 GenbankFormat.java
--- src/org/biojavax/bio/seq/io/GenbankFormat.java    28 Jun 2006 17:02:47
-0000    1.63
+++ src/org/biojavax/bio/seq/io/GenbankFormat.java    1 Jul 2006 20:34:48
-0000
@@ -274,6 +274,9 @@
                 Matcher m = lp.matcher(loc);
                 if (m.matches()) {
                     rlistener.setName(m.group(1));
+                    // default accession to locus name for sources that 
do
not have accessions proper.
+                    accession = m.group(1);
+                    rlistener.setAccession(accession);
                     rlistener.setDivision(m.group(5));
                     rlistener.addSequenceProperty(Terms.getMolTypeTerm(),
m.group(3));
 rlistener.addSequenceProperty(Terms.getDateUpdatedTerm
(),m.group(6));
_______________________________________________
biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev




From mark.schreiber at novartis.com  Mon Jul  3 22:44:21 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Tue, 4 Jul 2006 10:44:21 +0800
Subject: [Biojava-dev] Problem with SimpleDocRefTest
Message-ID: <OFC5C82EC7.6B27CCA8-ON482571A1.000EFAC6-482571A1.000F0C03@EU.novartis.net>

Works now. There were other problems, also fixed.





Richard Holland <richard.holland at ebi.ac.uk>
Sent by: biojava-dev-bounces at lists.open-bio.org
06/30/2006 05:11 PM

 
        To:     george waldon <gwaldon at geneinfinity.org>
        cc:     biojava-dev at lists.open-bio.org, Mark Schreiber 
<mark.schreiber at novartis.com>
        Subject:        Re: [Biojava-dev] Problem with SimpleDocRefTest


The SimpleDocRef constructor changed recently to include document titles
and I don't think the test was updated to match it. Sorry about that -
the head branch of CVS is always under development so cannot always be
guaranteed to work out 100%.

Mark, can you update the tests?

cheers,
Richard

On Thu, 2006-06-29 at 16:33 -0700, george waldon wrote:
> Hi,
> 
> I am trying to run the tests but my compiler complains about 
org.biojavax.SimpleDocRefTest at compilation:
> missing constructor SimpleDocRef(java.util.List, java.lang.String)
> 
> Was-It expected to interpretate that as SimpleDocRef(java.util.List, 
java.lang.String, null) (the three-argument constructor)?
> 
> Thanks,
> George
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416

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




From mark.schreiber at novartis.com  Mon Jul  3 22:43:11 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Tue, 4 Jul 2006 10:43:11 +0800
Subject: [Biojava-dev] developers should use unit tests and watch for
	javadoc errors
Message-ID: <OFE8F7F840.84605A8A-ON482571A1.000D11FB-482571A1.000EF0CB@EU.novartis.net>

Hi all -

There are quite a few new developers with CVS accounts so I would like to 
draw your attention to Unit testing.

BioJava uses JUnit Tests and has ant tasks for these (runtests for 
example). To enable this you pretty much only need to put the JUnit jar 
into your ant lib directory. Then from the biojava root type ant runtests.

I just did a CVS download and build after a few weeks break and found a 
few of the tests no longer passed. Changes had been made to the source 
code which compiled and presumably solved some problem but along the way 
had introduced subtle errors that caused the unit tests to fail. A 
particularly subtle one was a change that caused the compareTo() method to 
fail. You are not likely to notice this until you come to sort something 
and even then you may not pick it up.

If you make changes to the source code please run the Unit tests. Often 
changes in other parts of the code may affect the behaivour of methods you 
haven't touched (such as the compareTo example above).

I would also make a plea for people to contribute more Unit tests. The 
coverage is patchy and the more we have the more biojava will be bug free 
which means more of your programs will be bug free. If you use a certain 
class a lot and the Unit tests for it don't exist or are inadequate it 
would be a good idea to make or improve one so you can be sure of good 
behaivour. The unit tests for the biojavax objects are probably the best 
examples we have. They try to test every method, including the often 
neglected but very important compareTo(), equals(), hashCode() and 
toString(). They also try to test the behaivour described in the javadocs 
of the methods. If you want to write a Unit test take one of these as a 
template.

Finally a word about javadocs. One the whole the number and quality of 
javadocs has vastly improved over the last year. If you add or modify 
javadocs run the ant javadoc-biojava task and check for warnings. This 
allows you to avoid common errors such as misspelled @param names or @see 
tags that can't locate the class you want to reference. It's a good check 
if you have been copying and pasting javadoc comments.

In conclusion some basic guidelines for developers:

* New classes should have full javadocs and a JUnit test (inlcuding equals 
etc).
* New methods should have javadocs (not required if it is a private 
method) and add a test of the method to the JUnit test.
* Before any commit run the JUnit tests to make sure you haven't broken 
anything and run the javadoc task to make sure your @params etc are all 
correct.

If you observe this behaivour biojava will be a lot more stable and better 
documented which will give us a better reputation and mean that your code 
works more often.

Sorry for the sermon.

- 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 richard.holland at ebi.ac.uk  Tue Jul  4 04:05:52 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Tue, 04 Jul 2006 09:05:52 +0100
Subject: [Biojava-dev] Accession defaults for GenbankFormat
In-Reply-To: <d2f7533b0607030840g53cb18eeif5e38e9efa9ce010@mail.gmail.com>
References: <d2f7533b0607030840g53cb18eeif5e38e9efa9ce010@mail.gmail.com>
Message-ID: <1152000352.3948.32.camel@texas.ebi.ac.uk>

That seems like a good idea to me. I've made the change in CVS.

cheers,
Richard

On Mon, 2006-07-03 at 11:40 -0400, Bubba Puryear wrote:
> Hey all,
> 
>    I'm using biojava for an internal app for my client that has about 5000
> internally developed genbank records. The majority of these records do not
> have ACCESSION fields, since they didn't come from a public data source.
> (Many of these were created using Invitrogen's Vector NTI and saved as
> files)
> 
>   Because there is no accession number for these records, I get problems
> when I try to use RichSequence and friends with this data. I've made a patch
> for GenbankFormat.java that sets the accession to the locus name of the
> record during parsing. If/When the accession field is parsed, this value is
> over written, so I think it should be ok generally. I also have a test case
> and test data file.
> 
>   The registration page thing discouraged attachments for this list -- how
> should I provide these files? Thanks in advance,
> Bubba
> 
> ps - The patch is small, I can inline it here:
> 
> Index: src/org/biojavax/bio/seq/io/GenbankFormat.java
> ===================================================================
> RCS file:
> /home/repository/biojava/biojava-live/src/org/biojavax/bio/seq/io/GenbankFormat.java,v
> retrieving revision 1.63
> diff -u -r1.63 GenbankFormat.java
> --- src/org/biojavax/bio/seq/io/GenbankFormat.java    28 Jun 2006 17:02:47
> -0000    1.63
> +++ src/org/biojavax/bio/seq/io/GenbankFormat.java    1 Jul 2006 20:34:48
> -0000
> @@ -274,6 +274,9 @@
>                  Matcher m = lp.matcher(loc);
>                  if (m.matches()) {
>                      rlistener.setName(m.group(1));
> +                    // default accession to locus name for sources that do
> not have accessions proper.
> +                    accession = m.group(1);
> +                    rlistener.setAccession(accession);
>                      rlistener.setDivision(m.group(5));
>                      rlistener.addSequenceProperty(Terms.getMolTypeTerm(),
> m.group(3));
>                      rlistener.addSequenceProperty(Terms.getDateUpdatedTerm
> (),m.group(6));
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416


From richard.holland at ebi.ac.uk  Tue Jul  4 04:55:48 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Tue, 04 Jul 2006 09:55:48 +0100
Subject: [Biojava-dev] developers should use unit tests and watch
	for	javadoc errors
In-Reply-To: <OFE8F7F840.84605A8A-ON482571A1.000D11FB-482571A1.000EF0CB@EU.novartis.net>
References: <OFE8F7F840.84605A8A-ON482571A1.000D11FB-482571A1.000EF0CB@EU.novartis.net>
Message-ID: <1152003348.3948.46.camel@texas.ebi.ac.uk>

Hello all.

In addition to this, be careful with Java versions. BioJava is written
for Java 1.4. All binaries in CVS have been compiled with 1.4. BioJava
will compile successfully under 1.5 with a few extra warnings, but you
should not check any 1.5-compiled binaries back into CVS as then others
may not be able to use them.

Note also that the current version of JUnit (4.1) was compiled with 1.5.
If you want to run JUnit against BioJava using 1.4, you have to find and
download JUnit 3.8.1, which was the last release of JUnit to be compiled
with 1.4.

cheers,
Richard

On Tue, 2006-07-04 at 10:43 +0800, mark.schreiber at novartis.com wrote:
> Hi all -
> 
> There are quite a few new developers with CVS accounts so I would like to 
> draw your attention to Unit testing.
> 
> BioJava uses JUnit Tests and has ant tasks for these (runtests for 
> example). To enable this you pretty much only need to put the JUnit jar 
> into your ant lib directory. Then from the biojava root type ant runtests.
> 
> I just did a CVS download and build after a few weeks break and found a 
> few of the tests no longer passed. Changes had been made to the source 
> code which compiled and presumably solved some problem but along the way 
> had introduced subtle errors that caused the unit tests to fail. A 
> particularly subtle one was a change that caused the compareTo() method to 
> fail. You are not likely to notice this until you come to sort something 
> and even then you may not pick it up.
> 
> If you make changes to the source code please run the Unit tests. Often 
> changes in other parts of the code may affect the behaivour of methods you 
> haven't touched (such as the compareTo example above).
> 
> I would also make a plea for people to contribute more Unit tests. The 
> coverage is patchy and the more we have the more biojava will be bug free 
> which means more of your programs will be bug free. If you use a certain 
> class a lot and the Unit tests for it don't exist or are inadequate it 
> would be a good idea to make or improve one so you can be sure of good 
> behaivour. The unit tests for the biojavax objects are probably the best 
> examples we have. They try to test every method, including the often 
> neglected but very important compareTo(), equals(), hashCode() and 
> toString(). They also try to test the behaivour described in the javadocs 
> of the methods. If you want to write a Unit test take one of these as a 
> template.
> 
> Finally a word about javadocs. One the whole the number and quality of 
> javadocs has vastly improved over the last year. If you add or modify 
> javadocs run the ant javadoc-biojava task and check for warnings. This 
> allows you to avoid common errors such as misspelled @param names or @see 
> tags that can't locate the class you want to reference. It's a good check 
> if you have been copying and pasting javadoc comments.
> 
> In conclusion some basic guidelines for developers:
> 
> * New classes should have full javadocs and a JUnit test (inlcuding equals 
> etc).
> * New methods should have javadocs (not required if it is a private 
> method) and add a test of the method to the JUnit test.
> * Before any commit run the JUnit tests to make sure you haven't broken 
> anything and run the javadoc task to make sure your @params etc are all 
> correct.
> 
> If you observe this behaivour biojava will be a lot more stable and better 
> documented which will give us a better reputation and mean that your code 
> works more often.
> 
> Sorry for the sermon.
> 
> - 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
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416


From bubba.puryear at gmail.com  Tue Jul  4 12:51:23 2006
From: bubba.puryear at gmail.com (Bubba Puryear)
Date: Tue, 4 Jul 2006 12:51:23 -0400
Subject: [Biojava-dev] Exception wrapping in SimpleRichObjectBuilder
Message-ID: <d2f7533b0607040951m166da1cfoea49f1abdd5cdbb3@mail.gmail.com>

One last patch for the day - just added some exception wrapping that aided
me in some debugging earler:

Index: src/org/biojavax/SimpleRichObjectBuilder.java
===================================================================
RCS file:
/home/repository/biojava/biojava-live/src/org/biojavax/SimpleRichObjectBuilder.java,v
retrieving revision 1.7
diff -u -r1.7 SimpleRichObjectBuilder.java
--- src/org/biojavax/SimpleRichObjectBuilder.java       27 Apr 2006 10:16:29
-0000      1.7
+++ src/org/biojavax/SimpleRichObjectBuilder.java       4 Jul 2006 19:54:14
-0000
@@ -32,6 +32,7 @@
  * Creates objects and returns them, and stores them in an internal
  * map of singletons for reference. Takes up a lot of memory!
  * @author Richard Holland
+ * @author Bubba Puryear
  * @since 1.5
  */
 public class SimpleRichObjectBuilder implements RichObjectBuilder {
@@ -75,7 +76,7 @@
                 if (i<(paramsList.size()-1)) paramsstuff.append(",");
             }
             paramsstuff.append(")");
-            throw new IllegalArgumentException("Could not find constructor
for "+paramsstuff);
+            throw new IllegalArgumentException("Could not find constructor
for "+paramsstuff, e);
         }
     }

From richard.holland at ebi.ac.uk  Wed Jul  5 04:21:02 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Wed, 05 Jul 2006 09:21:02 +0100
Subject: [Biojava-dev] Exception wrapping in SimpleRichObjectBuilder
In-Reply-To: <d2f7533b0607040951m166da1cfoea49f1abdd5cdbb3@mail.gmail.com>
References: <d2f7533b0607040951m166da1cfoea49f1abdd5cdbb3@mail.gmail.com>
Message-ID: <1152087662.3948.80.camel@texas.ebi.ac.uk>

Unfortunately, the IllegalArgumentException(String, Throwable)
constructor is a Java 1.5 feature, and is not present in Java 1.4 As
BioJava is currently 1.4-compatible, I can't make this change exactly as
you make it. However, I did make the equivalent change in the 1.4
syntax:

	IllegalArgumentException ie = new IllegalArgumentException(.....);
	ie.initCause(e); 
	throw ie;

This change has been made in CVS.

cheers,
Richard

On Tue, 2006-07-04 at 12:51 -0400, Bubba Puryear wrote:
> One last patch for the day - just added some exception wrapping that aided
> me in some debugging earler:
> 
> Index: src/org/biojavax/SimpleRichObjectBuilder.java
> ===================================================================
> RCS file:
> /home/repository/biojava/biojava-live/src/org/biojavax/SimpleRichObjectBuilder.java,v
> retrieving revision 1.7
> diff -u -r1.7 SimpleRichObjectBuilder.java
> --- src/org/biojavax/SimpleRichObjectBuilder.java       27 Apr 2006 10:16:29
> -0000      1.7
> +++ src/org/biojavax/SimpleRichObjectBuilder.java       4 Jul 2006 19:54:14
> -0000
> @@ -32,6 +32,7 @@
>   * Creates objects and returns them, and stores them in an internal
>   * map of singletons for reference. Takes up a lot of memory!
>   * @author Richard Holland
> + * @author Bubba Puryear
>   * @since 1.5
>   */
>  public class SimpleRichObjectBuilder implements RichObjectBuilder {
> @@ -75,7 +76,7 @@
>                  if (i<(paramsList.size()-1)) paramsstuff.append(",");
>              }
>              paramsstuff.append(")");
> -            throw new IllegalArgumentException("Could not find constructor
> for "+paramsstuff);
> +            throw new IllegalArgumentException("Could not find constructor
> for "+paramsstuff, e);
>          }
>      }
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416


From bubba.puryear at gmail.com  Wed Jul  5 09:38:29 2006
From: bubba.puryear at gmail.com (Bubba Puryear)
Date: Wed, 5 Jul 2006 09:38:29 -0400
Subject: [Biojava-dev] Exception wrapping in SimpleRichObjectBuilder
In-Reply-To: <1152087662.3948.80.camel@texas.ebi.ac.uk>
References: <d2f7533b0607040951m166da1cfoea49f1abdd5cdbb3@mail.gmail.com>
	<1152087662.3948.80.camel@texas.ebi.ac.uk>
Message-ID: <d2f7533b0607050638y4d00a2e9jb3cd41fc8065c20e@mail.gmail.com>

Dang - forgot about that. Sorry. Thanks for the fix, though!

On 7/5/06, Richard Holland <richard.holland at ebi.ac.uk> wrote:
> Unfortunately, the IllegalArgumentException(String, Throwable)
> constructor is a Java 1.5 feature, and is not present in Java 1.4 As
> BioJava is currently 1.4-compatible, I can't make this change exactly as
> you make it. However, I did make the equivalent change in the 1.4
> syntax:
>
>         IllegalArgumentException ie = new IllegalArgumentException(.....);
>         ie.initCause(e);
>         throw ie;
>
> This change has been made in CVS.
>
> cheers,
> Richard
>
> On Tue, 2006-07-04 at 12:51 -0400, Bubba Puryear wrote:
> > One last patch for the day - just added some exception wrapping that aided
> > me in some debugging earler:
> >
> > Index: src/org/biojavax/SimpleRichObjectBuilder.java
> > ===================================================================
> > RCS file:
> > /home/repository/biojava/biojava-live/src/org/biojavax/SimpleRichObjectBuilder.java,v
> > retrieving revision 1.7
> > diff -u -r1.7 SimpleRichObjectBuilder.java
> > --- src/org/biojavax/SimpleRichObjectBuilder.java       27 Apr 2006 10:16:29
> > -0000      1.7
> > +++ src/org/biojavax/SimpleRichObjectBuilder.java       4 Jul 2006 19:54:14
> > -0000
> > @@ -32,6 +32,7 @@
> >   * Creates objects and returns them, and stores them in an internal
> >   * map of singletons for reference. Takes up a lot of memory!
> >   * @author Richard Holland
> > + * @author Bubba Puryear
> >   * @since 1.5
> >   */
> >  public class SimpleRichObjectBuilder implements RichObjectBuilder {
> > @@ -75,7 +76,7 @@
> >                  if (i<(paramsList.size()-1)) paramsstuff.append(",");
> >              }
> >              paramsstuff.append(")");
> > -            throw new IllegalArgumentException("Could not find constructor
> > for "+paramsstuff);
> > +            throw new IllegalArgumentException("Could not find constructor
> > for "+paramsstuff, e);
> >          }
> >      }
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> --
> Richard Holland (BioMart Team)
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> UNITED KINGDOM
> Tel: +44-(0)1223-494416
>
>

From ap3 at sanger.ac.uk  Thu Jul  6 14:44:42 2006
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Thu, 6 Jul 2006 19:44:42 +0100
Subject: [Biojava-dev] biojava wiki and Jmol
Message-ID: <f1c60ed25a12b4e80587b9a826141791@sanger.ac.uk>

Hi!

I will commit some new protein structure functionality to CVS soon 
(structure alignments).
For this it would be nice if I could show some examples in 3D with the 
Jmol applet in
the BioJava Wiki pages.

Could somebody with admin rights install the Jmol-wiki extension for 
MediaWiki? - not sure who to contact about that...
instructions would be here:
http://wiki.jmol.org/index.php/MediaWiki#Installation

Thanks! :-)
Andreas

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
			 +44 (0) 1223 49 6891


From mark.schreiber at novartis.com  Thu Jul  6 20:56:04 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 7 Jul 2006 08:56:04 +0800
Subject: [Biojava-dev] [Biojava-l] biojava wiki and Jmol
Message-ID: <OFD9C3155C.42A0849E-ON482571A4.0005193F-482571A4.00052204@EU.novartis.net>

Be my guest!!





Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx>
Sent by: biojava-l-bounces at lists.open-bio.org
07/07/2006 05:45 AM

 
        To:     Andreas Prlic <ap3 at sanger.ac.uk>
        cc:     biojava-dev at biojava.org, biojava-l at biojava.org, (bcc: Mark 
Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] biojava wiki and Jmol


Hi Andreas,

I have admin privileges for the open-bio.org webserver. Unless Mark 
Schreiber (who appears to be the website admin for BioJava) has other 
opinion, I can help you with this and get the extension installed and 
configured for the wiki.

Regards,
Mauricio.

Andreas Prlic wrote:
> Hi!
> 
> I will commit some new protein structure functionality to CVS soon 
> (structure alignments).
> For this it would be nice if I could show some examples in 3D with the 
> Jmol applet in
> the BioJava Wiki pages.
> 
> Could somebody with admin rights install the Jmol-wiki extension for 
> MediaWiki? - not sure who to contact about that...
> instructions would be here:
> http://wiki.jmol.org/index.php/MediaWiki#Installation
> 
> Thanks! :-)
> Andreas
> 
> -----------------------------------------------------------------------
> 
> Andreas Prlic      Wellcome Trust Sanger Institute
>                                Hinxton, Cambridge CB10 1SA, UK
>                                                 +44 (0) 1223 49 6891
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM

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





From bugzilla-daemon at newportal.open-bio.org  Thu Jul  6 22:20:42 2006
From: bugzilla-daemon at newportal.open-bio.org (bugzilla-daemon at newportal.open-bio.org)
Date: Thu, 6 Jul 2006 22:20:42 -0400
Subject: [Biojava-dev] [Bug 2038] New: test bug
Message-ID: <bug-2038-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2038

           Summary: test bug
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: trivial
          Priority: P2
         Component: Others
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: mark.schreiber at novartis.com
                CC: mark.schreiber at novartis.com


testing bugzilla please ignore!


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From bugzilla-daemon at newportal.open-bio.org  Thu Jul  6 22:21:37 2006
From: bugzilla-daemon at newportal.open-bio.org (bugzilla-daemon at newportal.open-bio.org)
Date: Thu, 6 Jul 2006 22:21:37 -0400
Subject: [Biojava-dev] [Bug 2038] test bug
In-Reply-To: <bug-2038-485@http.bugzilla.open-bio.org/>
Message-ID: <200607070221.k672LbcU017978@newportal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2038


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




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From mark.schreiber at novartis.com  Thu Jul  6 22:29:57 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 7 Jul 2006 10:29:57 +0800
Subject: [Biojava-dev] submission of bug reports and requests for enhancement
Message-ID: <OFDF2201FF.B33DC5D9-ON482571A4.000D52A3-482571A4.000DBA74@EU.novartis.net>

Hello all -

Biojava now has a working bug reporting and tracking system based on 
bugzilla. You can submit and track bugs or requests for enhancement at 
http://bugzilla.open-bio.org/ (I will add this link to the biojava wiki).

>From now on this should be the prefered way to report a bug in biojava. 
This is so we don't forget about the bugs that we haven't dealt with and 
the new features people want that we should add.

By default bugs will be 'assigned' to biojava-dev but from time to time I 
may reassign really bad ones to the appropriate person to clear them more 
quickly.

Please make use of this so we can make biojava better.

Thanks,

- 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 bugzilla-daemon at newportal.open-bio.org  Thu Jul  6 22:31:18 2006
From: bugzilla-daemon at newportal.open-bio.org (bugzilla-daemon at newportal.open-bio.org)
Date: Thu, 6 Jul 2006 22:31:18 -0400
Subject: [Biojava-dev] [Bug 2005] test bug
In-Reply-To: <bug-2005-485@http.bugzilla.open-bio.org/>
Message-ID: <200607070231.k672VIAV018929@newportal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2005


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




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From michael.tran at acpfg.com.au  Tue Jul  4 06:44:07 2006
From: michael.tran at acpfg.com.au (Michael Tran)
Date: Tue, 4 Jul 2006 20:14:07 +0930
Subject: [Biojava-dev] Java API for Global Alignment
References: <mailman.4967.1151566574.2084.biojava-l@lists.open-bio.org>
Message-ID: <D3C986810EBCCE488A9DCA95463794F146F35A@kaneda.acpfg.local>

Hi All,
 
Looking for a Java API to do global alignments (something like a clustalw alignment).
 
Looking at the BioJava API 1.4 (see below) does not appear to have such a class.
 
org.biojava.bio.alignment <https://mail.acpfg.com.au/org/biojava/bio/alignment/package-summary.html>  
Interfaces  
AlignmentElement <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/AlignmentElement.html>  
ARAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/ARAlignment.html>  
EditableAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/EditableAlignment.html>  
QualitativeAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/QualitativeAlignment.html>  
UnequalLengthAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/UnequalLengthAlignment.html> 	
Classes  
AbstractULAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/AbstractULAlignment.html>  
FlexibleAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/FlexibleAlignment.html>  
SimpleAlignmentElement <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/SimpleAlignmentElement.html> 	
Exceptions  
IllegalAlignmentEditException <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/IllegalAlignmentEditException.html> 	

Help is appreciated.
 
Cheers,
ST


From bubba.puryear at gmail.com  Tue Jul  4 12:48:10 2006
From: bubba.puryear at gmail.com (Bubba Puryear)
Date: Tue, 4 Jul 2006 12:48:10 -0400
Subject: [Biojava-dev] Some more light parser changes
Message-ID: <d2f7533b0607040948s5d7adb20we1564542829fd36d@mail.gmail.com>

Greetings again,

I've made some slight adjustments to GenbankFormat.java (biojavax)
that allow me to get biojavax to parse all 292M of genbank records
that I have access to. There are three things here:

1. Made the regex for locus lines slightly more tolerant. (made
modifed date field optional - some of the older records I have don't
include the date)

2. The previous checkin for no accessions was slighly incomplete - the
accession has to be set on the RichListener - not just assigned to the
local accession variable (which I believe is only used for logging)

3. I needed a larger readAheadLimit on the BufferedReader for parsing sections.

All the tests run (locally anyway) with these changes and pass. Thanks
for your consideration.

Bubba
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From bubba.puryear at gmail.com  Tue Jul  4 12:39:34 2006
From: bubba.puryear at gmail.com (Bubba Puryear)
Date: Tue, 4 Jul 2006 12:39:34 -0400
Subject: [Biojava-dev] Test for GenbankFormat (biojavax) and data file
Message-ID: <d2f7533b0607040939w2a673b0dxaabd19072d10af72@mail.gmail.com>

I've attached a simple high-level test I wrote for parsing a genbank
file with no accession field. I've also included the test file.

FYI,
Bubba
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From arareko at campus.iztacala.unam.mx  Thu Jul  6 17:45:34 2006
From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra)
Date: Thu, 06 Jul 2006 16:45:34 -0500
Subject: [Biojava-dev] [Biojava-l] biojava wiki and Jmol
In-Reply-To: <f1c60ed25a12b4e80587b9a826141791@sanger.ac.uk>
References: <f1c60ed25a12b4e80587b9a826141791@sanger.ac.uk>
Message-ID: <44AD847E.9030306@campus.iztacala.unam.mx>

Hi Andreas,

I have admin privileges for the open-bio.org webserver. Unless Mark 
Schreiber (who appears to be the website admin for BioJava) has other 
opinion, I can help you with this and get the extension installed and 
configured for the wiki.

Regards,
Mauricio.

Andreas Prlic wrote:
> Hi!
> 
> I will commit some new protein structure functionality to CVS soon 
> (structure alignments).
> For this it would be nice if I could show some examples in 3D with the 
> Jmol applet in
> the BioJava Wiki pages.
> 
> Could somebody with admin rights install the Jmol-wiki extension for 
> MediaWiki? - not sure who to contact about that...
> instructions would be here:
> http://wiki.jmol.org/index.php/MediaWiki#Installation
> 
> Thanks! :-)
> Andreas
> 
> -----------------------------------------------------------------------
> 
> Andreas Prlic      Wellcome Trust Sanger Institute
>                                Hinxton, Cambridge CB10 1SA, UK
> 			 +44 (0) 1223 49 6891
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM


From russ at kepler-eng.com  Fri Jul  7 09:11:23 2006
From: russ at kepler-eng.com (Russ Kepler)
Date: Fri, 7 Jul 2006 07:11:23 -0600
Subject: [Biojava-dev] Java API for Global Alignment
In-Reply-To: <D3C986810EBCCE488A9DCA95463794F146F35A@kaneda.acpfg.local>
References: <mailman.4967.1151566574.2084.biojava-l@lists.open-bio.org>
	<D3C986810EBCCE488A9DCA95463794F146F35A@kaneda.acpfg.local>
Message-ID: <200607070711.23576.russ@kepler-eng.com>

On Tuesday 04 July 2006 04:44 am, Michael Tran wrote:

> Looking for a Java API to do global alignments (something like a clustalw
> alignment).

I think most folks have simply implemented a parser for clustalw output to 
generate a FlexibleAlignment when they needed that.  I've got one, and a 
parser for the Paracel CAML output from their genomic scale assembler as 
well.

From arareko at campus.iztacala.unam.mx  Fri Jul  7 10:23:05 2006
From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra)
Date: Fri, 07 Jul 2006 09:23:05 -0500
Subject: [Biojava-dev] [Biojava-l] biojava wiki and Jmol
In-Reply-To: <OFD9C3155C.42A0849E-ON482571A4.0005193F-482571A4.00052204@EU.novartis.net>
References: <OFD9C3155C.42A0849E-ON482571A4.0005193F-482571A4.00052204@EU.novartis.net>
Message-ID: <44AE6E49.9030107@campus.iztacala.unam.mx>

Mark and Andreas,

The Jmol extension is installed now and should be working. I configured 
it with all the steps from the installation page. For the moment, I've 
only added *.cml files to the allowed extensions to upload. If you want 
to upload other types of files, please let me know and I'll perform the 
necessary steps.

Andreas - please try to upload some files and play with the Jmol wiki 
tags to see if everything works as it should.

Regards,
Mauricio.

PS. I'm Cc'ing this to some BioPerl friends to see if someone gets 
interested in having this for our wiki also ;)

mark.schreiber at novartis.com wrote:
> Be my guest!!
> 
> 
> Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx>
> Sent by: biojava-l-bounces at lists.open-bio.org
> 07/07/2006 05:45 AM
> 
>  
>         To:     Andreas Prlic <ap3 at sanger.ac.uk>
>         cc:     biojava-dev at biojava.org, biojava-l at biojava.org, (bcc: Mark 
> Schreiber/GP/Novartis)
>         Subject:        Re: [Biojava-l] biojava wiki and Jmol
> 
> 
> Hi Andreas,
> 
> I have admin privileges for the open-bio.org webserver. Unless Mark 
> Schreiber (who appears to be the website admin for BioJava) has other 
> opinion, I can help you with this and get the extension installed and 
> configured for the wiki.
> 
> Regards,
> Mauricio.
> 
> Andreas Prlic wrote:
>> Hi!
>>
>> I will commit some new protein structure functionality to CVS soon 
>> (structure alignments).
>> For this it would be nice if I could show some examples in 3D with the 
>> Jmol applet in
>> the BioJava Wiki pages.
>>
>> Could somebody with admin rights install the Jmol-wiki extension for 
>> MediaWiki? - not sure who to contact about that...
>> instructions would be here:
>> http://wiki.jmol.org/index.php/MediaWiki#Installation
>>
>> Thanks! :-)
>> Andreas
>>
>> -----------------------------------------------------------------------
>>
>> Andreas Prlic      Wellcome Trust Sanger Institute
>>                                Hinxton, Cambridge CB10 1SA, UK
>>                                                 +44 (0) 1223 49 6891
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM


From mark.schreiber at novartis.com  Sun Jul  9 21:38:09 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Mon, 10 Jul 2006 09:38:09 +0800
Subject: [Biojava-dev] Java API for Global Alignment
Message-ID: <OFA65CDA5D.65657CD1-ON482571A7.0008CA76-482571A7.0008FCB6@EU.novartis.net>

Hi -

There is not one in BioJava 1.4 although you can do it with an HMM. There 
is an implementation of the NW algorithm in the CVS as well as the SW 
algorithm. These can be downloaded from CVS and will be in the next build 
or snapshot.

- 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





Russ Kepler <russ at kepler-eng.com>
Sent by: biojava-dev-bounces at lists.open-bio.org
07/07/2006 09:11 PM

 
        To:     biojava-dev at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-dev] Java API for Global Alignment


On Tuesday 04 July 2006 04:44 am, Michael Tran wrote:

> Looking for a Java API to do global alignments (something like a 
clustalw
> alignment).

I think most folks have simply implemented a parser for clustalw output to 

generate a FlexibleAlignment when they needed that.  I've got one, and a 
parser for the Paracel CAML output from their genomic scale assembler as 
well.
_______________________________________________
biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev




From mark.schreiber at novartis.com  Fri Jul 14 03:12:27 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 14 Jul 2006 15:12:27 +0800
Subject: [Biojava-dev] [Off Topic] Getting JNDI resources from a Java
	application
Message-ID: <OFFFABF86D.C162A6B4-ON482571AB.00273991-482571AB.00279782@EU.novartis.net>

Hi -

I have a application running in JBoss with a web front end but I would 
like to make a standalone application with a GUI that runs in another JVM.

How can that application get access to resources in the application 
servers JNDI registry (notably the DataSource). I'm guessing I need RMI?? 
Does anyone know of a blueprint or best practice for this sort of thing?

- 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 mark.schreiber at novartis.com  Fri Jul 14 04:38:52 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 14 Jul 2006 16:38:52 +0800
Subject: [Biojava-dev] [Off Topic] Getting JNDI resources from a Java
 application
Message-ID: <OF455B6B7D.2E38347C-ON482571AB.002F72A2-482571AB.002F810E@EU.novartis.net>

Sounds perfect.

Do you have a code snippet?

- Mark





Andy Yates <ady at sanger.ac.uk>
07/14/2006 04:36 PM

 
        To:     mark.schreiber at novartis.com
        cc:     biojava-dev at biojava.org
        Subject:        Re: [Biojava-dev] [Off Topic] Getting JNDI resources from a Java 
application


Hi,

Best thing to use is Spring. You can get Spring to remote any object in 
about 5 lines of code and if you use Spring in your GUI application then 
it won't care about where the DataSource comes from; only that its got 
one.

Andy Yates


mark.schreiber at novartis.com wrote:
> Hi -
> 
> I have a application running in JBoss with a web front end but I would 
> like to make a standalone application with a GUI that runs in another 
JVM.
> 
> How can that application get access to resources in the application 
> servers JNDI registry (notably the DataSource). I'm guessing I need 
RMI?? 
> Does anyone know of a blueprint or best practice for this sort of thing?
> 
> - 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
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 




From ady at sanger.ac.uk  Fri Jul 14 04:36:37 2006
From: ady at sanger.ac.uk (Andy Yates)
Date: Fri, 14 Jul 2006 09:36:37 +0100
Subject: [Biojava-dev] [Off Topic] Getting JNDI resources from a Java
 application
In-Reply-To: <OFFFABF86D.C162A6B4-ON482571AB.00273991-482571AB.00279782@EU.novartis.net>
References: <OFFFABF86D.C162A6B4-ON482571AB.00273991-482571AB.00279782@EU.novartis.net>
Message-ID: <44B75795.1030205@sanger.ac.uk>

Hi,

Best thing to use is Spring. You can get Spring to remote any object in 
about 5 lines of code and if you use Spring in your GUI application then 
it won't care about where the DataSource comes from; only that its got one.

Andy Yates


mark.schreiber at novartis.com wrote:
> Hi -
> 
> I have a application running in JBoss with a web front end but I would 
> like to make a standalone application with a GUI that runs in another JVM.
> 
> How can that application get access to resources in the application 
> servers JNDI registry (notably the DataSource). I'm guessing I need RMI?? 
> Does anyone know of a blueprint or best practice for this sort of thing?
> 
> - 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
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

From bugzilla-daemon at newportal.open-bio.org  Fri Jul 14 12:27:51 2006
From: bugzilla-daemon at newportal.open-bio.org (bugzilla-daemon at newportal.open-bio.org)
Date: Fri, 14 Jul 2006 12:27:51 -0400
Subject: [Biojava-dev] [Bug 2046] New: Cannot read in more than one
	serialized ProfileHMM object, attempt crashes
Message-ID: <bug-2046-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2046

           Summary: Cannot read in more than one serialized ProfileHMM
                    object, attempt crashes
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: critical
          Priority: P1
         Component: dist/dp
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: toddri at eden.rutgers.edu


The following small demo code illustrates the problem.  For me, the second
attempt of reading in the same serialized ProfileHMM object fails (with the
same error from running the code when the 2 serialized objects are different). 
Very repeatable.


------------------------------------------------------------------------

/*
 * SerializeProfile.java
 *
 * Created on April 27, 2006, 11:29 AM
 *
 * To change this template, choose Tools | Template Manager
 * and open the template in the editor.
 */

//package hmm;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import org.biojava.bio.dist.DistributionFactory ;
import org.biojava.bio.dp.BaumWelchTrainer;
import org.biojava.bio.dp.DP;
import org.biojava.bio.dp.DPFactory;
import org.biojava.bio.dp.ModelTrainer;
import org.biojava.bio.dp.ProfileHMM;
import org.biojava.bio.dp.SimpleModelTrainer ;
import org.biojava.bio.dp.StoppingCriteria;
import org.biojava.bio.dp.TrainingAlgorithm;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.db.HashSequenceDB ;
import org.biojava.bio.seq.db.SequenceDB;

/**
 *
 * @author Mark Schreiber
 */
public class SerializeProfile {

    /**
     * Creates a new instance of SerializeProfile
     */
    public SerializeProfile() {
    }

    public void testSerialize(ProfileHMM hmm) throws Exception{
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        ObjectOutputStream oos = new ObjectOutputStream(bos);
        System.out.println("Writing HMM");
        oos.writeObject(hmm);
        oos.flush();
        System.out.println("Wrote "+bos.size()+" bytes");
        oos.close();

        ByteArrayInputStream bis = new ByteArrayInputStream(bos.toByteArray());
        ObjectInputStream ois = new ObjectInputStream(bis);
        System.out.println("Reading HMM");
        ProfileHMM hmm2 = (ProfileHMM)ois.readObject();
        ois.close();
        System.out.println("Read HMM");

        ByteArrayInputStream bis2 = new
ByteArrayInputStream(bos.toByteArray());
        ObjectInputStream ois2 = new ObjectInputStream(bis2);
        System.out.println("Reading HMM again!");
        ProfileHMM hmm3 = (ProfileHMM)ois2.readObject();
        ois2.close();
        System.out.println("Read HMM again.");
    }

    public ProfileHMM generateProfile() throws Exception{
               /*
                * Make a profile HMM over the DNA Alphabet with 12 'columns'
and default
                * DistributionFactories to construct the transition and
emmission
                * Distributions
                */
        ProfileHMM hmm = new ProfileHMM(DNATools.getDNA(),
                12,
                DistributionFactory.DEFAULT,
                DistributionFactory.DEFAULT,
                "my profilehmm");

        //create the Dynamic Programming matrix for the model.
        DP dp = DPFactory.DEFAULT.createDP(hmm);

        //Database to hold the training set
        SequenceDB db = new HashSequenceDB();

        //code here to load the training set
        Sequence seq = DNATools.createDNASequence("aaaggctagctg", "seq1");
        db.addSequence(seq);
        seq = DNATools.createDNASequence("aaaggcgagctg", "seq2");
        db.addSequence(seq);
        seq = DNATools.createDNASequence("aaattctagctg", "seq3");
        db.addSequence(seq);

        //train the model to have uniform parameters
        ModelTrainer mt = new SimpleModelTrainer();
        //register the model to train
        mt.registerModel(hmm);
        //as no other counts are being used the null weight will cause
everything to be uniform
        mt.setNullModelWeight(1.0);
        mt.train();

        //create a BW trainer for the dp matrix generated from the HMM
        BaumWelchTrainer bwt = new BaumWelchTrainer(dp);

        //anonymous implementation of the stopping criteria interface to stop
after 20 iterations
        StoppingCriteria stopper = new StoppingCriteria(){
            public boolean isTrainingComplete(TrainingAlgorithm ta){
                return (ta.getCycle() > 20);
            }
        };

       /*
        * optimize the dp matrix to reflect the training set in db using a null
model
        * weight of 1.0 and the Stopping criteria defined above.
        */
        bwt.train(db,1.0,stopper);


        return hmm;
    }

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) throws Exception{
        SerializeProfile sp = new SerializeProfile();
        ProfileHMM hmm = sp.generateProfile();
        sp.testSerialize(hmm);
    }

}


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From bugzilla-daemon at newportal.open-bio.org  Mon Jul 17 04:33:35 2006
From: bugzilla-daemon at newportal.open-bio.org (bugzilla-daemon at newportal.open-bio.org)
Date: Mon, 17 Jul 2006 04:33:35 -0400
Subject: [Biojava-dev] [Bug 2046] Cannot read in more than one serialized
	ProfileHMM object, attempt crashes
In-Reply-To: <bug-2046-485@http.bugzilla.open-bio.org/>
Message-ID: <200607170833.k6H8XZl9030328@newportal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2046





------- Comment #1 from holland at ebi.ac.uk  2006-07-17 04:33 -------
Could you post the full stacktrace please?


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From mmccormi at fhcrc.org  Mon Jul 17 11:43:27 2006
From: mmccormi at fhcrc.org (Michael McCormick)
Date: Mon, 17 Jul 2006 08:43:27 -0700
Subject: [Biojava-dev] [Off Topic] Getting JNDI resources from a Java
	application
In-Reply-To: <OFFFABF86D.C162A6B4-ON482571AB.00273991-482571AB.00279782@EU.novartis.net>
References: <OFFFABF86D.C162A6B4-ON482571AB.00273991-482571AB.00279782@EU.novartis.net>
Message-ID: <61EF645F-796B-4A71-8D97-ECF69FD1AAE6@fhcrc.org>

Hi Mark,

You can also achieve this by using standard J2EE/JEE conventions  
instead of creating a dependency on Spring. We have several external  
applications that take advantage of reusable services deployed on our  
JBoss instance.

This page details some standard J2EE/JEE patterns and includes code  
samples as well. From your description, you will want to take a look  
at the ServiceLocator, SessionFacade, and BusinessDelegate patterns.  
The JBoss forums and wiki are a good resource as well.
http://java.sun.com/blueprints/corej2eepatterns/Patterns/

Let me know if you have any further questions.

Mike

Michael McCormick
Systems Analyst
Geraghty Lab
Fred Hutchinson Cancer Research Center
mmccormi at fhcrc.org
206.667.75811


On Jul 14, 2006, at 12:12 AM, mark.schreiber at novartis.com wrote:

Hi -

I have a application running in JBoss with a web front end but I would
like to make a standalone application with a GUI that runs in another  
JVM.

How can that application get access to resources in the application
servers JNDI registry (notably the DataSource). I'm guessing I need  
RMI??
Does anyone know of a blueprint or best practice for this sort of thing?

- 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

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


From debesis at gmail.com  Fri Jul 21 04:32:47 2006
From: debesis at gmail.com (=?WINDOWS-1252?Q?Valdemaras_Rep=9Ays?=)
Date: Fri, 21 Jul 2006 11:32:47 +0300
Subject: [Biojava-dev] Question regarding
	org.biojava.bio.seq.db.WebSequenceDB
Message-ID: <ec12348a0607210132y5ed5e924n2e474a53a2540a7a@mail.gmail.com>

Hi,
I'm using the org.biojava.bio.seq.db.WebSequenceDB.getSequence(String id)
method.

Every time i invoke it it prints a few lines to System.err and these lines
are not errors:
query is
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=protein&uid=15625528&dopt=FASTA
got data from
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=protein&uid=15625528&dopt=FASTA

My application uses this method a lot and the log becomes stuffed with these
not important messages..

Could someone, please, remove these two System.err.println lines from the
method?
Or i can do it myself if you give me a cvs account.

By the way, cvs currently is not working: cvs [login aborted]: connect to
code.open-bio.org(207.154.17.72):2401 failed: Connection timed out. But I
hope it' temprary.

Thanks,
Valdemaras Rep?ys


From richard.holland at ebi.ac.uk  Fri Jul 21 04:58:29 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Fri, 21 Jul 2006 09:58:29 +0100
Subject: [Biojava-dev] Question
	regarding	org.biojava.bio.seq.db.WebSequenceDB
In-Reply-To: <ec12348a0607210132y5ed5e924n2e474a53a2540a7a@mail.gmail.com>
References: <ec12348a0607210132y5ed5e924n2e474a53a2540a7a@mail.gmail.com>
Message-ID: <1153472310.3955.21.camel@localhost.localdomain>

I've commented the lines out in the head branch of CVS for biojava-live.

cheers,
Richard

On Fri, 2006-07-21 at 11:32 +0300, Valdemaras Rep?ys wrote:
> Hi,
> I'm using the org.biojava.bio.seq.db.WebSequenceDB.getSequence(String id)
> method.
> 
> Every time i invoke it it prints a few lines to System.err and these lines
> are not errors:
> query is
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=protein&uid=15625528&dopt=FASTA
> got data from
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=protein&uid=15625528&dopt=FASTA
> 
> My application uses this method a lot and the log becomes stuffed with these
> not important messages..
> 
> Could someone, please, remove these two System.err.println lines from the
> method?
> Or i can do it myself if you give me a cvs account.
> 
> By the way, cvs currently is not working: cvs [login aborted]: connect to
> code.open-bio.org(207.154.17.72):2401 failed: Connection timed out. But I
> hope it' temprary.
> 
> Thanks,
> Valdemaras Rep?ys
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416


From bugzilla-daemon at newportal.open-bio.org  Mon Jul 31 11:35:43 2006
From: bugzilla-daemon at newportal.open-bio.org (bugzilla-daemon at newportal.open-bio.org)
Date: Mon, 31 Jul 2006 11:35:43 -0400
Subject: [Biojava-dev] [Bug 2046] Cannot read in more than one serialized
	ProfileHMM object, attempt crashes
In-Reply-To: <bug-2046-485@http.bugzilla.open-bio.org/>
Message-ID: <200607311535.k6VFZhI5010172@newportal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2046





------- Comment #2 from toddri at eden.rutgers.edu  2006-07-31 11:35 -------
Here is the output and the full stacktrace:

Writing HMM
Wrote 22561 bytes
Reading HMM
Read HMM
Reading HMM again!
Exception in thread "main" java.io.IOException: Symbol in serialized stream
can't be found in the alphabet
        at
org.biojava.bio.dist.SimpleDistribution.readObject(SimpleDistribution.java:97)
        at sun.reflect.GeneratedMethodAccessor5.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:919)
        at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1813)
        at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1713)
        at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1299)
        at java.io.ObjectInputStream.readObject(ObjectInputStream.java:339)
        at java.util.HashMap.readObject(HashMap.java:1013)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:919)
        at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1813)
        at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1713)
        at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1299)
        at
java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1912)
        at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1836)
        at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1713)
        at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1299)
        at java.io.ObjectInputStream.readObject(ObjectInputStream.java:339)
        at SerializeProfile.testSerialize(SerializeProfile.java:61)
        at SerializeProfile.main(SerializeProfile.java:126)


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From darin.london at duke.edu  Mon Jul  3 12:41:33 2006
From: darin.london at duke.edu (Darin London)
Date: Mon, 03 Jul 2006 08:41:33 -0400
Subject: [Biojava-dev] Call For Birds of a Feather Suggestions
Message-ID: <44A9107D.2050304@duke.edu>

The BOSC organizing comittee is currently seeking suggestions for Birds
of a Feather meeting ideas. Birds of a Feather meetings are one of the
more popular activities at BOSC, occurring at the end of each days
session. These are free-form meetings organized by the attendees
themselves to discuss one or a few topics of interest in greater detail.
BOF?s have been formed to allow developers and users of individual OBF
software to meet each other face-to-face to discuss the project, or to
discuss completely new ideas, and even start new software development
projects. These meetings offer a unique opportunity for individuals to
explore more about the activities of the various Open Source Projects,
and, in some cases, even take an active role influencing the future of
Open Source Software development. If you would like to create a BOF,
just sign up for a wiki account, login, and edit the <a
href="http://www.open-bio.org/wiki/BOSC_2006/Birds-of-a-Feather">BOSC
2006 Birds of a Feather page</a>.


From bubba.puryear at gmail.com  Mon Jul  3 15:40:40 2006
From: bubba.puryear at gmail.com (Bubba Puryear)
Date: Mon, 3 Jul 2006 11:40:40 -0400
Subject: [Biojava-dev] Accession defaults for GenbankFormat
Message-ID: <d2f7533b0607030840g53cb18eeif5e38e9efa9ce010@mail.gmail.com>

Hey all,

   I'm using biojava for an internal app for my client that has about 5000
internally developed genbank records. The majority of these records do not
have ACCESSION fields, since they didn't come from a public data source.
(Many of these were created using Invitrogen's Vector NTI and saved as
files)

  Because there is no accession number for these records, I get problems
when I try to use RichSequence and friends with this data. I've made a patch
for GenbankFormat.java that sets the accession to the locus name of the
record during parsing. If/When the accession field is parsed, this value is
over written, so I think it should be ok generally. I also have a test case
and test data file.

  The registration page thing discouraged attachments for this list -- how
should I provide these files? Thanks in advance,
Bubba

ps - The patch is small, I can inline it here:

Index: src/org/biojavax/bio/seq/io/GenbankFormat.java
===================================================================
RCS file:
/home/repository/biojava/biojava-live/src/org/biojavax/bio/seq/io/GenbankFormat.java,v
retrieving revision 1.63
diff -u -r1.63 GenbankFormat.java
--- src/org/biojavax/bio/seq/io/GenbankFormat.java    28 Jun 2006 17:02:47
-0000    1.63
+++ src/org/biojavax/bio/seq/io/GenbankFormat.java    1 Jul 2006 20:34:48
-0000
@@ -274,6 +274,9 @@
                 Matcher m = lp.matcher(loc);
                 if (m.matches()) {
                     rlistener.setName(m.group(1));
+                    // default accession to locus name for sources that do
not have accessions proper.
+                    accession = m.group(1);
+                    rlistener.setAccession(accession);
                     rlistener.setDivision(m.group(5));
                     rlistener.addSequenceProperty(Terms.getMolTypeTerm(),
m.group(3));
                     rlistener.addSequenceProperty(Terms.getDateUpdatedTerm
(),m.group(6));


From mark.schreiber at novartis.com  Tue Jul  4 02:19:21 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Tue, 4 Jul 2006 10:19:21 +0800
Subject: [Biojava-dev] Accession defaults for GenbankFormat
Message-ID: <OF4CDD72D6.AC92F35C-ON482571A1.000CAACF-482571A1.000CC21D@EU.novartis.net>

This seems reasonable. Can you forsee any problems Richard?

- 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





"Bubba Puryear" <bubba.puryear at gmail.com>
Sent by: biojava-dev-bounces at lists.open-bio.org
07/03/2006 11:40 PM

 
        To:     biojava-dev at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] Accession defaults for GenbankFormat


Hey all,

   I'm using biojava for an internal app for my client that has about 5000
internally developed genbank records. The majority of these records do not
have ACCESSION fields, since they didn't come from a public data source.
(Many of these were created using Invitrogen's Vector NTI and saved as
files)

  Because there is no accession number for these records, I get problems
when I try to use RichSequence and friends with this data. I've made a 
patch
for GenbankFormat.java that sets the accession to the locus name of the
record during parsing. If/When the accession field is parsed, this value 
is
over written, so I think it should be ok generally. I also have a test 
case
and test data file.

  The registration page thing discouraged attachments for this list -- how
should I provide these files? Thanks in advance,
Bubba

ps - The patch is small, I can inline it here:

Index: src/org/biojavax/bio/seq/io/GenbankFormat.java
===================================================================
RCS file:
/home/repository/biojava/biojava-live/src/org/biojavax/bio/seq/io/GenbankFormat.java,v
retrieving revision 1.63
diff -u -r1.63 GenbankFormat.java
--- src/org/biojavax/bio/seq/io/GenbankFormat.java    28 Jun 2006 17:02:47
-0000    1.63
+++ src/org/biojavax/bio/seq/io/GenbankFormat.java    1 Jul 2006 20:34:48
-0000
@@ -274,6 +274,9 @@
                 Matcher m = lp.matcher(loc);
                 if (m.matches()) {
                     rlistener.setName(m.group(1));
+                    // default accession to locus name for sources that 
do
not have accessions proper.
+                    accession = m.group(1);
+                    rlistener.setAccession(accession);
                     rlistener.setDivision(m.group(5));
                     rlistener.addSequenceProperty(Terms.getMolTypeTerm(),
m.group(3));
 rlistener.addSequenceProperty(Terms.getDateUpdatedTerm
(),m.group(6));
_______________________________________________
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biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev





From mark.schreiber at novartis.com  Tue Jul  4 02:44:21 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Tue, 4 Jul 2006 10:44:21 +0800
Subject: [Biojava-dev] Problem with SimpleDocRefTest
Message-ID: <OFC5C82EC7.6B27CCA8-ON482571A1.000EFAC6-482571A1.000F0C03@EU.novartis.net>

Works now. There were other problems, also fixed.





Richard Holland <richard.holland at ebi.ac.uk>
Sent by: biojava-dev-bounces at lists.open-bio.org
06/30/2006 05:11 PM

 
        To:     george waldon <gwaldon at geneinfinity.org>
        cc:     biojava-dev at lists.open-bio.org, Mark Schreiber 
<mark.schreiber at novartis.com>
        Subject:        Re: [Biojava-dev] Problem with SimpleDocRefTest


The SimpleDocRef constructor changed recently to include document titles
and I don't think the test was updated to match it. Sorry about that -
the head branch of CVS is always under development so cannot always be
guaranteed to work out 100%.

Mark, can you update the tests?

cheers,
Richard

On Thu, 2006-06-29 at 16:33 -0700, george waldon wrote:
> Hi,
> 
> I am trying to run the tests but my compiler complains about 
org.biojavax.SimpleDocRefTest at compilation:
> missing constructor SimpleDocRef(java.util.List, java.lang.String)
> 
> Was-It expected to interpretate that as SimpleDocRef(java.util.List, 
java.lang.String, null) (the three-argument constructor)?
> 
> Thanks,
> George
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416

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





From mark.schreiber at novartis.com  Tue Jul  4 02:43:11 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Tue, 4 Jul 2006 10:43:11 +0800
Subject: [Biojava-dev] developers should use unit tests and watch for
	javadoc errors
Message-ID: <OFE8F7F840.84605A8A-ON482571A1.000D11FB-482571A1.000EF0CB@EU.novartis.net>

Hi all -

There are quite a few new developers with CVS accounts so I would like to 
draw your attention to Unit testing.

BioJava uses JUnit Tests and has ant tasks for these (runtests for 
example). To enable this you pretty much only need to put the JUnit jar 
into your ant lib directory. Then from the biojava root type ant runtests.

I just did a CVS download and build after a few weeks break and found a 
few of the tests no longer passed. Changes had been made to the source 
code which compiled and presumably solved some problem but along the way 
had introduced subtle errors that caused the unit tests to fail. A 
particularly subtle one was a change that caused the compareTo() method to 
fail. You are not likely to notice this until you come to sort something 
and even then you may not pick it up.

If you make changes to the source code please run the Unit tests. Often 
changes in other parts of the code may affect the behaivour of methods you 
haven't touched (such as the compareTo example above).

I would also make a plea for people to contribute more Unit tests. The 
coverage is patchy and the more we have the more biojava will be bug free 
which means more of your programs will be bug free. If you use a certain 
class a lot and the Unit tests for it don't exist or are inadequate it 
would be a good idea to make or improve one so you can be sure of good 
behaivour. The unit tests for the biojavax objects are probably the best 
examples we have. They try to test every method, including the often 
neglected but very important compareTo(), equals(), hashCode() and 
toString(). They also try to test the behaivour described in the javadocs 
of the methods. If you want to write a Unit test take one of these as a 
template.

Finally a word about javadocs. One the whole the number and quality of 
javadocs has vastly improved over the last year. If you add or modify 
javadocs run the ant javadoc-biojava task and check for warnings. This 
allows you to avoid common errors such as misspelled @param names or @see 
tags that can't locate the class you want to reference. It's a good check 
if you have been copying and pasting javadoc comments.

In conclusion some basic guidelines for developers:

* New classes should have full javadocs and a JUnit test (inlcuding equals 
etc).
* New methods should have javadocs (not required if it is a private 
method) and add a test of the method to the JUnit test.
* Before any commit run the JUnit tests to make sure you haven't broken 
anything and run the javadoc task to make sure your @params etc are all 
correct.

If you observe this behaivour biojava will be a lot more stable and better 
documented which will give us a better reputation and mean that your code 
works more often.

Sorry for the sermon.

- 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 richard.holland at ebi.ac.uk  Tue Jul  4 08:05:52 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Tue, 04 Jul 2006 09:05:52 +0100
Subject: [Biojava-dev] Accession defaults for GenbankFormat
In-Reply-To: <d2f7533b0607030840g53cb18eeif5e38e9efa9ce010@mail.gmail.com>
References: <d2f7533b0607030840g53cb18eeif5e38e9efa9ce010@mail.gmail.com>
Message-ID: <1152000352.3948.32.camel@texas.ebi.ac.uk>

That seems like a good idea to me. I've made the change in CVS.

cheers,
Richard

On Mon, 2006-07-03 at 11:40 -0400, Bubba Puryear wrote:
> Hey all,
> 
>    I'm using biojava for an internal app for my client that has about 5000
> internally developed genbank records. The majority of these records do not
> have ACCESSION fields, since they didn't come from a public data source.
> (Many of these were created using Invitrogen's Vector NTI and saved as
> files)
> 
>   Because there is no accession number for these records, I get problems
> when I try to use RichSequence and friends with this data. I've made a patch
> for GenbankFormat.java that sets the accession to the locus name of the
> record during parsing. If/When the accession field is parsed, this value is
> over written, so I think it should be ok generally. I also have a test case
> and test data file.
> 
>   The registration page thing discouraged attachments for this list -- how
> should I provide these files? Thanks in advance,
> Bubba
> 
> ps - The patch is small, I can inline it here:
> 
> Index: src/org/biojavax/bio/seq/io/GenbankFormat.java
> ===================================================================
> RCS file:
> /home/repository/biojava/biojava-live/src/org/biojavax/bio/seq/io/GenbankFormat.java,v
> retrieving revision 1.63
> diff -u -r1.63 GenbankFormat.java
> --- src/org/biojavax/bio/seq/io/GenbankFormat.java    28 Jun 2006 17:02:47
> -0000    1.63
> +++ src/org/biojavax/bio/seq/io/GenbankFormat.java    1 Jul 2006 20:34:48
> -0000
> @@ -274,6 +274,9 @@
>                  Matcher m = lp.matcher(loc);
>                  if (m.matches()) {
>                      rlistener.setName(m.group(1));
> +                    // default accession to locus name for sources that do
> not have accessions proper.
> +                    accession = m.group(1);
> +                    rlistener.setAccession(accession);
>                      rlistener.setDivision(m.group(5));
>                      rlistener.addSequenceProperty(Terms.getMolTypeTerm(),
> m.group(3));
>                      rlistener.addSequenceProperty(Terms.getDateUpdatedTerm
> (),m.group(6));
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416



From richard.holland at ebi.ac.uk  Tue Jul  4 08:55:48 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Tue, 04 Jul 2006 09:55:48 +0100
Subject: [Biojava-dev] developers should use unit tests and watch
	for	javadoc errors
In-Reply-To: <OFE8F7F840.84605A8A-ON482571A1.000D11FB-482571A1.000EF0CB@EU.novartis.net>
References: <OFE8F7F840.84605A8A-ON482571A1.000D11FB-482571A1.000EF0CB@EU.novartis.net>
Message-ID: <1152003348.3948.46.camel@texas.ebi.ac.uk>

Hello all.

In addition to this, be careful with Java versions. BioJava is written
for Java 1.4. All binaries in CVS have been compiled with 1.4. BioJava
will compile successfully under 1.5 with a few extra warnings, but you
should not check any 1.5-compiled binaries back into CVS as then others
may not be able to use them.

Note also that the current version of JUnit (4.1) was compiled with 1.5.
If you want to run JUnit against BioJava using 1.4, you have to find and
download JUnit 3.8.1, which was the last release of JUnit to be compiled
with 1.4.

cheers,
Richard

On Tue, 2006-07-04 at 10:43 +0800, mark.schreiber at novartis.com wrote:
> Hi all -
> 
> There are quite a few new developers with CVS accounts so I would like to 
> draw your attention to Unit testing.
> 
> BioJava uses JUnit Tests and has ant tasks for these (runtests for 
> example). To enable this you pretty much only need to put the JUnit jar 
> into your ant lib directory. Then from the biojava root type ant runtests.
> 
> I just did a CVS download and build after a few weeks break and found a 
> few of the tests no longer passed. Changes had been made to the source 
> code which compiled and presumably solved some problem but along the way 
> had introduced subtle errors that caused the unit tests to fail. A 
> particularly subtle one was a change that caused the compareTo() method to 
> fail. You are not likely to notice this until you come to sort something 
> and even then you may not pick it up.
> 
> If you make changes to the source code please run the Unit tests. Often 
> changes in other parts of the code may affect the behaivour of methods you 
> haven't touched (such as the compareTo example above).
> 
> I would also make a plea for people to contribute more Unit tests. The 
> coverage is patchy and the more we have the more biojava will be bug free 
> which means more of your programs will be bug free. If you use a certain 
> class a lot and the Unit tests for it don't exist or are inadequate it 
> would be a good idea to make or improve one so you can be sure of good 
> behaivour. The unit tests for the biojavax objects are probably the best 
> examples we have. They try to test every method, including the often 
> neglected but very important compareTo(), equals(), hashCode() and 
> toString(). They also try to test the behaivour described in the javadocs 
> of the methods. If you want to write a Unit test take one of these as a 
> template.
> 
> Finally a word about javadocs. One the whole the number and quality of 
> javadocs has vastly improved over the last year. If you add or modify 
> javadocs run the ant javadoc-biojava task and check for warnings. This 
> allows you to avoid common errors such as misspelled @param names or @see 
> tags that can't locate the class you want to reference. It's a good check 
> if you have been copying and pasting javadoc comments.
> 
> In conclusion some basic guidelines for developers:
> 
> * New classes should have full javadocs and a JUnit test (inlcuding equals 
> etc).
> * New methods should have javadocs (not required if it is a private 
> method) and add a test of the method to the JUnit test.
> * Before any commit run the JUnit tests to make sure you haven't broken 
> anything and run the javadoc task to make sure your @params etc are all 
> correct.
> 
> If you observe this behaivour biojava will be a lot more stable and better 
> documented which will give us a better reputation and mean that your code 
> works more often.
> 
> Sorry for the sermon.
> 
> - 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
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416



From bubba.puryear at gmail.com  Tue Jul  4 16:51:23 2006
From: bubba.puryear at gmail.com (Bubba Puryear)
Date: Tue, 4 Jul 2006 12:51:23 -0400
Subject: [Biojava-dev] Exception wrapping in SimpleRichObjectBuilder
Message-ID: <d2f7533b0607040951m166da1cfoea49f1abdd5cdbb3@mail.gmail.com>

One last patch for the day - just added some exception wrapping that aided
me in some debugging earler:

Index: src/org/biojavax/SimpleRichObjectBuilder.java
===================================================================
RCS file:
/home/repository/biojava/biojava-live/src/org/biojavax/SimpleRichObjectBuilder.java,v
retrieving revision 1.7
diff -u -r1.7 SimpleRichObjectBuilder.java
--- src/org/biojavax/SimpleRichObjectBuilder.java       27 Apr 2006 10:16:29
-0000      1.7
+++ src/org/biojavax/SimpleRichObjectBuilder.java       4 Jul 2006 19:54:14
-0000
@@ -32,6 +32,7 @@
  * Creates objects and returns them, and stores them in an internal
  * map of singletons for reference. Takes up a lot of memory!
  * @author Richard Holland
+ * @author Bubba Puryear
  * @since 1.5
  */
 public class SimpleRichObjectBuilder implements RichObjectBuilder {
@@ -75,7 +76,7 @@
                 if (i<(paramsList.size()-1)) paramsstuff.append(",");
             }
             paramsstuff.append(")");
-            throw new IllegalArgumentException("Could not find constructor
for "+paramsstuff);
+            throw new IllegalArgumentException("Could not find constructor
for "+paramsstuff, e);
         }
     }


From richard.holland at ebi.ac.uk  Wed Jul  5 08:21:02 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Wed, 05 Jul 2006 09:21:02 +0100
Subject: [Biojava-dev] Exception wrapping in SimpleRichObjectBuilder
In-Reply-To: <d2f7533b0607040951m166da1cfoea49f1abdd5cdbb3@mail.gmail.com>
References: <d2f7533b0607040951m166da1cfoea49f1abdd5cdbb3@mail.gmail.com>
Message-ID: <1152087662.3948.80.camel@texas.ebi.ac.uk>

Unfortunately, the IllegalArgumentException(String, Throwable)
constructor is a Java 1.5 feature, and is not present in Java 1.4 As
BioJava is currently 1.4-compatible, I can't make this change exactly as
you make it. However, I did make the equivalent change in the 1.4
syntax:

	IllegalArgumentException ie = new IllegalArgumentException(.....);
	ie.initCause(e); 
	throw ie;

This change has been made in CVS.

cheers,
Richard

On Tue, 2006-07-04 at 12:51 -0400, Bubba Puryear wrote:
> One last patch for the day - just added some exception wrapping that aided
> me in some debugging earler:
> 
> Index: src/org/biojavax/SimpleRichObjectBuilder.java
> ===================================================================
> RCS file:
> /home/repository/biojava/biojava-live/src/org/biojavax/SimpleRichObjectBuilder.java,v
> retrieving revision 1.7
> diff -u -r1.7 SimpleRichObjectBuilder.java
> --- src/org/biojavax/SimpleRichObjectBuilder.java       27 Apr 2006 10:16:29
> -0000      1.7
> +++ src/org/biojavax/SimpleRichObjectBuilder.java       4 Jul 2006 19:54:14
> -0000
> @@ -32,6 +32,7 @@
>   * Creates objects and returns them, and stores them in an internal
>   * map of singletons for reference. Takes up a lot of memory!
>   * @author Richard Holland
> + * @author Bubba Puryear
>   * @since 1.5
>   */
>  public class SimpleRichObjectBuilder implements RichObjectBuilder {
> @@ -75,7 +76,7 @@
>                  if (i<(paramsList.size()-1)) paramsstuff.append(",");
>              }
>              paramsstuff.append(")");
> -            throw new IllegalArgumentException("Could not find constructor
> for "+paramsstuff);
> +            throw new IllegalArgumentException("Could not find constructor
> for "+paramsstuff, e);
>          }
>      }
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416



From bubba.puryear at gmail.com  Wed Jul  5 13:38:29 2006
From: bubba.puryear at gmail.com (Bubba Puryear)
Date: Wed, 5 Jul 2006 09:38:29 -0400
Subject: [Biojava-dev] Exception wrapping in SimpleRichObjectBuilder
In-Reply-To: <1152087662.3948.80.camel@texas.ebi.ac.uk>
References: <d2f7533b0607040951m166da1cfoea49f1abdd5cdbb3@mail.gmail.com>
	<1152087662.3948.80.camel@texas.ebi.ac.uk>
Message-ID: <d2f7533b0607050638y4d00a2e9jb3cd41fc8065c20e@mail.gmail.com>

Dang - forgot about that. Sorry. Thanks for the fix, though!

On 7/5/06, Richard Holland <richard.holland at ebi.ac.uk> wrote:
> Unfortunately, the IllegalArgumentException(String, Throwable)
> constructor is a Java 1.5 feature, and is not present in Java 1.4 As
> BioJava is currently 1.4-compatible, I can't make this change exactly as
> you make it. However, I did make the equivalent change in the 1.4
> syntax:
>
>         IllegalArgumentException ie = new IllegalArgumentException(.....);
>         ie.initCause(e);
>         throw ie;
>
> This change has been made in CVS.
>
> cheers,
> Richard
>
> On Tue, 2006-07-04 at 12:51 -0400, Bubba Puryear wrote:
> > One last patch for the day - just added some exception wrapping that aided
> > me in some debugging earler:
> >
> > Index: src/org/biojavax/SimpleRichObjectBuilder.java
> > ===================================================================
> > RCS file:
> > /home/repository/biojava/biojava-live/src/org/biojavax/SimpleRichObjectBuilder.java,v
> > retrieving revision 1.7
> > diff -u -r1.7 SimpleRichObjectBuilder.java
> > --- src/org/biojavax/SimpleRichObjectBuilder.java       27 Apr 2006 10:16:29
> > -0000      1.7
> > +++ src/org/biojavax/SimpleRichObjectBuilder.java       4 Jul 2006 19:54:14
> > -0000
> > @@ -32,6 +32,7 @@
> >   * Creates objects and returns them, and stores them in an internal
> >   * map of singletons for reference. Takes up a lot of memory!
> >   * @author Richard Holland
> > + * @author Bubba Puryear
> >   * @since 1.5
> >   */
> >  public class SimpleRichObjectBuilder implements RichObjectBuilder {
> > @@ -75,7 +76,7 @@
> >                  if (i<(paramsList.size()-1)) paramsstuff.append(",");
> >              }
> >              paramsstuff.append(")");
> > -            throw new IllegalArgumentException("Could not find constructor
> > for "+paramsstuff);
> > +            throw new IllegalArgumentException("Could not find constructor
> > for "+paramsstuff, e);
> >          }
> >      }
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> --
> Richard Holland (BioMart Team)
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> UNITED KINGDOM
> Tel: +44-(0)1223-494416
>
>


From ap3 at sanger.ac.uk  Thu Jul  6 18:44:42 2006
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Thu, 6 Jul 2006 19:44:42 +0100
Subject: [Biojava-dev] biojava wiki and Jmol
Message-ID: <f1c60ed25a12b4e80587b9a826141791@sanger.ac.uk>

Hi!

I will commit some new protein structure functionality to CVS soon 
(structure alignments).
For this it would be nice if I could show some examples in 3D with the 
Jmol applet in
the BioJava Wiki pages.

Could somebody with admin rights install the Jmol-wiki extension for 
MediaWiki? - not sure who to contact about that...
instructions would be here:
http://wiki.jmol.org/index.php/MediaWiki#Installation

Thanks! :-)
Andreas

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
			 +44 (0) 1223 49 6891



From mark.schreiber at novartis.com  Fri Jul  7 00:56:04 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 7 Jul 2006 08:56:04 +0800
Subject: [Biojava-dev] [Biojava-l] biojava wiki and Jmol
Message-ID: <OFD9C3155C.42A0849E-ON482571A4.0005193F-482571A4.00052204@EU.novartis.net>

Be my guest!!





Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx>
Sent by: biojava-l-bounces at lists.open-bio.org
07/07/2006 05:45 AM

 
        To:     Andreas Prlic <ap3 at sanger.ac.uk>
        cc:     biojava-dev at biojava.org, biojava-l at biojava.org, (bcc: Mark 
Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] biojava wiki and Jmol


Hi Andreas,

I have admin privileges for the open-bio.org webserver. Unless Mark 
Schreiber (who appears to be the website admin for BioJava) has other 
opinion, I can help you with this and get the extension installed and 
configured for the wiki.

Regards,
Mauricio.

Andreas Prlic wrote:
> Hi!
> 
> I will commit some new protein structure functionality to CVS soon 
> (structure alignments).
> For this it would be nice if I could show some examples in 3D with the 
> Jmol applet in
> the BioJava Wiki pages.
> 
> Could somebody with admin rights install the Jmol-wiki extension for 
> MediaWiki? - not sure who to contact about that...
> instructions would be here:
> http://wiki.jmol.org/index.php/MediaWiki#Installation
> 
> Thanks! :-)
> Andreas
> 
> -----------------------------------------------------------------------
> 
> Andreas Prlic      Wellcome Trust Sanger Institute
>                                Hinxton, Cambridge CB10 1SA, UK
>                                                 +44 (0) 1223 49 6891
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM

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






From bugzilla-daemon at newportal.open-bio.org  Fri Jul  7 02:20:42 2006
From: bugzilla-daemon at newportal.open-bio.org (bugzilla-daemon at newportal.open-bio.org)
Date: Thu, 6 Jul 2006 22:20:42 -0400
Subject: [Biojava-dev] [Bug 2038] New: test bug
Message-ID: <bug-2038-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2038

           Summary: test bug
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: trivial
          Priority: P2
         Component: Others
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: mark.schreiber at novartis.com
                CC: mark.schreiber at novartis.com


testing bugzilla please ignore!


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From bugzilla-daemon at newportal.open-bio.org  Fri Jul  7 02:21:37 2006
From: bugzilla-daemon at newportal.open-bio.org (bugzilla-daemon at newportal.open-bio.org)
Date: Thu, 6 Jul 2006 22:21:37 -0400
Subject: [Biojava-dev] [Bug 2038] test bug
In-Reply-To: <bug-2038-485@http.bugzilla.open-bio.org/>
Message-ID: <200607070221.k672LbcU017978@newportal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2038


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




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From mark.schreiber at novartis.com  Fri Jul  7 02:29:57 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 7 Jul 2006 10:29:57 +0800
Subject: [Biojava-dev] submission of bug reports and requests for enhancement
Message-ID: <OFDF2201FF.B33DC5D9-ON482571A4.000D52A3-482571A4.000DBA74@EU.novartis.net>

Hello all -

Biojava now has a working bug reporting and tracking system based on 
bugzilla. You can submit and track bugs or requests for enhancement at 
http://bugzilla.open-bio.org/ (I will add this link to the biojava wiki).

>From now on this should be the prefered way to report a bug in biojava. 
This is so we don't forget about the bugs that we haven't dealt with and 
the new features people want that we should add.

By default bugs will be 'assigned' to biojava-dev but from time to time I 
may reassign really bad ones to the appropriate person to clear them more 
quickly.

Please make use of this so we can make biojava better.

Thanks,

- 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 bugzilla-daemon at newportal.open-bio.org  Fri Jul  7 02:31:18 2006
From: bugzilla-daemon at newportal.open-bio.org (bugzilla-daemon at newportal.open-bio.org)
Date: Thu, 6 Jul 2006 22:31:18 -0400
Subject: [Biojava-dev] [Bug 2005] test bug
In-Reply-To: <bug-2005-485@http.bugzilla.open-bio.org/>
Message-ID: <200607070231.k672VIAV018929@newportal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2005


mark.schreiber at novartis.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




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From michael.tran at acpfg.com.au  Tue Jul  4 10:44:07 2006
From: michael.tran at acpfg.com.au (Michael Tran)
Date: Tue, 4 Jul 2006 20:14:07 +0930
Subject: [Biojava-dev] Java API for Global Alignment
References: <mailman.4967.1151566574.2084.biojava-l@lists.open-bio.org>
Message-ID: <D3C986810EBCCE488A9DCA95463794F146F35A@kaneda.acpfg.local>

Hi All,
 
Looking for a Java API to do global alignments (something like a clustalw alignment).
 
Looking at the BioJava API 1.4 (see below) does not appear to have such a class.
 
org.biojava.bio.alignment <https://mail.acpfg.com.au/org/biojava/bio/alignment/package-summary.html>  
Interfaces  
AlignmentElement <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/AlignmentElement.html>  
ARAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/ARAlignment.html>  
EditableAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/EditableAlignment.html>  
QualitativeAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/QualitativeAlignment.html>  
UnequalLengthAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/UnequalLengthAlignment.html> 	
Classes  
AbstractULAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/AbstractULAlignment.html>  
FlexibleAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/FlexibleAlignment.html>  
SimpleAlignmentElement <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/SimpleAlignmentElement.html> 	
Exceptions  
IllegalAlignmentEditException <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/IllegalAlignmentEditException.html> 	

Help is appreciated.
 
Cheers,
ST



From bubba.puryear at gmail.com  Tue Jul  4 16:48:10 2006
From: bubba.puryear at gmail.com (Bubba Puryear)
Date: Tue, 4 Jul 2006 12:48:10 -0400
Subject: [Biojava-dev] Some more light parser changes
Message-ID: <d2f7533b0607040948s5d7adb20we1564542829fd36d@mail.gmail.com>

Greetings again,

I've made some slight adjustments to GenbankFormat.java (biojavax)
that allow me to get biojavax to parse all 292M of genbank records
that I have access to. There are three things here:

1. Made the regex for locus lines slightly more tolerant. (made
modifed date field optional - some of the older records I have don't
include the date)

2. The previous checkin for no accessions was slighly incomplete - the
accession has to be set on the RichListener - not just assigned to the
local accession variable (which I believe is only used for logging)

3. I needed a larger readAheadLimit on the BufferedReader for parsing sections.

All the tests run (locally anyway) with these changes and pass. Thanks
for your consideration.

Bubba
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From bubba.puryear at gmail.com  Tue Jul  4 16:39:34 2006
From: bubba.puryear at gmail.com (Bubba Puryear)
Date: Tue, 4 Jul 2006 12:39:34 -0400
Subject: [Biojava-dev] Test for GenbankFormat (biojavax) and data file
Message-ID: <d2f7533b0607040939w2a673b0dxaabd19072d10af72@mail.gmail.com>

I've attached a simple high-level test I wrote for parsing a genbank
file with no accession field. I've also included the test file.

FYI,
Bubba
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From arareko at campus.iztacala.unam.mx  Thu Jul  6 21:45:34 2006
From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra)
Date: Thu, 06 Jul 2006 16:45:34 -0500
Subject: [Biojava-dev] [Biojava-l] biojava wiki and Jmol
In-Reply-To: <f1c60ed25a12b4e80587b9a826141791@sanger.ac.uk>
References: <f1c60ed25a12b4e80587b9a826141791@sanger.ac.uk>
Message-ID: <44AD847E.9030306@campus.iztacala.unam.mx>

Hi Andreas,

I have admin privileges for the open-bio.org webserver. Unless Mark 
Schreiber (who appears to be the website admin for BioJava) has other 
opinion, I can help you with this and get the extension installed and 
configured for the wiki.

Regards,
Mauricio.

Andreas Prlic wrote:
> Hi!
> 
> I will commit some new protein structure functionality to CVS soon 
> (structure alignments).
> For this it would be nice if I could show some examples in 3D with the 
> Jmol applet in
> the BioJava Wiki pages.
> 
> Could somebody with admin rights install the Jmol-wiki extension for 
> MediaWiki? - not sure who to contact about that...
> instructions would be here:
> http://wiki.jmol.org/index.php/MediaWiki#Installation
> 
> Thanks! :-)
> Andreas
> 
> -----------------------------------------------------------------------
> 
> Andreas Prlic      Wellcome Trust Sanger Institute
>                                Hinxton, Cambridge CB10 1SA, UK
> 			 +44 (0) 1223 49 6891
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM



From russ at kepler-eng.com  Fri Jul  7 13:11:23 2006
From: russ at kepler-eng.com (Russ Kepler)
Date: Fri, 7 Jul 2006 07:11:23 -0600
Subject: [Biojava-dev] Java API for Global Alignment
In-Reply-To: <D3C986810EBCCE488A9DCA95463794F146F35A@kaneda.acpfg.local>
References: <mailman.4967.1151566574.2084.biojava-l@lists.open-bio.org>
	<D3C986810EBCCE488A9DCA95463794F146F35A@kaneda.acpfg.local>
Message-ID: <200607070711.23576.russ@kepler-eng.com>

On Tuesday 04 July 2006 04:44 am, Michael Tran wrote:

> Looking for a Java API to do global alignments (something like a clustalw
> alignment).

I think most folks have simply implemented a parser for clustalw output to 
generate a FlexibleAlignment when they needed that.  I've got one, and a 
parser for the Paracel CAML output from their genomic scale assembler as 
well.


From arareko at campus.iztacala.unam.mx  Fri Jul  7 14:23:05 2006
From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra)
Date: Fri, 07 Jul 2006 09:23:05 -0500
Subject: [Biojava-dev] [Biojava-l] biojava wiki and Jmol
In-Reply-To: <OFD9C3155C.42A0849E-ON482571A4.0005193F-482571A4.00052204@EU.novartis.net>
References: <OFD9C3155C.42A0849E-ON482571A4.0005193F-482571A4.00052204@EU.novartis.net>
Message-ID: <44AE6E49.9030107@campus.iztacala.unam.mx>

Mark and Andreas,

The Jmol extension is installed now and should be working. I configured 
it with all the steps from the installation page. For the moment, I've 
only added *.cml files to the allowed extensions to upload. If you want 
to upload other types of files, please let me know and I'll perform the 
necessary steps.

Andreas - please try to upload some files and play with the Jmol wiki 
tags to see if everything works as it should.

Regards,
Mauricio.

PS. I'm Cc'ing this to some BioPerl friends to see if someone gets 
interested in having this for our wiki also ;)

mark.schreiber at novartis.com wrote:
> Be my guest!!
> 
> 
> Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx>
> Sent by: biojava-l-bounces at lists.open-bio.org
> 07/07/2006 05:45 AM
> 
>  
>         To:     Andreas Prlic <ap3 at sanger.ac.uk>
>         cc:     biojava-dev at biojava.org, biojava-l at biojava.org, (bcc: Mark 
> Schreiber/GP/Novartis)
>         Subject:        Re: [Biojava-l] biojava wiki and Jmol
> 
> 
> Hi Andreas,
> 
> I have admin privileges for the open-bio.org webserver. Unless Mark 
> Schreiber (who appears to be the website admin for BioJava) has other 
> opinion, I can help you with this and get the extension installed and 
> configured for the wiki.
> 
> Regards,
> Mauricio.
> 
> Andreas Prlic wrote:
>> Hi!
>>
>> I will commit some new protein structure functionality to CVS soon 
>> (structure alignments).
>> For this it would be nice if I could show some examples in 3D with the 
>> Jmol applet in
>> the BioJava Wiki pages.
>>
>> Could somebody with admin rights install the Jmol-wiki extension for 
>> MediaWiki? - not sure who to contact about that...
>> instructions would be here:
>> http://wiki.jmol.org/index.php/MediaWiki#Installation
>>
>> Thanks! :-)
>> Andreas
>>
>> -----------------------------------------------------------------------
>>
>> Andreas Prlic      Wellcome Trust Sanger Institute
>>                                Hinxton, Cambridge CB10 1SA, UK
>>                                                 +44 (0) 1223 49 6891
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM



From mark.schreiber at novartis.com  Mon Jul 10 01:38:09 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Mon, 10 Jul 2006 09:38:09 +0800
Subject: [Biojava-dev] Java API for Global Alignment
Message-ID: <OFA65CDA5D.65657CD1-ON482571A7.0008CA76-482571A7.0008FCB6@EU.novartis.net>

Hi -

There is not one in BioJava 1.4 although you can do it with an HMM. There 
is an implementation of the NW algorithm in the CVS as well as the SW 
algorithm. These can be downloaded from CVS and will be in the next build 
or snapshot.

- 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





Russ Kepler <russ at kepler-eng.com>
Sent by: biojava-dev-bounces at lists.open-bio.org
07/07/2006 09:11 PM

 
        To:     biojava-dev at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-dev] Java API for Global Alignment


On Tuesday 04 July 2006 04:44 am, Michael Tran wrote:

> Looking for a Java API to do global alignments (something like a 
clustalw
> alignment).

I think most folks have simply implemented a parser for clustalw output to 

generate a FlexibleAlignment when they needed that.  I've got one, and a 
parser for the Paracel CAML output from their genomic scale assembler as 
well.
_______________________________________________
biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev





From mark.schreiber at novartis.com  Fri Jul 14 07:12:27 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 14 Jul 2006 15:12:27 +0800
Subject: [Biojava-dev] [Off Topic] Getting JNDI resources from a Java
	application
Message-ID: <OFFFABF86D.C162A6B4-ON482571AB.00273991-482571AB.00279782@EU.novartis.net>

Hi -

I have a application running in JBoss with a web front end but I would 
like to make a standalone application with a GUI that runs in another JVM.

How can that application get access to resources in the application 
servers JNDI registry (notably the DataSource). I'm guessing I need RMI?? 
Does anyone know of a blueprint or best practice for this sort of thing?

- 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 mark.schreiber at novartis.com  Fri Jul 14 08:38:52 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 14 Jul 2006 16:38:52 +0800
Subject: [Biojava-dev] [Off Topic] Getting JNDI resources from a Java
 application
Message-ID: <OF455B6B7D.2E38347C-ON482571AB.002F72A2-482571AB.002F810E@EU.novartis.net>

Sounds perfect.

Do you have a code snippet?

- Mark





Andy Yates <ady at sanger.ac.uk>
07/14/2006 04:36 PM

 
        To:     mark.schreiber at novartis.com
        cc:     biojava-dev at biojava.org
        Subject:        Re: [Biojava-dev] [Off Topic] Getting JNDI resources from a Java 
application


Hi,

Best thing to use is Spring. You can get Spring to remote any object in 
about 5 lines of code and if you use Spring in your GUI application then 
it won't care about where the DataSource comes from; only that its got 
one.

Andy Yates


mark.schreiber at novartis.com wrote:
> Hi -
> 
> I have a application running in JBoss with a web front end but I would 
> like to make a standalone application with a GUI that runs in another 
JVM.
> 
> How can that application get access to resources in the application 
> servers JNDI registry (notably the DataSource). I'm guessing I need 
RMI?? 
> Does anyone know of a blueprint or best practice for this sort of thing?
> 
> - 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
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 





From ady at sanger.ac.uk  Fri Jul 14 08:36:37 2006
From: ady at sanger.ac.uk (Andy Yates)
Date: Fri, 14 Jul 2006 09:36:37 +0100
Subject: [Biojava-dev] [Off Topic] Getting JNDI resources from a Java
 application
In-Reply-To: <OFFFABF86D.C162A6B4-ON482571AB.00273991-482571AB.00279782@EU.novartis.net>
References: <OFFFABF86D.C162A6B4-ON482571AB.00273991-482571AB.00279782@EU.novartis.net>
Message-ID: <44B75795.1030205@sanger.ac.uk>

Hi,

Best thing to use is Spring. You can get Spring to remote any object in 
about 5 lines of code and if you use Spring in your GUI application then 
it won't care about where the DataSource comes from; only that its got one.

Andy Yates


mark.schreiber at novartis.com wrote:
> Hi -
> 
> I have a application running in JBoss with a web front end but I would 
> like to make a standalone application with a GUI that runs in another JVM.
> 
> How can that application get access to resources in the application 
> servers JNDI registry (notably the DataSource). I'm guessing I need RMI?? 
> Does anyone know of a blueprint or best practice for this sort of thing?
> 
> - 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
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 


From bugzilla-daemon at newportal.open-bio.org  Fri Jul 14 16:27:51 2006
From: bugzilla-daemon at newportal.open-bio.org (bugzilla-daemon at newportal.open-bio.org)
Date: Fri, 14 Jul 2006 12:27:51 -0400
Subject: [Biojava-dev] [Bug 2046] New: Cannot read in more than one
	serialized ProfileHMM object, attempt crashes
Message-ID: <bug-2046-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2046

           Summary: Cannot read in more than one serialized ProfileHMM
                    object, attempt crashes
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: critical
          Priority: P1
         Component: dist/dp
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: toddri at eden.rutgers.edu


The following small demo code illustrates the problem.  For me, the second
attempt of reading in the same serialized ProfileHMM object fails (with the
same error from running the code when the 2 serialized objects are different). 
Very repeatable.


------------------------------------------------------------------------

/*
 * SerializeProfile.java
 *
 * Created on April 27, 2006, 11:29 AM
 *
 * To change this template, choose Tools | Template Manager
 * and open the template in the editor.
 */

//package hmm;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import org.biojava.bio.dist.DistributionFactory ;
import org.biojava.bio.dp.BaumWelchTrainer;
import org.biojava.bio.dp.DP;
import org.biojava.bio.dp.DPFactory;
import org.biojava.bio.dp.ModelTrainer;
import org.biojava.bio.dp.ProfileHMM;
import org.biojava.bio.dp.SimpleModelTrainer ;
import org.biojava.bio.dp.StoppingCriteria;
import org.biojava.bio.dp.TrainingAlgorithm;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.db.HashSequenceDB ;
import org.biojava.bio.seq.db.SequenceDB;

/**
 *
 * @author Mark Schreiber
 */
public class SerializeProfile {

    /**
     * Creates a new instance of SerializeProfile
     */
    public SerializeProfile() {
    }

    public void testSerialize(ProfileHMM hmm) throws Exception{
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        ObjectOutputStream oos = new ObjectOutputStream(bos);
        System.out.println("Writing HMM");
        oos.writeObject(hmm);
        oos.flush();
        System.out.println("Wrote "+bos.size()+" bytes");
        oos.close();

        ByteArrayInputStream bis = new ByteArrayInputStream(bos.toByteArray());
        ObjectInputStream ois = new ObjectInputStream(bis);
        System.out.println("Reading HMM");
        ProfileHMM hmm2 = (ProfileHMM)ois.readObject();
        ois.close();
        System.out.println("Read HMM");

        ByteArrayInputStream bis2 = new
ByteArrayInputStream(bos.toByteArray());
        ObjectInputStream ois2 = new ObjectInputStream(bis2);
        System.out.println("Reading HMM again!");
        ProfileHMM hmm3 = (ProfileHMM)ois2.readObject();
        ois2.close();
        System.out.println("Read HMM again.");
    }

    public ProfileHMM generateProfile() throws Exception{
               /*
                * Make a profile HMM over the DNA Alphabet with 12 'columns'
and default
                * DistributionFactories to construct the transition and
emmission
                * Distributions
                */
        ProfileHMM hmm = new ProfileHMM(DNATools.getDNA(),
                12,
                DistributionFactory.DEFAULT,
                DistributionFactory.DEFAULT,
                "my profilehmm");

        //create the Dynamic Programming matrix for the model.
        DP dp = DPFactory.DEFAULT.createDP(hmm);

        //Database to hold the training set
        SequenceDB db = new HashSequenceDB();

        //code here to load the training set
        Sequence seq = DNATools.createDNASequence("aaaggctagctg", "seq1");
        db.addSequence(seq);
        seq = DNATools.createDNASequence("aaaggcgagctg", "seq2");
        db.addSequence(seq);
        seq = DNATools.createDNASequence("aaattctagctg", "seq3");
        db.addSequence(seq);

        //train the model to have uniform parameters
        ModelTrainer mt = new SimpleModelTrainer();
        //register the model to train
        mt.registerModel(hmm);
        //as no other counts are being used the null weight will cause
everything to be uniform
        mt.setNullModelWeight(1.0);
        mt.train();

        //create a BW trainer for the dp matrix generated from the HMM
        BaumWelchTrainer bwt = new BaumWelchTrainer(dp);

        //anonymous implementation of the stopping criteria interface to stop
after 20 iterations
        StoppingCriteria stopper = new StoppingCriteria(){
            public boolean isTrainingComplete(TrainingAlgorithm ta){
                return (ta.getCycle() > 20);
            }
        };

       /*
        * optimize the dp matrix to reflect the training set in db using a null
model
        * weight of 1.0 and the Stopping criteria defined above.
        */
        bwt.train(db,1.0,stopper);


        return hmm;
    }

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) throws Exception{
        SerializeProfile sp = new SerializeProfile();
        ProfileHMM hmm = sp.generateProfile();
        sp.testSerialize(hmm);
    }

}


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Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
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From bugzilla-daemon at newportal.open-bio.org  Mon Jul 17 08:33:35 2006
From: bugzilla-daemon at newportal.open-bio.org (bugzilla-daemon at newportal.open-bio.org)
Date: Mon, 17 Jul 2006 04:33:35 -0400
Subject: [Biojava-dev] [Bug 2046] Cannot read in more than one serialized
	ProfileHMM object, attempt crashes
In-Reply-To: <bug-2046-485@http.bugzilla.open-bio.org/>
Message-ID: <200607170833.k6H8XZl9030328@newportal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2046





------- Comment #1 from holland at ebi.ac.uk  2006-07-17 04:33 -------
Could you post the full stacktrace please?


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------- You are receiving this mail because: -------
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From mmccormi at fhcrc.org  Mon Jul 17 15:43:27 2006
From: mmccormi at fhcrc.org (Michael McCormick)
Date: Mon, 17 Jul 2006 08:43:27 -0700
Subject: [Biojava-dev] [Off Topic] Getting JNDI resources from a Java
	application
In-Reply-To: <OFFFABF86D.C162A6B4-ON482571AB.00273991-482571AB.00279782@EU.novartis.net>
References: <OFFFABF86D.C162A6B4-ON482571AB.00273991-482571AB.00279782@EU.novartis.net>
Message-ID: <61EF645F-796B-4A71-8D97-ECF69FD1AAE6@fhcrc.org>

Hi Mark,

You can also achieve this by using standard J2EE/JEE conventions  
instead of creating a dependency on Spring. We have several external  
applications that take advantage of reusable services deployed on our  
JBoss instance.

This page details some standard J2EE/JEE patterns and includes code  
samples as well. From your description, you will want to take a look  
at the ServiceLocator, SessionFacade, and BusinessDelegate patterns.  
The JBoss forums and wiki are a good resource as well.
http://java.sun.com/blueprints/corej2eepatterns/Patterns/

Let me know if you have any further questions.

Mike

Michael McCormick
Systems Analyst
Geraghty Lab
Fred Hutchinson Cancer Research Center
mmccormi at fhcrc.org
206.667.75811


On Jul 14, 2006, at 12:12 AM, mark.schreiber at novartis.com wrote:

Hi -

I have a application running in JBoss with a web front end but I would
like to make a standalone application with a GUI that runs in another  
JVM.

How can that application get access to resources in the application
servers JNDI registry (notably the DataSource). I'm guessing I need  
RMI??
Does anyone know of a blueprint or best practice for this sort of thing?

- 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

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



From debesis at gmail.com  Fri Jul 21 08:32:47 2006
From: debesis at gmail.com (=?WINDOWS-1252?Q?Valdemaras_Rep=9Ays?=)
Date: Fri, 21 Jul 2006 11:32:47 +0300
Subject: [Biojava-dev] Question regarding
	org.biojava.bio.seq.db.WebSequenceDB
Message-ID: <ec12348a0607210132y5ed5e924n2e474a53a2540a7a@mail.gmail.com>

Hi,
I'm using the org.biojava.bio.seq.db.WebSequenceDB.getSequence(String id)
method.

Every time i invoke it it prints a few lines to System.err and these lines
are not errors:
query is
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=protein&uid=15625528&dopt=FASTA
got data from
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=protein&uid=15625528&dopt=FASTA

My application uses this method a lot and the log becomes stuffed with these
not important messages..

Could someone, please, remove these two System.err.println lines from the
method?
Or i can do it myself if you give me a cvs account.

By the way, cvs currently is not working: cvs [login aborted]: connect to
code.open-bio.org(207.154.17.72):2401 failed: Connection timed out. But I
hope it' temprary.

Thanks,
Valdemaras Rep?ys



From richard.holland at ebi.ac.uk  Fri Jul 21 08:58:29 2006
From: richard.holland at ebi.ac.uk (Richard Holland)
Date: Fri, 21 Jul 2006 09:58:29 +0100
Subject: [Biojava-dev] Question
	regarding	org.biojava.bio.seq.db.WebSequenceDB
In-Reply-To: <ec12348a0607210132y5ed5e924n2e474a53a2540a7a@mail.gmail.com>
References: <ec12348a0607210132y5ed5e924n2e474a53a2540a7a@mail.gmail.com>
Message-ID: <1153472310.3955.21.camel@localhost.localdomain>

I've commented the lines out in the head branch of CVS for biojava-live.

cheers,
Richard

On Fri, 2006-07-21 at 11:32 +0300, Valdemaras Rep?ys wrote:
> Hi,
> I'm using the org.biojava.bio.seq.db.WebSequenceDB.getSequence(String id)
> method.
> 
> Every time i invoke it it prints a few lines to System.err and these lines
> are not errors:
> query is
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=protein&uid=15625528&dopt=FASTA
> got data from
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=protein&uid=15625528&dopt=FASTA
> 
> My application uses this method a lot and the log becomes stuffed with these
> not important messages..
> 
> Could someone, please, remove these two System.err.println lines from the
> method?
> Or i can do it myself if you give me a cvs account.
> 
> By the way, cvs currently is not working: cvs [login aborted]: connect to
> code.open-bio.org(207.154.17.72):2401 failed: Connection timed out. But I
> hope it' temprary.
> 
> Thanks,
> Valdemaras Rep?ys
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416



From bugzilla-daemon at newportal.open-bio.org  Mon Jul 31 15:35:43 2006
From: bugzilla-daemon at newportal.open-bio.org (bugzilla-daemon at newportal.open-bio.org)
Date: Mon, 31 Jul 2006 11:35:43 -0400
Subject: [Biojava-dev] [Bug 2046] Cannot read in more than one serialized
	ProfileHMM object, attempt crashes
In-Reply-To: <bug-2046-485@http.bugzilla.open-bio.org/>
Message-ID: <200607311535.k6VFZhI5010172@newportal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2046





------- Comment #2 from toddri at eden.rutgers.edu  2006-07-31 11:35 -------
Here is the output and the full stacktrace:

Writing HMM
Wrote 22561 bytes
Reading HMM
Read HMM
Reading HMM again!
Exception in thread "main" java.io.IOException: Symbol in serialized stream
can't be found in the alphabet
        at
org.biojava.bio.dist.SimpleDistribution.readObject(SimpleDistribution.java:97)
        at sun.reflect.GeneratedMethodAccessor5.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:919)
        at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1813)
        at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1713)
        at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1299)
        at java.io.ObjectInputStream.readObject(ObjectInputStream.java:339)
        at java.util.HashMap.readObject(HashMap.java:1013)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at
java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:919)
        at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1813)
        at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1713)
        at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1299)
        at
java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1912)
        at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1836)
        at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1713)
        at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1299)
        at java.io.ObjectInputStream.readObject(ObjectInputStream.java:339)
        at SerializeProfile.testSerialize(SerializeProfile.java:61)
        at SerializeProfile.main(SerializeProfile.java:126)


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