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" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
01/05/2006 06:07 PM
To: Mark Schreiber/GP/[EMAIL PROTECTED]
cc: [EMAIL PROTECTED], biojava-l@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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: 05 January 2006 01:22
To: Jolyon Holdstock
Cc: biojava-l@biojava.org; [EMAIL PROTECTED]
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" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
01/04/2006 06:54 PM
To: <biojava-l@biojava.org>,
<[EMAIL PROTECTED]>
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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: 04 January 2006 01:10
To: Jolyon Holdstock
Cc: biojava-l@biojava.org; [EMAIL PROTECTED]
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" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
01/03/2006 10:21 PM
To: <biojava-l@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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