On 11 Jan 2006, at 10:45, Christian Köberle wrote:
Hi,
exists a way to get Features from a FeatureHolder sorted by Location?
You guarantee a specific iteration order from a FeatureHolder (unless
you write your own implementation). You can, however, dump some
features into a List or Set
On 5 Jan 2006, at 10:07, Jolyon Holdstock wrote:
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
On 8 Dec 2005, at 14:16, Tamas Horvath wrote:
I know this is not strictly BioJava, but here's my problem:
I create a shell script file that would run a GROMACS MD
simulationI generate the necessary input and config files
I can make the generated shell script runnable
I cannot actually run th
Hi Felix,
This doesn't look like a problem specific to GenbankSequenceDB
itself, but a problem with initialising some core BioJava machinary
(from the exception you report, it looks like the static initializer
for the FeatureFilter.OnlyChildren class is failing -- I assume the
real proble
On 14 Apr 2005, at 11:58, [EMAIL PROTECTED] wrote:
Hi!
I have added features to a sequence file using
StrandedFeature.Template as a
template and RangeLocation class to define the locations. The sequence
is saved
in Genbank format after the addition of all features. I want to output
the
features
On 12 Apr 2005, at 15:17, Joel Björkman wrote:
Hello!
I have a tiny question...
I have a program that dies with the error message: "Can't build DAS
url"...
I'm 90% sure that the error comes from a dtd-URL-fault since it looks
lite
this in the XML file.
The "Can't build DAS url" error isn't DTD re
On 18 Mar 2005, at 09:20, Joel Björkman wrote:
Hello!
I'm new to org.biojava.bio.program.das and I have a couple of
questions regarding fetching features and sequences from dazzle
servers...
At the moment I'm only interested in getting the sequence and
annotations from ensembl's database, which sho
On 26 Jan 2005, at 19:55, Michael Heuer wrote:
Hello,
I would like to use the dazzle GFFAnnotationSource to display predicted
transcripts on the Ensembl web interface, but it's a little bit
difficult
to follow tags through from the GFF file to what ends up on the Ensembl
web interface.
I imagine
On 24 Jan 2005, at 09:17, [EMAIL PROTECTED] wrote:
BioJava uses (or at least can use) the PackedSymbolList for large
sequences. It uses an array of longs to represent the packed bits.
There may be some advantage to using a ByteBuffer, hard to know.
The main reason I was thinking for using MappedByt
On 24 Jan 2005, at 02:48, Richard HOLLAND wrote:
It's a compressed binary format. I doubt BioJava would be able to read
it without a lot of effort as the current parser framework is set up
for
text input only.
Nib support probably wouldn't fit into the text-oriented parsing
framework, but I'm sur
On 16 Dec 2004, at 12:35, Christian Storm wrote:
Is there a way of adapting org.biojava.bio.seq classes / interfaces to
an interface?
I would like to add functionality to some of the interfaces in
org.biojava.bio.seq, i.e. sequence and feature, by adapting them to an
existing interface.
I see
Hi Richard,
We've had a problem very much like this when using BioSQL with a MySQL
database -- the issue occurs when you have two "ontology terms" (which
are used for a number of different purposes -- feature types,
annotation keys, etc) which differ only by name. For example
"organism" and "O
On 21 Nov 2004, at 08:52, James Diggans wrote:
Certainly. I was asking the list to inquire whether this was an
intentional design choice (i.e. making the class noisy regardless of
calling class) or whether anyone would be averse to fixing it to just
simply be:
>> } catch (Exception e) {
>>
On Tue, Nov 16, 2004 at 11:09:43AM +0100, Dirk Habighorst wrote:
> Hi,
>
> running the TestDAS example (biojava-live) causes the following exception:
>
> Exception in thread "main" org.biojava.bio.BioRuntimeException:
> org.biojava.bio.BioException: DAS error (status code = 401) connecting to
>
On 13 Nov 2004, at 19:47, Koen van der Drift wrote:
On Nov 10, 2004, at 4:35 AM, Koen van der Drift wrote:
So far I was treating biojava and my own code as 2 different targets
in the same project. I will try to make just one target and post here
if it worked. Thanks all for the comments,
To foll
On Fri, Nov 12, 2004 at 10:01:13AM +0800, [EMAIL PROTECTED] wrote:
>
> Bascially there is absolutely no failsafe way to know if a fasta file is
> DNA or Protein (or RNA). It's perfectly reasonable to have a short peptide
> which contains only acg and t although it becomes very unlikely with
> l
On 10 Nov 2004, at 00:17, Koen van der Drift wrote:
Hi,
I have been able to build biojava using Apple's Xcode 1.5. I also was
able to make a separate small Xcode project and run some code that
uses biojava. What I would like to be able to do is, is to debug my
code including the code it uses from
On Mon, Nov 01, 2004 at 03:49:39PM +0100, Can Gencer wrote:
> Hello everyone,
>
> We are trying to parse a quite large multiple BLAST results file (around
> 4GB), and the computer available has 1GB of RAM. However, when the code
> in the cookbook is used (
> "http://www.biojava.org/docs/bj_in_ange
On Tue, Jul 27, 2004 at 09:41:28AM +0800, [EMAIL PROTECTED] wrote:
> Hi -
>
> I have checked in GenbankXmlFormat.java which was kindly developed by Alan
> Li. This is a useful new functionality, take it out for some stress
> testing!
Thanks for checking this in Mark.
Was there also a correspon
On 26 Jul 2004, at 10:47, [EMAIL PROTECTED] wrote:
Hi all,
Is it possible to remove a feature in a SimpleGappedSequence
in 1.3 ? in 1.4 ?
And if not, why not ?
Hi again David,
Yes, there was definitely a bug here. I've just checked in a fix (and
tests). Thanks for spotting this.
If you're not f
On 26 Jul 2004, at 10:47, [EMAIL PROTECTED] wrote:
Hi all,
Is it possible to remove a feature in a SimpleGappedSequence
in 1.3 ? in 1.4 ?
And if not, why not ?
Hi David,
I'm not sure about 1.3. In 1.4pre1 you certainly can in principle, but
there seems to be a bug which means that it's only possi
On 29 Jun 2004, at 15:49, [EMAIL PROTECTED] wrote:
Thomas,
Seems the version is different from mine. In my version
DistributionLogo is extension of Component and there are no
setRenderingHints(hints) or setPreferedSize() methods.
Hmmm, do you know what version of BioJava you're using? Those method
On 28 Jun 2004, at 21:44, [EMAIL PROTECTED] wrote:
I am trying to use DistributionLogo class to represent a PSSM for a
transcription factor. I can generate DistributionLogos for each
position but can't merge them together to form a nice looking
single logo to be displayed on a panel. Basically,I d
On Mon, Jun 07, 2004 at 12:00:19PM +0800, [EMAIL PROTECTED] wrote:
> Hi -
>
> Slightly off topic but,
>
> I am making an application that will display a heat map based on the value
> of a variable. I'm wondering if anyone has some sample code for generating
> a color on a gradient between color
Hi,
There's now a biojava 1.4pre1 release available for download and
testing:
http://www.biojava.org/download14.html
BioJava 1.4 includes many new features, including regular expressions
on SymbolLists and macromolecular structure APIs, plus the usual
bug-fixes and performance improvement
On 21 May 2004, at 06:55, [EMAIL PROTECTED] wrote:
Hi -
I'm going to start using BioSQL fairly intensively soon and I was
wondering at what level the biojava bindings to biosql control
transactions. Specifically: if I get a reference to a Sequence object
from
my SequenceDB does that reference lock
On 14 May 2004, at 11:21, Matthew Pocock wrote:
I think for the sake of useability, we could either relax the location
constraint to allow point locations at 0, or in the sp parser,
re-write these as <1 - what do people think?
Ugh.
I'm not sure "<1" will appeal to people who are into round-trip
Hi,
I've just released a new version of Dazzle modular DAS server. It's
available from the usual place:
http://www.biojava.org/dazzle/
The main change since version 1.00 is the addition of a new plugin
which allows Dazzle annotation servers to be set up backed by SQL
databases in the L
On 10 May 2004, at 20:44, Thomas Down wrote:
On 10 May 2004, at 20:12, Bradford Powell wrote:
Hi,
I'm not sure if I am missing something here, but I'm confused as to
why
the field readingFrame in FramedFeature.Template is declared static.
None
of the fields (that I've looked
On 10 May 2004, at 20:12, Bradford Powell wrote:
Hi,
I'm not sure if I am missing something here, but I'm confused as to why
the field readingFrame in FramedFeature.Template is declared static.
None
of the fields (that I've looked at) in similar *Feature.Template
classes
are static. I would thi
the page.
I'd also like to add some kind of "BioJava application directory", but
this is only really worthwhile if there's a significant number of
entries. If you've written something with Biojava and want to tell the
world about it, please sent me a link.
Thanks!
Hi...
After four years of only minor changes to the main biojava.org website,
we've finally decided to make a break. The first stage of the website
improvements is now complete: there's a totally new style for all the
main pages, based on the biopython.org stylesheet, and I've fixed some
of t
I've just put out a new release of the Dazzle modular DAS server. The
new release features improvements to the plugin API, updates to work
with the BioJava 1.4 release, and many minor fixes.
You can download either source or a prebuilt web-application skeleton
from:
http://www.biojava.or
On 12 Mar 2004, at 12:03, David Huen wrote:
On Friday 12 Mar 2004 11:17 am, Matthew Pocock wrote:
Hi,
The parser shouldn't be throwing a NPE. However, the NCBI blast xml
output didn't used to be well-formed XML, so was not parseable by any
XML parser. I don't know if this has since been fixed by
On 12 Mar 2004, at 06:00, [EMAIL PROTECTED] wrote:
When you call the train() method of the BaumWelchTrainer you supply it
with a SequenceDB. The sequences from this DB are used to optimize the
weights of the model.
However, I have a bad feeling that when you train your model with the
BaumWelchTrai
Once upon a time, Dan Bolser wrote:
>
>
> Test.java uses or overrides a deprecated API.
> [javac] Note: Recompile with -deprecation for details.
> [javac] 100 errors
>
Once upon a time, Toralf Kirsten wrote:
> Hi,
> I have to extract data from the GenBank XML files.
> For this purpose I use the biojava API. But I get a parser error.
>
> java.lang.StringIndexOutOfBoundsException: String index out of range: 12
> at java.lang.String.substring(String.java:1477)
> at
Once upon a time, Benjamin Schuster-Boeckler wrote:
> Benjamin Schuster-Boeckler wrote:
>
> >As I understood the principle, a FeatureFilter will be used to test
> >one Feature after the other through it's accept(Feature f) method. Now
> >my problem is that this is _far_ too slow. I need to check
On Mon, Nov 24, 2003 at 02:48:43PM +, Lorna Morris wrote:
> I'm trying to submit some biojava files I've changed to the mailing list
> but I get this message:
> ---
>
> Your mail to 'Biojava-l' with the subject
>
>EmblFileFormer
>
> Is being held until the list moderator can re
On Thu, Sep 18, 2003 at 04:45:06PM +0800, [EMAIL PROTECTED] wrote:
> Dear all:
>
>There is a problem in biojava when using biofetch behind a firewall. There is no
> way
> to get the httpURLconnection object and set the http proxy. I think there are two
> solutions:
> 1. Modify biofetch of th
Once upon a time, Derek Gatherer wrote:
> Hi
>
> I have a couple of questions regarding codon bias measurements.
>
> 1) Is there a codon usage object in Biojava?
> 2) How easy would it be to integrate it into Artemis (to add things to the
> Graph menu)?
>
> I've seen references to
> CrossProduc
Once upon a time, martin gomez wrote:
> hi everyone,
>
> i'm new here and i've been lurking around for some time now. i was wondering
> if there have been any applets created out there that uses biojava. also, is
> there a list of biojava apps somewhere? i've been to
> http://www.biojava.org/docs/
Once upon a time, Schreiber, Mark wrote:
> These are great!
>
> As a wish list suggestion (only if it is possible and it can be done
> in a reasonable amount of time). Could the name of the person
> commiting be added to the file. This will be useful for me when
> backporting to biojava1.3 bra
Once upon a time, Michael Heuer wrote:
> > [EMAIL PROTECTED] mailing list (which is, after all,
> > intended for people who are participating in, or at least
> > actively following, development). If there's anyone
> > who strongly considers this to be silly/evil/spammy,
> > please speak up soon.
>
On Mon, Aug 18, 2003 at 12:29:10PM +0800, Ng Peck Leng wrote:
> Hi,
>
> I've seen someone talk about running a PDB2XML demo program. May I know where
> I download it from? Thanks in advance!
If you download the source code distribution, you'll find this
program in the demos/nativeapps/ directory
Once upon a time, Francois Pepin wrote:
>
> I personally think that the class in a good shape now (I hope no one has
> started using the API that I just broke yet).
Yes, it's looking good. I've been giving it a fairly heavy hammering
this weekend, and it's holding out okay.
I have just checked
Once upon a time, Matthew Pocock wrote:
> Last time I checked, CVS notification sent messages
> /per file/ rather than per commit. That's painfull.
> Perhaps a daily single cvs mail would be better?
Okay, I've set this up as a nightly job. At the moment, the
reports are just being sent to a test
On Fri, Aug 15, 2003 at 01:23:13PM +0200, Einar Andreas R?dland wrote:
> Hi,
>
> I'm trying to download BioJava, but get 'Access forbidden!' on the
> following links:
>
> http://biojava.org/download/
> http://www.biojava.org/download/
> http://www.biojava.org/download/binaries/
The biojav
Once upon a time, Thomas Down wrote:
>
> A lot of these issues could probably be addressed by something
> like:
>
> public class ExecTools {
Okay, I've had a first stab at this -- you can see what I
ended up with in org.biojava.utils.ProcessTools. In my
tests so far, it
Once upon a time, Halfdan Rydbeck wrote:
>
> I have been trying to install BioJava on a Windows 2000 machine for a
> day now but cant get it to work.
> Maybe you could help me out here?
>
> I store my .jar-files (biojava-1.30-jdk14, bytecode-0.92,
> jakarta-regexp, xerces) in C:\biojava.
>
> M
Once upon a time, Ryan Golhar wrote:
> I'm looking through the documentation for biojava 1.3, and cannot find
> any reference to performing a BLAST search, or performing any type of
> SmithWaterman local alignment. If its there, and I'm just not looking
> in the right place, can someone please dir
Once upon a time, Patrick McConnell wrote:
>
> Or, even better would be some sort of Parameters class to encapsulate all
> those parameters, providing optional parameters. Then, you could do
> something like this:
>
>NCBIBlastParameters params = new NCBIBlastParameters();
>params.addPara
Once upon a time, Francois Pepin wrote:
> I've added it to the cvs as org.biojava.utils.ExecRunner. It make take a
> little while to be replicated in the anonymous cvs.
Sorry, our two solutions seem to have crossed in cyberspace :-(.
As far as I can tell, ExecRunner has:
- Use of Windows cmd
Hi...
There seems to be quite a bit of interest in this subject, so
I thought I'd post an update.
Francois Pepin has kindly merged in some functionality from
ExecRunner. You can now specify a single command line
String, instead of an arguments array, and on Windows
platforms that will be process
On Mon, Aug 11, 2003 at 11:59:46AM +1200, Schreiber, Mark wrote:
>
> What is the best way to invoke a native bioinformatics program in Java.
> People have reported that controlling processes directly has been patchy
> in Java, is this still the case or have JVMs evolved? If not then what
> is the
The feature you're looking at isn't actually a `top level' feature
in BioJava, because it is fully contained by a clone of the
genome assembly. When accessing ensembl sequences, you need
to search the whole feature hierarchy. If you try:
Iterator fi = seq.filter(FeatureFilter.all).features()
Once upon a time, Karin Lagesen wrote:
> I am using the SeqIOTools.readFastaDNA() method to get hold sequences
> which are stored in a file. These are as far as I can tell in the
> correct fasta format. However, whenever the fasta description line
> contains a paranthesis, like this for instance:
>
Once upon a time, Schreiber, Mark wrote:
> > An alternate approach, which BioJava *will* help you with, is
> > to calculate both the forward and the backward DP matrices,
> > then multiply these together and normalize by the overall
> > backwards/forwards probability. This then tells you the
>
On Thu, Jul 17, 2003 at 01:24:41PM +1200, Schreiber, Mark wrote:
>
> On a more theoretical note if one calculated the probability of the
> viterbi path and compared that to the forward probability would that be
> a good way of infering confidence in the predictions fit to the model?
> Eg If the Vi
Hi...
A user at Sanger has just pointed out that the sample data
in SCF files is always represented as unsigned bytes or
shorts. The BioJava parser got this right for SCFv2 files,
but not for SCFv3.
I've just checked in a small patch to fix this. Rhett: could
you check that this is okay?
We sh
Once upon a time, Yu Wang wrote:
> Dear Sr/Madam,
>
> I am trying to build NetBSD package for biojava1.3, and I want to build
> everything from source so when this package is ported to some other OS, it
> still work.
Okay, there's now a bytecode-0.92.tar.gz file in:
http://www.biojava.org/do
Once upon a time, Yu Wang wrote:
> Dear Sr/Madam,
>
> I am trying to build NetBSD package for biojava1.3, and I want to build
> everything from source so when this package is ported to some other OS, it
> still work.
> Could you please tell me how I can get source codes for bytecode.jar,
> xerces.
Once upon a time, Sylvain Foisy wrote:
> Hi,
>
> I did my daily cvs update stuff and collected the mods that you described in
> the mailing list. I end up with these errors:
Some files got moved around during this change. Because the BioJava
build scripts make a copy of the source tree before co
Once upon a time, Y D Sun wrote:
> >
> > The complement(xxx..yyy) stuff is the feature's location,
> > rather than part of the qualifier-value data. In BioJava,
> > this will be represented by a feature having a location from
> > xxx to yyy, and being on the negative strand.
> >
>
> I want t
Once upon a time, Y D Sun wrote:
> Dear all,
>
> How to filter the complement feature in CDS? I get the features in a CDS
> table using the following code:
>
> Map m = f.getAnnotation().asMap(); // f is a
> Feature containing a CDS table
>
> String ge = m.get("gene
Once upon a time, Y D Sun wrote:
> Dear all,
>
> Is there a method in BioJava that returns a sub-sequence using a
> Location parameter (not subStr() or subList() with two integers - start
> and end)? This consideration comes from my requirement to get the
> nucleotide sub-sequence corresponding to
Once upon a time, Alberto Ambesi wrote:
> Thank you for your help!
> Now I have another problem, on the same code. Apparently, the
> iterator on 'transcripts' extracts multiple copies of same features, if the
> gene has more than one transcript. I just can't figure why. I adjusted my
Once upon a time, Viswanathan Ramachandran wrote:
> Hi,
> The latest Jun 15 2003 version source code is not
> unzipping properly. It gives this message:
>
> "Error reading header after processing 0 entries"
It's working fine for me.
Could you tell me how you downloaded the biojava-1.30.tar.gz f
Once upon a time, Matthew Muller wrote:
> I was using org.biojava.bio.seq.genomic.TranslatedRegion to bind a protein sequence
> to it's mRNA sequence. I see that in BioJava 1.3, the whole package has been
> dropped.
>
> I want an object model that links mRNA, protein translations, and Feature
Once upon a time, Hilmar Lapp wrote:
> I feel I'm stupid but I can't find the ontology stuff you guys wrote at
> the hackathon. Can you give me a hint? I thought there's got to be a
> Term class or interface or something?
In CVS HEAD BioJava (not the 1.3x series), look in the
org.biojava.bio.ont
Once upon a time, Keith James wrote:
>
> It may also be worth noting that you /can/ do this:
>
> while (seqI.hasNext())
> {
> Sequence seq = seqI.nextSequence();
>
> for (Iterator i = seq.features(); i.hasNext();)
> {
> i.next();
> i.remove();
> }
> }
>
> which i
Once upon a time, Vasa Curcin wrote:
> Is it just me or are the .html files for the stable 1.30 version in docs
> section all 0KB in length?
I'm very sorry -- a lot of the files do seem to be truncated.
The only explanation I can think of is that the machine where
I built the release ran out of d
Once upon a time, Juguang Xiao wrote:
> HI guys,
>
> I may miss or ignore some relevant emails before, sorry about that. I
> am just keen to know whether there is any biojava API equivalent to
> bioperl-db? Thanks
Yes there is. Better still, it uses the same SQL schema, and
should in princip
ses Hohman
Nimesh Singh
Paul Seed
Rhett Sutphin
Robin Emig
Ron Kuhn
Russell Smithies
Samiul Hasan
Thad Welch
Thomas Down
I hope you all find it useful,
Thomas.
___
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.o
Once upon a time, Stephen Montgomery wrote:
> Searching the archives, there was some talk/submissions regarding
> putting in Smith-Waterman in biojava.
> It doesn't look like this ever made it in though.
> I wasn't able to track down where the code may have ended up. (a google
> search shows a
On Tue, Jun 10, 2003 at 10:15:31AM +0100, Y D Sun wrote:
>
> How long it takes to add a sequence to the database in your case? For
> me, it takes 10 hours to insert a BA40 sequence to DB.
Okay, I think I may have found the problem...
Could you try again without the accelerators file loaded?
Once upon a time, Y D Sun wrote:
>
> I would like to clarify one important point. Is biosqldb-pg.sql (you
> sent to me) the ONLY schema required to install in a database? Other two
> schemas, i.e., biosqldb-assembly-pg.sql and biosql-accelerators-pg.sql,
> are not required to install.
Yes, biosql
Once upon a time, Y D Sun wrote:
> I find that the elapsed time of filtering CDS for a sequence is
> proportional to the total number of sequences stored in a database. For
> exmaple, when there is only one sequence in the database, the filtering
> takes 5 seconds. If one more sequence is added to
Once upon a time, Y D Sun wrote:
> I find that the elapsed time of filtering CDS for a sequence is
> proportional to the total number of sequences stored in a database. For
> exmaple, when there is only one sequence in the database, the filtering
> takes 5 seconds. If one more sequence is added to
Once upon a time, David Huen wrote:
> On Thursday 05 Jun 2003 6:07 pm, Y D Sun wrote:
> > Having created the indices as following and restarted postmaster, the
> > performance of feature filtering is even worse. Maybe MySQL is a better
> > choice than PostgreSQL. Does anyone have the similar experi
On Fri, Jun 06, 2003 at 10:33:28AM +0100, Y D Sun wrote:
>
> > -Original Message-
> > From: Thomas Down [mailto:[EMAIL PROTECTED]
> > Sent: 05 June 2003 22:58
> > To: [EMAIL PROTECTED]
> > Cc: Y D Sun; Thomas Down; [EMAIL PROTECTED]
> > Subject: R
Once upon a time, Y D Sun wrote:
>
> Can I run the command in an existing db? Now I am running it in a db
> containing 10 sequences, but it is hanging there.
Really ought to work (and only take a second or so). Probably
best to avoid having anything else actually accessing the database
at the s
Sounds reasonable to me.
Do you have a CVS account to check this in?
Thomas.
Once upon a time, Stephen Montgomery wrote:
> Hi -
>
> Can I propose a small change to the
> org.biojava.bio.gff.program.gff.GFFParser class?
>
> In
>
>*protected* GFFRecord createRecord(GFFDocumentHandler
Once upon a time, Y D Sun wrote:
>
> > That said, the time you quote is very, very, slow. Where
> > did you get the BioSQL schema from? Some versions are
> > circulating which seem to be missing some critical "CREATE
> > INDEX" statements, which makes feature-filtering
> > substantially slower
Once upon a time, Y D Sun wrote:
> Hi,
>
> It seems that the implmentation for a sequence that is read from a plain
> text file (e.g. Embl file) or from a BioSQL database is different.
>
> I apply a feature filter to a sequence seq like:
>
> //make a Filter for "CDS" types
>
Once upon a time, Russell Smithies wrote:
> What was the cause of the missing messages?
> Mark and I haven't seen any posts for about 1 1/2 weeks.
Since some of the open-bio hardware was upgraded last
weekend, mail to biojava.org addresses has been sent to
the wrong server because of a stale DNS r
Once upon a time, Sylvain Foisy wrote:
> Hi to all,
>
> I have been having problems compiling biojava-live for that past few days
> now. My ant output is like this:
>
> compile:
> [javac] Compiling 48 source files to
> /Users/foisys/biojava-live/ant-build/classes/main
> [javac]
> /Users/
Once upon a time, Warth,Rainer,LAUSANNE,NRC/BAS wrote:
> HI,
> download the tarball from
>
>
> http://cvs.biojava.org/cgi-bin/viewcvs/viewcvs.cgi/biojava-live/?cvsroot=bio
> java
That will actually get you a snapshot of the CVS HEAD. The
1.3 series was actually branched. If you look at th
On Wed, Apr 02, 2003 at 11:29:50AM -0800, Ren, Zhen wrote:
>
> So, obviously the method SeqIOTools.readFastaProtein() uses a space (probably all
> kinds of whitespace) as delimiters to parse whatever into the name property in a
> sequence. My question is how I can specify my own delimiter and t
On Thu, Feb 27, 2003 at 09:54:52PM -0500, Chris Dagdigian wrote:
>
> Hi Sameer,
>
> I only manage the cvsweb installation at cvs.bioperl.org, not the actual
> BioJava project or codebase.
>
> I've cc'd this reply to the biojava mailing list where you will find
> people better equipped to answe
On Fri, Feb 14, 2003 at 10:10:34AM +0100, Karin Lagesen wrote:
> I have a Sequence which I have stuck several Features onto. I would
> now like to iterate over these features, in the order that they appear
> on the genome (i.e. a Feature from [7,10] comes before [8-20]). I see
> that there is an in
On Tue, Feb 11, 2003 at 10:48:05AM +, Phillip Lord wrote:
>
> In short, using all the memory you possibly can, but without actually
> crashing the JVM is fairly hard in Java. Or, if I am more honest, I
> never found a good way of doing it. Perhaps someone else has.
To be honest, I'd say that
On Sun, Feb 09, 2003 at 09:24:07PM +, Ewan Birney wrote:
>
>
> I know... this is a troll but it sort of resonates with me about the
> way Java development works - people have to fix on a JVM version to get
> real like-a-rock stability and work about bugs in that release, and
> Java is ju
On Mon, Feb 10, 2003 at 10:48:53AM +, David Huen wrote:
>
> > I have read the mailing list and found the link to the "Blast Java
> > Library" by Patrick McConnell. Can anyone tell me if this is the right
> > way to go? As I understand, an external program is called (the original
> > blast softw
On Sun, Feb 09, 2003 at 04:56:28PM -0500, Dave Keller wrote:
>
> >This is why I think i have alot of reluctance to move to Java; C is by far
> >my prefered strongly-typed, "non-scripting" language. But I am a
> >dinosaur...
> >
> >
> Nothing wrong with that, C is an excellent language and there i
On Wed, Feb 05, 2003 at 03:52:03PM +, Keith James wrote:
>
> I got bitten by this too, when porting some of the code. If you look
> in biojava-live/resources/org/biojava/bio/symbol/AlphabetManager.xml
> you will see that the default RNA alphabet contains only
> agcu-~. i.e. no ambiguity symbols
On Wed, Jan 29, 2003 at 01:41:46PM +0100, Stein Aerts wrote:
>
> The BioJava-Ensembl should be ideal. However, retrieving a gene with
> flanking sequence based on gene_stable_id using the code below takes a
> million years.
>
>Ensembl ens = new Ensembl(
> org.ensembl.db.sql
On Wed, Jan 29, 2003 at 09:58:18AM +, Ewan Birney wrote:
>
> (c) If you don't like Perl ( ... this is the biojava mailing list...) then
> there is a pretty complete and stable Java binding to Ensembl - it doesn't
> use BioJava - it is more just a vanilla Java binding to Ensembl. Craig
> mel
On Thu, Jan 23, 2003 at 03:38:45PM -0500, Simon Foote wrote:
> I've tried compiling a fresh checkout of biojava-live after my cvs
> update compiling failed and it also failed.
> There appears to be errors in numerous programs. The majority are
> relating to Sequence, see below for example:
>
>
On Wed, Jan 22, 2003 at 03:23:29PM +, Matthew Pocock wrote:
> Thanks for all the sudgestions. I got this working in the end. The bug
> appeared in JBoss as well as various tomcats. It was fixed by doing a
> totaly clean rebuild of biojava-live followed by a totaly clean rebuild
> of biojava-
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