[Biojava-l] Embl parser problem[Scanned]

Fri Jan 6 04:56:27 EST 2006

Hi Mark,

Thanks for your help.

I have deleted the original download and repeated the cvs checkout with
the command

cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/biojava checkout
-P biojava-live

I couldn't use -Pd with the checkout command (I'm using cvs 1.11.17).

I repeated the build and got the same error.

I checked the download and there is only one copy of the
ProjectedFeatureHolder in org.biojava.bio.seq.projection where it should
be; so I'm not sure why Ant believes there is a second one in
org.biojava.bio.seq

Jolyon

-----Original Message-----
From: mark.schreiber at novartis.com [mailto:mark.schreiber at novartis.com] 
Sent: 06 January 2006 01:11
To: Jolyon Holdstock
Cc: biojava-l at biojava.org; biojava-l-bounces at portal.open-bio.org
Subject: RE: [Biojava-l] Embl parser problem[Scanned]

There should only be one copy of the ProjectedFeatureHolder 
(org.biojava.bio.seq.projection.ProjectedFeatureHolder),
Try deleting your biojava-live directory and doing a fresh checkout,
make 
sure you use the -Pd options during the checkout.
- Mark

"Jolyon Holdstock" <jolyon.holdstock at ogt.co.uk>
Sent by: biojava-l-bounces at portal.open-bio.org
01/05/2006 06:07 PM

        To:     Mark Schreiber/GP/Novartis at PH
        cc:     biojava-l-bounces at portal.open-bio.org,
biojava-l at biojava.org
        Subject:        RE: [Biojava-l] Embl parser problem[Scanned]

Hi 

I ran cvs update -Pd and then repeated the Ant command.

I can see it has updated as I'm trying to compile an extra source file

[javac] Compiling 1280 source files

But the build fails with the same error.

Is there a work around I could use?

Thanks

Jolyon

-----Original Message-----
From: mark.schreiber at novartis.com [mailto:mark.schreiber at novartis.com] 
Sent: 05 January 2006 01:22
To: Jolyon Holdstock
Cc: biojava-l at biojava.org; biojava-l-bounces at portal.open-bio.org
Subject: RE: [Biojava-l] Embl parser problem[Scanned]

Hi -

When you do the CVS update or checkout make sure you use the -Pd
options.

The -d option prunes empty directories (old stuff not included in 
biojava-live anymore). It seems that you have got both an old copy and a

new copy of the projected feature holder.

The -P option pulls new directories (new packages since your last
update).

Or maybe i've got them mixed up, anyhow use both. Try doing a CVS upate 
-Pd and then running ant.

- Mark

"Jolyon Holdstock" <jolyon.holdstock at ogt.co.uk>
Sent by: biojava-l-bounces at portal.open-bio.org
01/04/2006 06:54 PM

        To:     <biojava-l at biojava.org>,
<biojava-l-bounces at portal.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        RE: [Biojava-l] Embl parser problem[Scanned]

Thanks for the help.
I have downloaded the dev version and tried to build it.
I have no experience with Ant (I'm running v1.6.1) and the build fails.
The output from this is:

Buildfile: build.xml

init:
     [echo] Building biojava-live
     [echo] Java Home:                       c:\j2sdk1.4.2_04\jre
     [echo] JUnit present:                   ${junit.present}
     [echo] JUnit supported by Ant:          true
     [echo] HSQLDB driver present:           ${sqlDriver.hsqldb}

prepare:

prepare-biojava:

compile-biojava:
    [javac] Compiling 1279 source files to
C:\Downloads\Java\BioJava\biojava-live\ant-build\classes\biojava
    [javac]
C:\Downloads\Java\BioJava\biojava-live\src\org\biojava\bio\seq\impl\RevC
ompSequence.java:47: reference to ProjectedFeatureHolder is ambiguous,
both class org.biojava.bio.seq.projection.ProjectedFeatureHolder in
org.biojava.bio.seq.projection and class
org.biojava.bio.seq.ProjectedFeatureHolder in org.biojava.bio.seq match
    [javac]     private ProjectedFeatureHolder pfh;
    [javac]             ^
    [javac] C:\Downloads\Java\BioJava\biojava-
live\src\org\biojava\bio\seq\impl\RevCompSequence.java:65: reference to
ProjectedFeatureHolder is ambiguous, both class
org.biojava.bio.seq.projection.ProjectedFeatureHolder in
org.biojava.bio.seq.projection and class
org.biojava.bio.seq.ProjectedFeatureHolder in org.biojava.bio.seq match
    [javac]         pfh = new ProjectedFeatureHolder(new
TranslateFlipContext(this,seq,seq.length()+1,true));
    [javac]                   ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -deprecation for details.
    [javac] 2 errors

-----Original Message-----
From: mark.schreiber at novartis.com [mailto:mark.schreiber at novartis.com] 
Sent: 04 January 2006 01:10
To: Jolyon Holdstock
Cc: biojava-l at biojava.org; biojava-l-bounces at portal.open-bio.org
Subject: Re: [Biojava-l] Embl parser problem[Scanned]

Hi -

A BioException would be expected when parsing an embl file via the
genbank 
option. I is surprising you don't get one when parsing a genbank file
via 
the embl option although it clearly has not worked properly.

You should only ever parse a file with the appropriate read method.

Please note that if you have access to CVS you could download the 
development version of the new parsers (biojavax) which do a much better

job.

- Mark

"Jolyon Holdstock" <jolyon.holdstock at ogt.co.uk>
Sent by: biojava-l-bounces at portal.open-bio.org
01/03/2006 10:21 PM

        To:     <biojava-l at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Embl parser problem

Hi,

I have an application using BioJava1.4pre1.4 that loads an embl or
genbank file.

If I load an embl file via the genbank option a BioException error is
thrown.

But if I load a genbank file via the embl option no BioException is
thrown and the sequence is created although it is not correct e.g.
sequence.length() returns 0

An example of code using the sequence file from the BioJava demos

String fileName =
"C:/Downloads/Java/BioJava/BioJava-1.4pre1/biojava-1.4pre1/demos/seq/AL1
21903.genbank"; 

try {

  seq = SeqIOTools.readEmbl(new BufferedReader(new
FileReader(fileName))).nextSequence();

  System.out.println("URN: " + seq.getURN());

  System.out.println("Length: " + seq.length());

}

catch (BioException BIOE) {

  System.out.println("BioException " + BIOE);

}

The output is:

URN: sequence/embl:SION

Length: 0

If I use the matching embl sequence from the demos the output is:

URN: sequence/embl:AL121903

Length: 80600

I've used BioJava1.4 with the same outcome. Should I be parsing the file
an alternative way?

Thanks,

Jolyon

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