From sylvain.foisy@bioneq.qc.ca  Sun Dec  1 01:22:53 2002
From: sylvain.foisy@bioneq.qc.ca (Sylvain Foisy)
Date: Sat, 30 Nov 2002 20:22:53 -0500
Subject: [Biojava-l] Behavior of the createRegex() method (MotifTool class)
Message-ID: <BA0ECE9D.2953%sylvain.foisy@bioneq.qc.ca>

Hi,


I used the createRegex() method to return a regular expression from a
sequence of DNA inputted by the user to scan a genome for that motif. I just
discovered an interesting thing about that method: if n is in the motif to
seek, the regex will not have n as a possibility.

Ok, I have that motif: atgnnnndgta.

CreateRegex would return: atg[atcg]{4}gta and it does

What if my sequence to scan contains n: atgagcngta, for exemple.
Java.util.regex would not find the pattern. Unless mistaken, the pattern
should be atg[atcgn]{4}gta.

Am I wrong? Any input would be appreciated

Sylvain

=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Sylvain Foisy, Ph. D
Directeur des operations
BioneQ - Reseau quebecois de bioinformatique
Universite de Montreal/Genome-Quebec
1260 rue Crescent, Bur. 201
Montreal, QC
H3G 2A9
Tel.: (514) 878-9911
Fax : (514) 878-2899
E-Mail:sylvain.foisy@bioneq.qc.ca
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=



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From s8814045@mail.cyut.edu.tw  Sun Dec  1 10:39:30 2002
From: s8814045@mail.cyut.edu.tw (kiro)
Date: Sun, 1 Dec 2002 18:39:30 +0800
Subject: [Biojava-l] (no subject)
Message-ID: <002201c29925$ee589e60$626a788c@kiro>



From kdj@sanger.ac.uk  Sun Dec  1 18:42:00 2002
From: kdj@sanger.ac.uk (Keith James)
Date: 01 Dec 2002 18:42:00 +0000
Subject: [Biojava-l] Behavior of the createRegex() method (MotifTool class)
In-Reply-To: <BA0ECE9D.2953%sylvain.foisy@bioneq.qc.ca>
References: <BA0ECE9D.2953%sylvain.foisy@bioneq.qc.ca>
Message-ID: <sc4fzthint3.fsf@adnah.sanger.ac.uk>

>>>>> "Sylvain" == Sylvain Foisy <sylvain.foisy@bioneq.qc.ca> writes:

    Sylvain> Hi, I used the createRegex() method to return a regular
    Sylvain> expression from a sequence of DNA inputted by the user to
    Sylvain> scan a genome for that motif. I just discovered an
    Sylvain> interesting thing about that method: if n is in the motif
    Sylvain> to seek, the regex will not have n as a possibility.

    Sylvain> Ok, I have that motif: atgnnnndgta.

    Sylvain> CreateRegex would return: atg[atcg]{4}gta and it does

    Sylvain> What if my sequence to scan contains n: atgagcngta, for
    Sylvain> exemple.  Java.util.regex would not find the
    Sylvain> pattern. Unless mistaken, the pattern should be
    Sylvain> atg[atcgn]{4}gta.

    Sylvain> Am I wrong? Any input would be appreciated

You are correct about the behaviour, but not about the solution. An
ambiguous target sequence could contain n, but could also contain r,
y, m, k, s, w, h, b, v and d. To match correctly the regex would have
to take into account that the symbols represented by n are a superset
of those represented by the other ambiguity symbols.

As MotifTools is generic (it will work for any alphabet) implementing
generation of regexes for searching ambiguous SymbolLists requires a
more complex algorithm than the current one. I'll take a look at this
as soon as I can.

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -


From matthew_pocock@yahoo.co.uk  Sun Dec  1 21:20:59 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Sun, 01 Dec 2002 21:20:59 +0000
Subject: [Biojava-l] Behavior of the createRegex() method (MotifTool class)
In-Reply-To: <sc4fzthint3.fsf@adnah.sanger.ac.uk>
References: <BA0ECE9D.2953%sylvain.foisy@bioneq.qc.ca> <sc4fzthint3.fsf@adnah.sanger.ac.uk>
Message-ID: <3DEA7D3B.5020602@yahoo.co.uk>

Well spotted Sylvain,

Keith, there's a method in AlphabetTools - getAllSymbols(). Feed it with 
  the matches() map of the symbol & cat together the tokens from each of 
these.

Matthew

Keith James wrote:
>>>>>>"Sylvain" == Sylvain Foisy <sylvain.foisy@bioneq.qc.ca> writes:
> 
> 
>     Sylvain> Hi, I used the createRegex() method to return a regular
>     Sylvain> expression from a sequence of DNA inputted by the user to
>     Sylvain> scan a genome for that motif. I just discovered an
>     Sylvain> interesting thing about that method: if n is in the motif
>     Sylvain> to seek, the regex will not have n as a possibility.
> 
>     Sylvain> Ok, I have that motif: atgnnnndgta.
> 
>     Sylvain> CreateRegex would return: atg[atcg]{4}gta and it does
> 
>     Sylvain> What if my sequence to scan contains n: atgagcngta, for
>     Sylvain> exemple.  Java.util.regex would not find the
>     Sylvain> pattern. Unless mistaken, the pattern should be
>     Sylvain> atg[atcgn]{4}gta.
> 
>     Sylvain> Am I wrong? Any input would be appreciated
> 
> You are correct about the behaviour, but not about the solution. An
> ambiguous target sequence could contain n, but could also contain r,
> y, m, k, s, w, h, b, v and d. To match correctly the regex would have
> to take into account that the symbols represented by n are a superset
> of those represented by the other ambiguity symbols.
> 
> As MotifTools is generic (it will work for any alphabet) implementing
> generation of regexes for searching ambiguous SymbolLists requires a
> more complex algorithm than the current one. I'll take a look at this
> as soon as I can.
> 
> Keith
> 


-- 
BioJava Consulting LTD - Support and training for BioJava
http://www.biojava.co.uk

__________________________________________________
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From kdj@sanger.ac.uk  Mon Dec  2 10:44:27 2002
From: kdj@sanger.ac.uk (Keith James)
Date: 02 Dec 2002 10:44:27 +0000
Subject: [Biojava-l] Behavior of the createRegex() method (MotifTool class)
In-Reply-To: <3DEA7D3B.5020602@yahoo.co.uk>
References: <BA0ECE9D.2953%sylvain.foisy@bioneq.qc.ca>
 <sc4fzthint3.fsf@adnah.sanger.ac.uk> <3DEA7D3B.5020602@yahoo.co.uk>
Message-ID: <sc4adjon1is.fsf@maul.i-did-not-set--mail-host-address--so-shoot-me>

>>>>> "Matthew" == Matthew Pocock <matthew_pocock@yahoo.co.uk> writes:

    Matthew> Well spotted Sylvain, Keith, there's a method in
    Matthew> AlphabetTools - getAllSymbols(). Feed it with the
    Matthew> matches() map of the symbol & cat together the tokens
    Matthew> from each of these.

I don't think this method is behaving as expected. Passing the
FiniteAlphabets from the following Symbols gets these results:

a -> getMatches() -> getAllSymbols -> tokenize -> -a
c -> getMatches() -> getAllSymbols -> tokenize -> -c
g -> getMatches() -> getAllSymbols -> tokenize -> -g
t -> getMatches() -> getAllSymbols -> tokenize -> -t
n -> getMatches() -> getAllSymbols -> tokenize -> tnn-nannnngncnnn

The code I am using is below (for a motif SymbolList with i Symbols).

Symbol sym = motif.symbolAt(i);
FiniteAlphabet ambiAlpha = (FiniteAlphabet) sym.getMatches();

Symbol [] ambiSyms = (Symbol [])
    AlphabetManager.getAllSymbols(ambiAlpha).toArray(new Symbol[0]);

// getAllSymbols returns a Set (i.e. unordered) so
// we convert to char array so we can sort tokens
char [] ambiChars = new char [ambiSyms.length];

for (int j = 0; j < ambiSyms.length; j++)
{
    ambiChars[j] =
        sToke.tokenizeSymbol(ambiSyms[j]).charAt(0);
}

Arrays.sort(ambiChars);
sb.append(ambiChars);

So the final character class for 'n' comes out as [-acgnnnnnnnnnnnt]

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -


From stein.aerts@esat.kuleuven.ac.be  Mon Dec  2 13:20:46 2002
From: stein.aerts@esat.kuleuven.ac.be (Stein Aerts)
Date: Mon, 02 Dec 2002 14:20:46 +0100
Subject: [Biojava-l] StrandedFeature.template
Message-ID: <3DEB5E2E.9030602@esat.kuleuven.ac.be>

Would there be a reason why there is no "score" and "frame" field in the 
Feature.template class? If they are not present in a Feature, then how 
can they be outputted using a GFFWriter?

Stein.


From td2@sanger.ac.uk  Mon Dec  2 14:48:12 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Mon, 2 Dec 2002 14:48:12 +0000
Subject: [Biojava-l] Behavior of the createRegex() method (MotifTool class)
In-Reply-To: <sc4adjon1is.fsf@maul.i-did-not-set--mail-host-address--so-shoot-me>
References: <BA0ECE9D.2953%sylvain.foisy@bioneq.qc.ca> <sc4fzthint3.fsf@adnah.sanger.ac.uk> <3DEA7D3B.5020602@yahoo.co.uk> <sc4adjon1is.fsf@maul.i-did-not-set--mail-host-address--so-shoot-me>
Message-ID: <20021202144812.GD124957@jabba.sanger.ac.uk>

On Mon, Dec 02, 2002 at 10:44:27AM +0000, Keith James wrote:
> 
> I don't think this method is behaving as expected. Passing the
> FiniteAlphabets from the following Symbols gets these results:
> 
> a -> getMatches() -> getAllSymbols -> tokenize -> -a
> c -> getMatches() -> getAllSymbols -> tokenize -> -c
> g -> getMatches() -> getAllSymbols -> tokenize -> -g
> t -> getMatches() -> getAllSymbols -> tokenize -> -t
> n -> getMatches() -> getAllSymbols -> tokenize -> tnn-nannnngncnnn

Okay, looks like I broke this when fixing serialization of
ambiguity-symbols.  Ugh, serialization...

It's fixed for now (see AlphabetManagerTest).  If we ever re-write
this code we *must* use some kind of globally unique names (URLs?)
for Symbols and Alphabets, otherwise we'll end up in this mess
again.

    Thomas.



From kdj@sanger.ac.uk  Mon Dec  2 16:04:40 2002
From: kdj@sanger.ac.uk (Keith James)
Date: 02 Dec 2002 16:04:40 +0000
Subject: [Biojava-l] Behavior of the createRegex() method (MotifTool class)
In-Reply-To: <20021202144812.GD124957@jabba.sanger.ac.uk>
References: <BA0ECE9D.2953%sylvain.foisy@bioneq.qc.ca>
 <sc4fzthint3.fsf@adnah.sanger.ac.uk> <3DEA7D3B.5020602@yahoo.co.uk>
 <sc4adjon1is.fsf@maul.i-did-not-set--mail-host-address--so-shoot-me>
 <20021202144812.GD124957@jabba.sanger.ac.uk>
Message-ID: <sc4y978l84n.fsf@maul.i-did-not-set--mail-host-address--so-shoot-me>

>>>>> "Thomas" == Thomas Down <td2@sanger.ac.uk> writes:

[...]

    Thomas> It's fixed for now (see AlphabetManagerTest).  If we ever
    Thomas> re-write this code we *must* use some kind of globally
    Thomas> unique names (URLs?)  for Symbols and Alphabets, otherwise
    Thomas> we'll end up in this mess again.

Thanks.

One final thing... the docs say "AtomicSymbol instances guarantee that
getMatches returns an Alphabet containing just that Symbol". But the
gap Symbol is returned by this method in every case. Or is the gap
Symbol specially "non-existent"? Elsewhere it states "every alphabet
contains gap, as there is no symbol that matches gap, so there is no
case where an alphabet doesn't contain a symbol that matches gap". I'm
just not sure what this means!

In short, what is the correct behaviour? I ask because currently the
SymbolList "acgt" generates the regex "[-a][-g][-c][-t]" under this
system.

cheers,

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -


From TDudgeon@OSIP.com  Mon Dec  2 16:56:58 2002
From: TDudgeon@OSIP.com (Dudgeon, Tim)
Date: Mon, 2 Dec 2002 11:56:58 -0500
Subject: [Biojava-l] Gene Ontology
Message-ID: <53340B0EBD7AD611A2A600065B3807957E5DB5@oxfordmail.osip.com>

There has been mention of a Gene Ontology API and/or browser within BioJava
in the past.
I've also started off down that route, but before I go too far I thought it
made sense to check whether there was any consensus here.
I don't want to reinvent the wheel yet again and will be happy to help get
something into BioJava.

What I'd like to see is an API to the GO database (probably with adaptors to
its various forms), plus some gui browser that can form a component of a
bigger tool.
Browser would probably initially use a JTree type appraach, but eventually
something that better reflected the fact that a GO term can have multiple
parents.

What's the state of play here?

Tim




=======================================
Dr. Tim Dudgeon
OSI Pharmaceuticals
Watlington Road, Oxford,
OX4 6LT, UK
tdudgeon@osip.com


From Peter.Andras@newcastle.ac.uk  Mon Dec  2 17:09:48 2002
From: Peter.Andras@newcastle.ac.uk (Peter Andras)
Date: Mon, 2 Dec 2002 17:09:48 -0000
Subject: [Biojava-l] Job in proteomics software development
Message-ID: <20CC6C4061CBB04A98656ED3209B203C26CB5B@bond.ncl.ac.uk>

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From p.lord@russet.org.uk  Mon Dec  2 18:14:18 2002
From: p.lord@russet.org.uk (Phillip Lord)
Date: 02 Dec 2002 18:14:18 +0000
Subject: [Biojava-l] Gene Ontology
In-Reply-To: <53340B0EBD7AD611A2A600065B3807957E5DB5@oxfordmail.osip.com>
References: <53340B0EBD7AD611A2A600065B3807957E5DB5@oxfordmail.osip.com>
Message-ID: <vfy978l24l.fsf@rpc71.cs.man.ac.uk>

>>>>> "Tim" == Dudgeon, Tim <TDudgeon@OSIP.com> writes:

  Tim> There has been mention of a Gene Ontology API and/or browser
  Tim> within BioJava in the past.  I've also started off down that
  Tim> route, but before I go too far I thought it made sense to check
  Tim> whether there was any consensus here.  I don't want to reinvent
  Tim> the wheel yet again and will be happy to help get something
  Tim> into BioJava.

  Tim> What I'd like to see is an API to the GO database (probably
  Tim> with adaptors to its various forms), plus some gui browser that
  Tim> can form a component of a bigger tool.  Browser would probably
  Tim> initially use a JTree type appraach, but eventually something
  Tim> that better reflected the fact that a GO term can have multiple
  Tim> parents.

  Tim> What's the state of play here?


It depends on how you want to represent GO. DAGEdit already contains
an API for representing GO, and adaptors for the database, and some of
the GO syntaxes. You should be able to pull these out and use them
directly as libraries. 

Alternatively, if you want to use more generic technology, you could
use some of the DAML+OIL/OWL API's, which are more than capable of
representing the GO DAG, then there are various tools and API's around
for representing these, as well as gui tools, or indeed editing
environments (such as Oiled (http://oiled.man.ac.uk) for instance...).

It's probably also worth reading the Ontology thread on the bioperl
list. It's a moot question how much of a GO representation you put
into biojava. It might make more sense to use a more generic DAG
representation, so that you get, for example, transitive closure, or
shortest path stuff for free. 

Cheers

Phil



From matthew_pocock@yahoo.co.uk  Mon Dec  2 18:16:50 2002
From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=)
Date: Mon, 2 Dec 2002 18:16:50 +0000 (GMT)
Subject: [Biojava-l] Gene Ontology
In-Reply-To: <53340B0EBD7AD611A2A600065B3807957E5DB5@oxfordmail.osip.com>
Message-ID: <20021202181650.15367.qmail@web14907.mail.yahoo.com>

Hi Tim,

It's one of those things that would have been nice to
have a long time ago, but nobody ever wrote. What is
the API for a GO term? I'm wondering if we can just
re-use the Annotation/AnnotationType interfaces and
suck this in as a constrained Map. 

Go terms have an ID and (possibly) a description. By
the isa relationship, they have a (single?) parent and
(possibly no) children. I'm assuming Go has a part-of
relationship (or it's inverse, has-a). What else does
a GO term have?

Then, there are go ontologies, or roots. These have a
root GO term.

We would need some way to map between a set of
database IDs and GO terms - GO -> all IDs with that
term, or perhaps (GO,seqDB) -> all features with that
term.

What have I missed off? What else would you need
API-wise for your GUI to work?

Matthew

 --- "Dudgeon, Tim" <TDudgeon@OSIP.com> wrote: > There
has been mention of a Gene Ontology API and/or
> browser within BioJava
> in the past.
> I've also started off down that route, but before I
> go too far I thought it
> made sense to check whether there was any consensus
> here.
> I don't want to reinvent the wheel yet again and
> will be happy to help get
> something into BioJava.
> 
> What I'd like to see is an API to the GO database
> (probably with adaptors to
> its various forms), plus some gui browser that can
> form a component of a
> bigger tool.
> Browser would probably initially use a JTree type
> appraach, but eventually
> something that better reflected the fact that a GO
> term can have multiple
> parents.
> 
> What's the state of play here?
> 
> Tim
> 
> 
> 
> 
> =======================================
> Dr. Tim Dudgeon
> OSI Pharmaceuticals
> Watlington Road, Oxford,
> OX4 6LT, UK
> tdudgeon@osip.com
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l 

__________________________________________________
Do You Yahoo!?
Everything you'll ever need on one web page
from News and Sport to Email and Music Charts
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From p.lord@russet.org.uk  Mon Dec  2 19:45:44 2002
From: p.lord@russet.org.uk (Phillip Lord)
Date: 02 Dec 2002 19:45:44 +0000
Subject: [Biojava-l] Gene Ontology
In-Reply-To: <20021202181650.15367.qmail@web14907.mail.yahoo.com>
References: <20021202181650.15367.qmail@web14907.mail.yahoo.com>
Message-ID: <vfn0nokxw7.fsf@rpc71.cs.man.ac.uk>

>>>>> "Matthew" == Matthew Pocock <matthew_pocock@yahoo.co.uk> writes:

  Matthew> Go terms have an ID and (possibly) a description. By the
  Matthew> isa relationship, they have a (single?) parent and
  Matthew> (possibly no) children. I'm assuming Go has a part-of
  Matthew> relationship (or it's inverse, has-a). What else does a GO
  Matthew> term have?

GO allows multiple parents along both is-a, and part-of. In the case
of GO, there are only two relationship types, but some of the GOBO
ontologies define others. It wouldn't really make sense to have an API
supporting GO, but not other DAG ontologies. 
        
It's also worth mentioning that the GO database has transitive closure
information pre-calculated, so you need methods for accessing paths,
if you want to advantage of this. I know from experience that graphing
around GO using the "get_parent" methods is very slow, over the SQL
database. (I won't bore you with the details, but I couldn't use the
path methods). If memory serves the GO perl API has first class Path
objects to allow this sort of access.


  Matthew> Then, there are go ontologies, or roots. These have a root
  Matthew> GO term.

  Matthew> We would need some way to map between a set of database IDs
  Matthew> and GO terms - GO -> all IDs with that term, or perhaps
  Matthew> (GO,seqDB) -> all features with that term.

Probably methods for saying "all ID's with that term, and any of its
children", which is generally what people are interested in. 

 
Cheers

Phil

From kdj@sanger.ac.uk  Tue Dec  3 10:02:27 2002
From: kdj@sanger.ac.uk (Keith James)
Date: 03 Dec 2002 10:02:27 +0000
Subject: [Biojava-l] Behavior of the createRegex() method (MotifTool class)
In-Reply-To: <sc4y978l84n.fsf@maul.i-did-not-set--mail-host-address--so-shoot-me>
References: <BA0ECE9D.2953%sylvain.foisy@bioneq.qc.ca>
 <sc4fzthint3.fsf@adnah.sanger.ac.uk> <3DEA7D3B.5020602@yahoo.co.uk>
 <sc4adjon1is.fsf@maul.i-did-not-set--mail-host-address--so-shoot-me>
 <20021202144812.GD124957@jabba.sanger.ac.uk>
 <sc4y978l84n.fsf@maul.i-did-not-set--mail-host-address--so-shoot-me>
Message-ID: <sc4n0nnh13g.fsf@maul.i-did-not-set--mail-host-address--so-shoot-me>

Following up my own post, but anyway... I've made the MotifTools test
pass again. However in trying to eliminate the gap character (which
I'm still not sure I should be doing) I tried to test for the gap
symbol in DNA using mySymbol == AlphabetManager.getGapSymbol() but
this didn't work (didn't return true for the DNA gap).

Stringifying the DNA gap object I get

org.biojava.bio.symbol.SimpleBasisSymbol: []

Can someone clarify the circumstances under which the various gap
Symbol(s) are equal (or ==) to each other?

ta,
Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -


From matthew_pocock@yahoo.co.uk  Tue Dec  3 11:15:03 2002
From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=)
Date: Tue, 3 Dec 2002 11:15:03 +0000 (GMT)
Subject: [Biojava-l] Behavior of the createRegex() method (MotifTool class)
In-Reply-To: <sc4n0nnh13g.fsf@maul.i-did-not-set--mail-host-address--so-shoot-me>
Message-ID: <20021203111503.21646.qmail@web14901.mail.yahoo.com>

Hi Keith,

You can simply call sym.getMatches().size() == 0, and
if true, it is a symbol with gaps. For all the cases
the regex stuff will be used for any time soon, this
is good enough.

Basicaly, two gaps are the same if they have the same
arrangement of nested [] in their toString(). This is
equivalent to them returning the same list of gap
symbols in their getSymbols() methods. It's a bit
complicated but it's the only way to do it without the
gap rules being totaly different from all other
symbols. I will add docs to package.html in Symbol
explaining gaps and why they are as they are.

Very quickly, the gap [] is the empty set of symbols.
It means 'there is nothing to see here, move on'. [-]
means 'there is nothing here and it takes up one unit
of your sequence'. [-,-] would be a gap in an
alignment of two sequences where both individual
sequences are gapped at that point. You could also
have symbols like [-,a] and [g,-] to represent gaps in
one or the other sequences. For aligning things like
DNA-Protein, you could end up with [-,-,-][-] (a gap
in the codon and in the protein sequence), [a,g,-][-]
(a gap in the protein sequence and a codon with an
insert at pos 3) and so on.

Damn those null sub-spaces and all their spawn.

Matthew

 --- Keith James <kdj@sanger.ac.uk> wrote: > 
> Following up my own post, but anyway... I've made
> the MotifTools test
> pass again. However in trying to eliminate the gap
> character (which
> I'm still not sure I should be doing) I tried to
> test for the gap
> symbol in DNA using mySymbol ==
> AlphabetManager.getGapSymbol() but
> this didn't work (didn't return true for the DNA
> gap).
> 
> Stringifying the DNA gap object I get
> 
> org.biojava.bio.symbol.SimpleBasisSymbol: []
> 
> Can someone clarify the circumstances under which
> the various gap
> Symbol(s) are equal (or ==) to each other?
> 
> ta,
> Keith
> 
> -- 
> 
> - Keith James <kdj@sanger.ac.uk> bioinformatics
> programming support -
> - Pathogen Sequencing Unit, The Wellcome Trust
> Sanger Institute, UK -
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l 

__________________________________________________
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Everything you'll ever need on one web page
from News and Sport to Email and Music Charts
http://uk.my.yahoo.com

From matthew_pocock@yahoo.co.uk  Tue Dec  3 11:27:39 2002
From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=)
Date: Tue, 3 Dec 2002 11:27:39 +0000 (GMT)
Subject: [Biojava-l] Gene Ontology
In-Reply-To: <vfn0nokxw7.fsf@rpc71.cs.man.ac.uk>
Message-ID: <20021203112739.95855.qmail@web14911.mail.yahoo.com>

 --- Phillip Lord <p.lord@russet.org.uk> wrote: >
>>>>> "Matthew" == Matthew Pocock
> <matthew_pocock@yahoo.co.uk> writes:
> 
>   Matthew> Go terms have an ID and (possibly) a
> description. By the
>   Matthew> isa relationship, they have a (single?)
> parent and
>   Matthew> (possibly no) children. I'm assuming Go
> has a part-of
>   Matthew> relationship (or it's inverse, has-a).
> What else does a GO
>   Matthew> term have?
> 
> GO allows multiple parents along both is-a, and
> part-of. In the case
> of GO, there are only two relationship types, but
> some of the GOBO
> ontologies define others. It wouldn't really make
> sense to have an API
> supporting GO, but not other DAG ontologies. 

OK - so GO is potentialy a DAG, not a tree (for any
given relation). Can you represent part-whole
hierachies (i.e. partative with cycles)? I can think
of a simple meta-data one:

|-> biological_process has-a (biological_process as
sub_process)*

You can remove the apparent cycle here by saying:

|-> sub_process is-a biological_process
&&  biological_process has-a (sub_process)*

but now we have to symultaneously reason over is-a and
part-of/has-a to figue anything out. I know this is
being pedantic, but are there cases when something
with an equivalent structure to this could/have been
built in GO?

>         
> It's also worth mentioning that the GO database has
> transitive closure
> information pre-calculated, so you need methods for
> accessing paths,
> if you want to advantage of this. I know from
> experience that graphing
> around GO using the "get_parent" methods is very
> slow, over the SQL
> database. (I won't bore you with the details, but I
> couldn't use the
> path methods). If memory serves the GO perl API has
> first class Path
> objects to allow this sort of access.

OK - worth knowing. Thanks.

My 2p is that we should suck GO in using whatever API
because it's usefull, and do it with beauty in BioJava
V2. If someone posts javacoc for GO APIs, we will
plump for one.

Matthew

__________________________________________________
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from News and Sport to Email and Music Charts
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From td2@sanger.ac.uk  Tue Dec  3 11:56:11 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Tue, 3 Dec 2002 11:56:11 +0000
Subject: [Biojava-l] Gene Ontology
In-Reply-To: <53340B0EBD7AD611A2A600065B3807957E5DB5@oxfordmail.osip.com>
References: <53340B0EBD7AD611A2A600065B3807957E5DB5@oxfordmail.osip.com>
Message-ID: <20021203115611.GB131506@jabba.sanger.ac.uk>

On Mon, Dec 02, 2002 at 11:56:58AM -0500, Dudgeon, Tim wrote:
> There has been mention of a Gene Ontology API and/or browser within BioJava
> in the past.
> I've also started off down that route, but before I go too far I thought it
> made sense to check whether there was any consensus here.
> I don't want to reinvent the wheel yet again and will be happy to help get
> something into BioJava.
> 
> What I'd like to see is an API to the GO database (probably with adaptors to
> its various forms), plus some gui browser that can form a component of a
> bigger tool.
> Browser would probably initially use a JTree type appraach, but eventually
> something that better reflected the fact that a GO term can have multiple
> parents.

I've only ever used GO mysql by talking directly to the database.
But if you want an API (especially one which helps you build a nice
viewer) you might want to look at GOET:

    http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gmod/goet/

[sorry, I can't find a proper website at the moment.  Although
it uses the org.goet namespace, www.goet.org appears to be owned
by the Global Organization for Ethical Time Travel]

     Thomas.

From p.lord@russet.org.uk  Tue Dec  3 12:17:09 2002
From: p.lord@russet.org.uk (Phillip Lord)
Date: 03 Dec 2002 12:17:09 +0000
Subject: [Biojava-l] Gene Ontology
In-Reply-To: <20021203112739.95855.qmail@web14911.mail.yahoo.com>
References: <20021203112739.95855.qmail@web14911.mail.yahoo.com>
Message-ID: <vf8yz7qou2.fsf@rpc71.cs.man.ac.uk>

>>>>> "Matthew" == Matthew Pocock <matthew_pocock@yahoo.co.uk> writes:

  >> GO allows multiple parents along both is-a, and part-of. In the
  >> case of GO, there are only two relationship types, but some of
  >> the GOBO ontologies define others. It wouldn't really make sense
  >> to have an API supporting GO, but not other DAG ontologies.

  Matthew> OK - so GO is potentialy a DAG, not a tree (for any given
  Matthew> relation). Can you represent part-whole hierachies
  Matthew> (i.e. partative with cycles)? 

No. Its a acyclic (hence DAG!). 


  Matthew> I can think of a simple meta-data one:

  Matthew> |-> biological_process has-a (biological_process as
  Matthew> sub_process)*

  Matthew> You can remove the apparent cycle here by saying:

  Matthew> |-> sub_process is-a biological_process &&
  Matthew> biological_process has-a (sub_process)*

I'm not sure that I am understanding what you are saying here. I don't
think that this is a cycle, because the arrows are the wrong way
around. 

So for instance

macrophagy has-a autophagic membrane degredation (the latter is a
subprocess of the former), 

autophagic membrane degradation is-a membrane degradation, which is-a
biological process. 


Actually there is a slight gotcha here. Although, logically, all
concepts should be a kind of something else, in GO this is not
explicitly represented in the DAG. So a "large ribosome subunit" is
part-of a "ribosome", but is not a kind of anything. We call these
"orphan nodes", and they make life slightly confusing, although the GO
people did them for sensible reasons (they didn't want terms like
"ribosome component", which are not, of themselves, useful for
annotating). 

There is a brief discussion of this, in one of my papers. 

http://www.cs.man.ac.uk/~phillord/download/publications/bioinf-sim-2002.pdf

It caused us a few problems, so our solution was, er, to fudge it. 


  Matthew> but now we have to symultaneously reason over is-a and
  Matthew> part-of/has-a to figue anything out. I know this is being
  Matthew> pedantic, but are there cases when something with an
  Matthew> equivalent structure to this could/have been built in GO?

You do have to graph over both link types.


  >> It's also worth mentioning that the GO database has transitive
  >> closure information pre-calculated, so you need methods for
  >> accessing paths, if you want to advantage of this. I know from
  >> experience that graphing around GO using the "get_parent" methods
  >> is very slow, over the SQL database. (I won't bore you with the
  >> details, but I couldn't use the path methods). If memory serves
  >> the GO perl API has first class Path objects to allow this sort
  >> of access.

  Matthew> OK - worth knowing. Thanks.

  Matthew> My 2p is that we should suck GO in using whatever API
  Matthew> because it's usefull, and do it with beauty in BioJava
  Matthew> V2. If someone posts javacoc for GO APIs, we will plump for
  Matthew> one.

I'd have a look at this lot first. I don't know what the future plans
are for it, but you could ask!

http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/geneontology/go-dev/java/dagedit/sources/org/bdgp/apps/dagedit/datamodel/

Cheers

Phil

From staff@absolutefrsmt.com  Tue Dec  3 23:57:56 2002
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Date: Tue,  3 Dec 2002 18:57:56 -0500 (EST)
Subject: [Biojava-l] Teen  Fisting
Message-ID: <20021203235756.28F1F18D24@mx.emailhowdy.com>

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From russell.smithies@xtra.co.nz  Wed Dec  4 05:03:39 2002
From: russell.smithies@xtra.co.nz (Russell Smithies)
Date: Wed, 4 Dec 2002 18:03:39 +1300
Subject: [Biojava-l] Re: gene ontology?
Message-ID: <000f01c29b52$82d42540$0100a8c0@lexx>

Has anyone looked at the gene ontology (or any other bits) in Duke
University's DBSR java resources?
http://mendel.mc.duke.edu:1755/libraries/dbsr/index.html
The documentation is non-existant so not sure whats in their packages
exactly

Russell


From matthew_pocock@yahoo.co.uk  Wed Dec  4 10:05:59 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Wed, 04 Dec 2002 10:05:59 +0000
Subject: [Biojava-l] Gene Ontology
In-Reply-To: <vf8yz7qou2.fsf@rpc71.cs.man.ac.uk>
References: <20021203112739.95855.qmail@web14911.mail.yahoo.com> <vf8yz7qou2.fsf@rpc71.cs.man.ac.uk>
Message-ID: <3DEDD387.1070107@yahoo.co.uk>

>   Matthew> OK - so GO is potentialy a DAG, not a tree (for any given
>   Matthew> relation). Can you represent part-whole hierachies
>   Matthew> (i.e. partative with cycles)? 
> 
> No. Its a acyclic (hence DAG!). 

But the graphs it validates can be cyclic, surely.


__________________________________________________
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from News and Sport to Email and Music Charts
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From p.lord@russet.org.uk  Wed Dec  4 14:15:44 2002
From: p.lord@russet.org.uk (Phillip Lord)
Date: 04 Dec 2002 14:15:44 +0000
Subject: [Biojava-l] Gene Ontology
In-Reply-To: <3DEDD387.1070107@yahoo.co.uk>
References: <20021203112739.95855.qmail@web14911.mail.yahoo.com>
 <vf8yz7qou2.fsf@rpc71.cs.man.ac.uk> <3DEDD387.1070107@yahoo.co.uk>
Message-ID: <vfsmxdyinj.fsf@rpc71.cs.man.ac.uk>

>>>>> "Matthew" == Matthew Pocock <matthew_pocock@yahoo.co.uk> writes:

  Matthew> OK - so GO is potentialy a DAG, not a tree (for any given
  Matthew> relation). Can you represent part-whole hierachies Matthew>
  >> (i.e. partative with cycles)? No. Its a acyclic (hence Matthew>
  >> DAG!).


  Matthew> But the graphs it validates can be cyclic, surely.

I'm sorry, but I am not sure that I understand what you are
asking. 

Phil

From MCCon012@mc.duke.edu  Wed Dec  4 19:46:12 2002
From: MCCon012@mc.duke.edu (Patrick McConnell)
Date: Wed, 4 Dec 2002 14:46:12 -0500
Subject: [Biojava-l] Re: DBSR
Message-ID: <OF56D344A1.D3DE5F29-ON85256C85.006C95CF-85256C85.006CCE65@notes.duke.edu>

---------------------- Forwarded by Patrick McConnell/CanCtr/mc/Duke on
12/04/2002 02:48 PM ---------------------------


Patrick McConnell
12/04/2002 02:45 PM

To:    Biojava-L<Biojava-L@Biojava. Org" <biojava-l@biojava.org>
cc:    "Russell Smithies" <russell_smithies@hotmail.com>

Subject:    Re: DBSR  (Document link: Patrick McConnell)

We have not produced any documentation because the library is primarily for
internal use.

We do have some code for building and manipulating GO trees, but it is
unlikely to be flexible and robust enough for use in BioJava.

In our system:

Every term is an object that extends from DefaultMutableTreeNode and
includes fields for the term id, accession, name, and description.  Where
one term has multiple parents, multiple nodes are created with the same
information.

Our viewer extends JTree and provides methods for marking nodes with custom
counts (used primarily for # of gene's annotated at that term, etc.),
tooltips, colors, etc.  We also provide methods to hide unmarked nodes and
the such.

We build our trees from the GO database using SQL (I think a MySQL driver
is hard-coded right now).  This is a slow process, so we first try to build
the tree via Java serialization from a File (our GO nodes are
serializable).

I would gladly donate the source "as is" if anyone is interested, but I do
not think I have the time to alter and maintain it for BioJava.

-Patrick




"Russell Smithies" <russell_smithies@hotmail.com> on 12/03/2002 09:48:26 PM

To:    mccon012@mc.duke.edu
cc:

Subject:    DBSR

Hi Patrick,

I was hunting about for a java BLAST parsers (I usually use BioJava) and
found your library on Duke's site.
I downloaded the .jar of DBSR but there's no documentation or javadoc.
Have I missed something or is it availible elsewhere?

thanx

Russell Smithies
University of Otago,
Dunedin
New Zealand





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From jon portuondo murguiondo <jon.portuondo01@campus.upf.es>  Thu Dec  5 10:43:44 2002
From: jon portuondo murguiondo <jon.portuondo01@campus.upf.es> (jon portuondo murguiondo)
Date: Thu, 5 Dec 2002 10:43:44
Subject: [Biojava-l] I search for java.jar
Message-ID: <1039081424.16522@mail.infomail.es>

Hello,
I have a problem when I try to execute the program PdbToXML. I think the problem is I don't have the java.jar library, but where I can find it? (I have linux). I would be very pleased you could help me.
The errors are the following (if you think the problem is not the java.jar library, tell me please!):
[jon@diana ~]$ java PdbToXMLConverter 1FS1.pdb 
Exception in thread "main" java.lang.NoClassDefFoundError: PdbToXMLConverter (wrong name: org/biojava/bio/program/PdbToXMLConverter)
        at java.lang.ClassLoader.defineClass0(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:502)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:123)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:250)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:54)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:193)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:186)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:299)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:265)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:255)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:315)


From infowebmail@yahoo.co.jp  Thu Dec  5 11:08:05 2002
From: infowebmail@yahoo.co.jp (infowebmail@yahoo.co.jp)
Date: Thu, 5 Dec 2002 20:08:05 +0900
Subject: [Biojava-l] =?ISO-2022-JP?B?GyRCTCQ+NUJ6OS05cCIoSXwzaCVKJV4lOyVpGyhC?=
Message-ID: <200212051107.gB5B7LJ9024149@pw600a.bioperl.org>

<$BAw?.<T(B>
$B%U%!%$%J%k%M%C%H(B

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$B$3$N$^$^$4JV?.$$$?$@$1$l$P!"EvJ}$N%j%9%H$+$i%"%I%l%9$r:o=|$$$?$7$^$9!#(B
$B"-!]!]!]"-!]!]!]"-!]!]!]"-!]!]!]"-!]!]!]"-!]!]!]"-!]!]!]"-!]!]!]"-(B
$B!!!!!!!!!!!!(Bwebmailjapan@yahoo.co.jp
**********************************************************************
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$B!!!!!!!!!!!!!!!!!!!!!HI|!!3h!I%J!!%^!!%;!!%i!!!*!!!!!!!!!!!!!!!!!!!!(B
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$B!!!!05E]E*B??t$N$*5RMM$N$4MWK>$K$*Ez$($7$F(B
$B!!!!A49q$N3'$5$s$,$49XF~=PMh$kMM$K$J$j$^$7$?!#(B
$B!!!!6=L#$,$"$k?M$O2<$N(BHP$B$r8+$KMh$F$/$@$5$$"v(B

$B!!!!!!!!!!!!(Bhttp://www.goo-girl.com/

$B(.(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(/(B
          $B")(B150-0002$B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B
          $BEl5~ET=BC+6h=BC+(B1-13-8$B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B
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          TEL 090-6710-3732$B!!!!!!!!!!!!(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B
$B(1(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(,(0(B

From artofselflove@clear.net.nz  Thu Dec  5 12:12:01 2002
From: artofselflove@clear.net.nz (artofselflove)
Date: Fri, 06 Dec 2002 01:12:01 +1300 (NZDT)
Subject: [Biojava-l] Protein Diets from New Zealand
Message-ID: <0H6N007V6B81M7@smtp2.clear.net.nz>

The Art of Self-Healing is a E-book containing a rotational 7 day protein diet which has been formulated by myself having practiced as a Naturopath in 
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From matthew_pocock@yahoo.co.uk  Thu Dec  5 12:54:23 2002
From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=)
Date: Thu, 5 Dec 2002 12:54:23 +0000 (GMT)
Subject: [Biojava-l] I search for java.jar
In-Reply-To: <1039081424.16522@mail.infomail.es>
Message-ID: <20021205125423.6206.qmail@web14908.mail.yahoo.com>

Hi,

Firstly, I think you will need to put biojava.jar into
your classpath rather than java.jar.

Seccondly, you are running the class
PdbToXMLConverter. Did you compile this yourself? If
you did, I think you may have a package statement on
the first non-comment, non-empty line that says:

package org.biojava.bio.program;

To make the program run, you eiter need the .class
file from compiling this to be in a directory
org/biojava/bio/program (relative to your classpath)
and type java
org.biojava.bio.program.PdbToXMLConverter 1FS1.pdb, or
you need to remove the package line from the file. If
you did not compile the application yourself, you will
probably find that putting biojava.jar into your path
and typing the new command-line works.

If you have any more trouble, drop us a line.

Matthew


 --- jon portuondo murguiondo
<jon.portuondo01@campus.upf.es> wrote: > Hello,
> I have a problem when I try to execute the program
> PdbToXML. I think the problem is I don't have the
> java.jar library, but where I can find it? (I have
> linux). I would be very pleased you could help me.
> The errors are the following (if you think the
> problem is not the java.jar library, tell me
> please!):
> [jon@diana ~]$ java PdbToXMLConverter 1FS1.pdb 
> Exception in thread "main"
> java.lang.NoClassDefFoundError: PdbToXMLConverter
> (wrong name:
> org/biojava/bio/program/PdbToXMLConverter)
>         at java.lang.ClassLoader.defineClass0(Native
> Method)
>         at
>
java.lang.ClassLoader.defineClass(ClassLoader.java:502)
>         at
>
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:123)
>         at
>
java.net.URLClassLoader.defineClass(URLClassLoader.java:250)
>         at
>
java.net.URLClassLoader.access$100(URLClassLoader.java:54)
>         at
>
java.net.URLClassLoader$1.run(URLClassLoader.java:193)
>         at
> java.security.AccessController.doPrivileged(Native
> Method)
>         at
>
java.net.URLClassLoader.findClass(URLClassLoader.java:186)
>         at
>
java.lang.ClassLoader.loadClass(ClassLoader.java:299)
>         at
>
sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:265)
>         at
>
java.lang.ClassLoader.loadClass(ClassLoader.java:255)
>         at
>
java.lang.ClassLoader.loadClassInternal(ClassLoader.java:315)
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l 

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From james@jamestaylor.org  Thu Dec  5 15:00:15 2002
From: james@jamestaylor.org (James Taylor)
Date: 05 Dec 2002 10:00:15 -0500
Subject: [Biojava-l] Re: Biojava-l -- confirmation of subscription -- request 786011
In-Reply-To: <20021205150004.26225.98843.Mailman@pw600a.bioperl.org>
References: <20021205150004.26225.98843.Mailman@pw600a.bioperl.org>
Message-ID: <1039100414.5728.4.camel@enki>

On Thu, 2002-12-05 at 10:00, biojava-l-request@biojava.org wrote:
> Biojava-l -- confirmation of subscription -- request 786011
> 
> We have received a request from 64.30.49.15 for subscription of your
> email address, <james@jamestaylor.org>, to the biojava-l@biojava.org
> mailing list.  To confirm the request, please send a message to
> biojava-l-request@biojava.org, and either:
> 
> - maintain the subject line as is (the reply's additional "Re:" is
> ok),
> 
> - or include the following line - and only the following line - in the
> message body: 
> 
> confirm 786011
> 
> (Simply sending a 'reply' to this message should work from most email
> interfaces, since that usually leaves the subject line in the right
> form.)
> 
> If you do not wish to subscribe to this list, please simply disregard
> this message.  Send questions to biojava-l-admin@biojava.org.
> 


From russell_smithies@hotmail.com  Fri Dec  6 03:58:29 2002
From: russell_smithies@hotmail.com (Russell Smithies)
Date: Fri, 06 Dec 2002 03:58:29 +0000
Subject: [Biojava-l] SimpleModelInState problem?
Message-ID: <F165RXf2LTrpwACkWHZ000002b6@hotmail.com>

I'm trying to create a reasonably complex markov model so have split it into 
bits to make it a little easier to handle.
I'm then trying to re-assemble the bits into another model by creating 
SimpleModelInState's from the sub-models.
The problem is that I keep getting errors and not sure why.
heres some code I did as a test, the top portion creates a sub-model (which 
compiles correctly) but when I try to add them to create the DP for, I get 
null pointer errors and was getting errors about null back pointers?

heres some testy code :
(sorry if HotMail munges it)  :-)



import java.util.*;

import org.biojava.bio.*;
import org.biojava.bio.dist.*;
import org.biojava.bio.dp.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;

public class modelInStateTest {
  public static void main(String[] args) throws Exception {

    // sequence to test
    SymbolList sl  = DNATools.createDNA("actgatcgactgtacgatgagatgcgactga"+
                                        
"tcgactgactgctgcgtatcgatcgatcgatgactgacg");
    int[] advance = { 1 };

    //create order n alphabet
    Alphabet orderNAlpha = AlphabetManager.getCrossProductAlphabet(
                                            Collections.nCopies(3, 
DNATools.getDNA()));

    //create uniform distribution for emission states
    Distribution uni_dist = new UniformDistribution(DNATools.getDNA());

    // create simple markov model
    SimpleMarkovModel mm = new SimpleMarkovModel(1, DNATools.getDNA(), 
"mm");

    //create emission states
    EmissionState es1 = new SimpleEmissionState("1_es", 
Annotation.EMPTY_ANNOTATION, advance, uni_dist);
    EmissionState es2 = new SimpleEmissionState("2_es", 
Annotation.EMPTY_ANNOTATION, advance, uni_dist);


    //  add states to model
    mm.addState(es1);
    mm.addState(es2);

    //  create transitions between all states
    mm.createTransition(mm.magicalState(), es1);
    mm.createTransition(mm.magicalState(), es2);
    mm.createTransition(es1, es1);
    mm.createTransition(es1, es2);
    mm.createTransition(es2, es2);
    mm.createTransition(es2, es1);
    mm.createTransition(es2, mm.magicalState());
    mm.createTransition(es1, mm.magicalState());

    //set weights on transitions
    mm.setWeights(mm.magicalState(), new 
UniformDistribution(mm.transitionsFrom(mm.magicalState())));
    mm.setWeights(es1, new UniformDistribution(mm.transitionsFrom(es1)));
    mm.setWeights(es2, new UniformDistribution(mm.transitionsFrom(es2)));

    sl = SymbolListViews.orderNSymbolList(sl, 3);

    SymbolList[] sla = { sl };

    //  create the dynamic programming object
    DP dp = DPFactory.DEFAULT.createDP(mm);

    //create statepath
    StatePath sp = dp.viterbi(sla, ScoreType.PROBABILITY);

    /////////     TRY TO CREATE SUB MODELS AND INTEGRATE THEM  
///////////////////////////

    SimpleMarkovModel mm2 = new SimpleMarkovModel(1, DNATools.getDNA(), 
"2_mm");

    //create states
    SimpleModelInState smis1 = new SimpleModelInState(mm, "1_smis");
    SimpleModelInState smis2 = new SimpleModelInState(mm, "2_smis");

    mm2.addState(smis1);
    mm2.addState(smis2);

    //  create transitions between all states
    mm2.createTransition(mm2.magicalState(), smis1);
    mm2.createTransition(mm2.magicalState(), smis2);
    mm2.createTransition(smis1, smis1);
    mm2.createTransition(smis1, smis2);
    mm2.createTransition(smis2, smis2);
    mm2.createTransition(smis2, smis1);
    mm2.createTransition(smis2, mm2.magicalState());
    mm2.createTransition(smis1, mm2.magicalState());

    //set weights on transitions
    mm2.setWeights(mm2.magicalState(), new 
UniformDistribution(mm2.transitionsFrom(mm2.magicalState())));
    mm2.setWeights(smis1, new 
UniformDistribution(mm2.transitionsFrom(smis1)));
    mm2.setWeights(smis2, new 
UniformDistribution(mm2.transitionsFrom(smis2)));

    //  create the dynamic programming object
    DP dp2 = DPFactory.DEFAULT.createDP(mm2);   //<<<<-----------------

    //create statepath
    StatePath sp2 = dp2.viterbi(sla, ScoreType.PROBABILITY);

    /*
    java.lang.NullPointerException
        at org.biojava.bio.dp.FlatModel.<init>(FlatModel.java:229)
        at org.biojava.bio.dp.DP.flatView(DP.java:96)
        at 
org.biojava.bio.dp.DPFactory$DefaultFactory.createDP(DPFactory.java:51)
        at markov.modelInStateTest.main(modelInStateTest.java:89)
    Exception in thread "main"
    */

  }
}




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From matthew_pocock@yahoo.co.uk  Fri Dec  6 09:40:44 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Fri, 06 Dec 2002 09:40:44 +0000
Subject: [Biojava-l] SimpleModelInState problem?
In-Reply-To: <F165RXf2LTrpwACkWHZ000002b6@hotmail.com>
References: <F165RXf2LTrpwACkWHZ000002b6@hotmail.com>
Message-ID: <3DF0709C.60805@yahoo.co.uk>

Hi Russell,

This code is my fault, and I haven't looked at the nested model support 
in a couple of years. Hopefully we will get time to look at it over the 
weekend.

Matthew

ps I'm writing a CpG finder using the lib today, so at least I have the 
right javadocs open.

Russell Smithies wrote:
> 
> I'm trying to create a reasonably complex markov model so have split it 
> into bits to make it a little easier to handle.
> I'm then trying to re-assemble the bits into another model by creating 
> SimpleModelInState's from the sub-models.
> The problem is that I keep getting errors and not sure why.
> heres some code I did as a test, the top portion creates a sub-model 
> (which compiles correctly) but when I try to add them to create the DP 
> for, I get null pointer errors and was getting errors about null back 
> pointers?
> 
> heres some testy code :
> (sorry if HotMail munges it)  :-)
> 
> 
> 
> import java.util.*;
> 
> import org.biojava.bio.*;
> import org.biojava.bio.dist.*;
> import org.biojava.bio.dp.*;
> import org.biojava.bio.seq.*;
> import org.biojava.bio.symbol.*;
> 
> public class modelInStateTest {
>  public static void main(String[] args) throws Exception {
> 
>    // sequence to test
>    SymbolList sl  = DNATools.createDNA("actgatcgactgtacgatgagatgcgactga"+
>                                        
> "tcgactgactgctgcgtatcgatcgatcgatgactgacg");
>    int[] advance = { 1 };
> 
>    //create order n alphabet
>    Alphabet orderNAlpha = AlphabetManager.getCrossProductAlphabet(
>                                            Collections.nCopies(3, 
> DNATools.getDNA()));
> 
>    //create uniform distribution for emission states
>    Distribution uni_dist = new UniformDistribution(DNATools.getDNA());
> 
>    // create simple markov model
>    SimpleMarkovModel mm = new SimpleMarkovModel(1, DNATools.getDNA(), 
> "mm");
> 
>    //create emission states
>    EmissionState es1 = new SimpleEmissionState("1_es", 
> Annotation.EMPTY_ANNOTATION, advance, uni_dist);
>    EmissionState es2 = new SimpleEmissionState("2_es", 
> Annotation.EMPTY_ANNOTATION, advance, uni_dist);
> 
> 
>    //  add states to model
>    mm.addState(es1);
>    mm.addState(es2);
> 
>    //  create transitions between all states
>    mm.createTransition(mm.magicalState(), es1);
>    mm.createTransition(mm.magicalState(), es2);
>    mm.createTransition(es1, es1);
>    mm.createTransition(es1, es2);
>    mm.createTransition(es2, es2);
>    mm.createTransition(es2, es1);
>    mm.createTransition(es2, mm.magicalState());
>    mm.createTransition(es1, mm.magicalState());
> 
>    //set weights on transitions
>    mm.setWeights(mm.magicalState(), new 
> UniformDistribution(mm.transitionsFrom(mm.magicalState())));
>    mm.setWeights(es1, new UniformDistribution(mm.transitionsFrom(es1)));
>    mm.setWeights(es2, new UniformDistribution(mm.transitionsFrom(es2)));
> 
>    sl = SymbolListViews.orderNSymbolList(sl, 3);
> 
>    SymbolList[] sla = { sl };
> 
>    //  create the dynamic programming object
>    DP dp = DPFactory.DEFAULT.createDP(mm);
> 
>    //create statepath
>    StatePath sp = dp.viterbi(sla, ScoreType.PROBABILITY);
> 
>    /////////     TRY TO CREATE SUB MODELS AND INTEGRATE THEM  
> ///////////////////////////
> 
>    SimpleMarkovModel mm2 = new SimpleMarkovModel(1, DNATools.getDNA(), 
> "2_mm");
> 
>    //create states
>    SimpleModelInState smis1 = new SimpleModelInState(mm, "1_smis");
>    SimpleModelInState smis2 = new SimpleModelInState(mm, "2_smis");
> 
>    mm2.addState(smis1);
>    mm2.addState(smis2);
> 
>    //  create transitions between all states
>    mm2.createTransition(mm2.magicalState(), smis1);
>    mm2.createTransition(mm2.magicalState(), smis2);
>    mm2.createTransition(smis1, smis1);
>    mm2.createTransition(smis1, smis2);
>    mm2.createTransition(smis2, smis2);
>    mm2.createTransition(smis2, smis1);
>    mm2.createTransition(smis2, mm2.magicalState());
>    mm2.createTransition(smis1, mm2.magicalState());
> 
>    //set weights on transitions
>    mm2.setWeights(mm2.magicalState(), new 
> UniformDistribution(mm2.transitionsFrom(mm2.magicalState())));
>    mm2.setWeights(smis1, new 
> UniformDistribution(mm2.transitionsFrom(smis1)));
>    mm2.setWeights(smis2, new 
> UniformDistribution(mm2.transitionsFrom(smis2)));
> 
>    //  create the dynamic programming object
>    DP dp2 = DPFactory.DEFAULT.createDP(mm2);   //<<<<-----------------
> 
>    //create statepath
>    StatePath sp2 = dp2.viterbi(sla, ScoreType.PROBABILITY);
> 
>    /*
>    java.lang.NullPointerException
>        at org.biojava.bio.dp.FlatModel.<init>(FlatModel.java:229)
>        at org.biojava.bio.dp.DP.flatView(DP.java:96)
>        at 
> org.biojava.bio.dp.DPFactory$DefaultFactory.createDP(DPFactory.java:51)
>        at markov.modelInStateTest.main(modelInStateTest.java:89)
>    Exception in thread "main"
>    */
> 
>  }
> }
> 
> 
> 
> 
> _________________________________________________________________
> The new MSN 8: advanced junk mail protection and 2 months FREE* 
> http://join.msn.com/?page=features/junkmail
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 


-- 
BioJava Consulting LTD - Support and training for BioJava
http://www.biojava.co.uk

__________________________________________________
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From hjm@tacgi.com  Fri Dec  6 19:42:31 2002
From: hjm@tacgi.com (Harry Mangalam)
Date: Fri, 06 Dec 2002 11:42:31 -0800
Subject: [Biojava-l] ANN: O'Reilly's 2003 Bioinformatics Technology Conference
Message-ID: <3DF0FDA7.7030902@tacgi.com>

Hi All,

This is an announcement for:

O'Reilly's 2003 Bioinformatics Technology Conference,
taking place February 3 - 6, 2003, in San Diego, California

More information at:
http://www.oreillynet.com/biocon2002/

NOTE to the Open Bio Foundation:
Furthermore, O'Reilly is extending a 20% registration discount to
OBFers. To take advantage of the discount, visit the conference web
site, and register using the OBF discount code "bio03open". The
discount means more if you register by December 16, which is the end
of the early-bird registration period.

It's an unusual but compelling mix of information technology, bit twiddlers,
academic researchers, industry types, headhunters, and standards setters (and
wannabes), brought together in in one 3 ring circus by the O'Reilly
organization, the people who document Open (and some closed) Source IT
with their retro-animal covered screeds on Perl, Python, apache, etc.

This year, the keynotes include emissions from the minds of:

  - Lincoln Stein - too-young godfather of Perl Bioinfo, CGI.pm,
      DAS, Moby, etc
  - Stephen Wolfram - ex-boy genius of Mathematica, author of
      'A New Kind of Science'
  - Suzi Lewis - Godmother of the Gene Ontology project
  - Alvis Brazma - Lead cheerleader for the MGED, MIAME gene
      expression standards.
  - James Gosling - programming god/demon (Java, NeWS, EMACS),
      Sun Fellow, Canadian
  - Damian Conway - nonpareil Perl Edutainment speaker, Author,
      Australian, singer
  - James Kent - late-blooming/exploding bioinformatics genome
      gnome from UCSC.
  - Francis Ouellette - longtime NCBI vet, now escaped to UBC
      Bioinformatics Ctr
  - and others

For a sense of what last year's conference was like, check out its coverage
page: http://www.oreillynet.com/biocon2002/

Disclaimer:  I don't work for O'Reilly, but I did attend the 2002 conference,
liked most things, didn't like some things, then got hit up by the organizers,
to assure more-of-the-former/less-of-the-latter and so have been volunteering
some time to help them do an even better job this year.

Apologies to those who have seen this in other related lists.

-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hjm@tacgi.com
             <<plain text preferred>>


From hjm@tacgi.com  Fri Dec  6 20:20:23 2002
From: hjm@tacgi.com (Harry Mangalam)
Date: Fri, 06 Dec 2002 12:20:23 -0800
Subject: [Biojava-l] Re: ANN: O'Reilly's 2003 Bioinformatics Technology Conference
In-Reply-To: <3DF0FDA7.7030902@tacgi.com>
References: <3DF0FDA7.7030902@tacgi.com>
Message-ID: <3DF10687.10208@tacgi.com>

Oops!  2003 conference URL should be:

http://conferences.oreilly.com/bio2003/

Sorry..

-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hjm@tacgi.com
             <<plain text preferred>>


From judithz@student.ethz.ch  Mon Dec  9 08:38:00 2002
From: judithz@student.ethz.ch (Zimmermann, Judith)
Date: Mon, 9 Dec 2002 09:38:00 +0100
Subject: [Biojava-l] SuffixTree
Message-ID: <65ABEA2ED2490A4085A4BD59E7427EDD7AB4F9@EXSTUD2.d.ethz.ch>

Dear receiver

 

I found your implementation of the suffix tree. You point out, that it uses little space. But I could not find any state of time complexity. 

 

What is the time complexity of the construction phase of a suffix tree of a given string? Which algorithm was implemented?

 

Thanks a lot for this information.

 

Greetings

Judith Zimmermann



From zren@amylin.com  Mon Dec  9 22:07:51 2002
From: zren@amylin.com (Ren, Zhen)
Date: Mon, 9 Dec 2002 14:07:51 -0800
Subject: [Biojava-l] SymbolParsers in Alphabet
Message-ID: <C527D913CB1168458AE19E0FECDE58DE0D365E@api-exch-1.amylin.com>

Hi, there,

The interface Alphabet has a method
    public SymbolTokenization getTokenization(java.lang.String name) throws BioException

Every alphabet should have a SymbolParser under the name 'token' that uses the symbol token characters to translate a string into a SymbolList. Likewise, there should be a SymbolParser under the name 'name' that uses symbol names to identify symbols.

I'd like to know how I can have these two SymbolParsers under the names 'token' and 'name' incorporated into an alphabet I intend to create by myself.

Thanks a lot.

Zhen


From td2@sanger.ac.uk  Mon Dec  9 23:16:06 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Mon, 9 Dec 2002 23:16:06 +0000
Subject: [Biojava-l] SymbolParsers in Alphabet
In-Reply-To: <C527D913CB1168458AE19E0FECDE58DE0D365E@api-exch-1.amylin.com>
References: <C527D913CB1168458AE19E0FECDE58DE0D365E@api-exch-1.amylin.com>
Message-ID: <20021209231605.GB174236@jabba.sanger.ac.uk>

On Mon, Dec 09, 2002 at 02:07:51PM -0800, Ren, Zhen wrote:
> Hi, there,
> 
> The interface Alphabet has a method
>     public SymbolTokenization getTokenization(java.lang.String name) throws BioException
> 
> Every alphabet should have a SymbolParser under the name 'token' that uses the symbol token characters to translate a string into a SymbolList. Likewise, there should be a SymbolParser under the name 'name' that uses symbol names to identify symbols.
> 
> I'd like to know how I can have these two SymbolParsers under the names 'token' and 'name' incorporated into an alphabet I intend to create by myself.

Hmmm, "SymbolParser" is an old interface name.  Its functionality
has been subsumed into SymbolTokenization, but a few references to
it survived in the javadoc for a while.  I think these are gone
now, if you get the latest CVS version.

Exactly how tokenizations are handled depends on the Alphabet
implementation.  If you write your own Alphabet, you can, of
coure, write a getTokenization method yourself.

If you're construction a SimpleAlphabet, getTokenization("name") is handled
automatically for you.  To add extra tokenizations, you can do
something like:

     CharacterTokenization toke = new CharacterTokenization(
         myAlphabet,
         false
     );
     toke.bindSymbol(symbol0, '0');
     toke.bindSymbol(symbol1, '1');
     myAlphabet.putTokenization("token", toke);

Hope this helps,

     Thomas.

From mark.schreiber@agresearch.co.nz  Tue Dec 10 03:46:43 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Tue, 10 Dec 2002 16:46:43 +1300
Subject: [Biojava-l] Biojava in Anger
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650126CFBC@inbox.agresearch.co.nz>

Hi -

I have setup some web pages that provide a cookbook, how to, kind of
approach to performing basic tasks in biojava. It's available at
http://bioconf.otago.ac.nz/biojava/

Comments, suggestions, flames and financial support all welcome.

Enjoy

Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From jon portuondo murguiondo <jon.portuondo01@campus.upf.es>  Tue Dec 10 12:14:42 2002
From: jon portuondo murguiondo <jon.portuondo01@campus.upf.es> (jon portuondo murguiondo)
Date: Tue, 10 Dec 2002 12:14:42
Subject: [Biojava-l] It's me once again
Message-ID: <1039518882.21896@mail.infomail.es>

Mensaje con FORMATO mime.
-------21896-----INFOMAIL-----
Content-Type: text/plain
Content-Transfer-Encoding: 8bit

Hi! I Haven't solved the problem. I remember you what problem I am refering to:
[jon@diana ~]$ java PdbToXMLConverter 1FS1.pdb
Exception in thread "main" java.lang.NoClassDefFoundError: PdbToXMLConverter (wrong name: org/biojava/bio/program/PdbToXMLConverter)
        at java.lang.ClassLoader.defineClass0(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:502)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:123)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:250)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:54)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:193)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:186)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:299)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:265)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:255)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:315)

I tried to put the .class in this directory (relative to my CLASSPATH) :/org/biojava/bio/program/PdbToXMLConverter.class
But it does'nt solve the problem.
If I put the .class in the directory where I run the program, the error is the same.
On the other hand, if the .class is ONLY in the package directory (the org/biojava....), I mean if I remove the .class from the current directory, the problem is: 

[jon@diana ~]$ java PdbToXMLConverter 1FS1.pdb
Exception in thread "main" java.lang.NoClassDefFoundError: PdbToXMLConverter
[jon@diana ~]$

I tried removing the package line "package org.biojava.bio.program" but the following error ocurred while compiling:

[jon@diana ~]$ javac PdbToXMLConverter2.java
PdbToXMLConverter2.java:69: invalid method declaration; return type required
    public PdbToXMLConverter(String poInput) {
           ^
1 error

Thanks for all, spetially to Mattew that suggest me to do this modifications I've explained. In the case you want to see the source code, it is attached.

-------21896-----INFOMAIL-----
Content-Type: application/octet-stream; name="PdbToXMLConverter.java"
Content-Transfer-Encoding: base64
Content-Disposition: inline; filename="PdbToXMLConverter.java"

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Y29kZQogKgogKiBUaGlzIGNvZGUgbWF5IGJlIGZyZWVseSBkaXN0cmlidXRl
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TGVzc2VyIEdlbmVyYWwgUHVibGljIExpY2VuY2UuICBUaGlzIHNob3VsZAog
KiBiZSBkaXN0cmlidXRlZCB3aXRoIHRoZSBjb2RlLiAgSWYgeW91IGRvIG5v
dCBoYXZlIGEgY29weSwKICogc2VlOgogKgogKiAgICAgIGh0dHA6Ly93d3cu
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-------21896-----INFOMAIL-------

From matthew_pocock@yahoo.co.uk  Tue Dec 10 17:16:01 2002
From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=)
Date: Tue, 10 Dec 2002 17:16:01 +0000 (GMT)
Subject: [Biojava-l] It's me once again
In-Reply-To: <1039518882.21896@mail.infomail.es>
Message-ID: <20021210171601.93080.qmail@web14907.mail.yahoo.com>

Hi,

Try reading through this tutorial. It should help fill
the gaps.

http://java.sun.com/docs/books/tutorial/java/interpack/packages.html

> I tried to put the .class in this directory
> (relative to my CLASSPATH)
> :/org/biojava/bio/program/PdbToXMLConverter.class
> But it does'nt solve the problem.
> If I put the .class in the directory where I run the
> program, the error is the same.
> On the other hand, if the .class is ONLY in the
> package directory (the org/biojava....), I mean if I
> remove the .class from the current directory, the
> problem is: 
> 
> [jon@diana ~]$ java PdbToXMLConverter 1FS1.pdb
> Exception in thread "main"
> java.lang.NoClassDefFoundError: PdbToXMLConverter
> [jon@diana ~]$

In this configuration, you would need to type:

java org.biojava.bio.program.PdbToXMLConverter
lFSl.pdb

Notice that the package prefix to the class matches
the package of the classes package & it's location.

> 
> I tried removing the package line "package
> org.biojava.bio.program" but the following error
> ocurred while compiling:
> 
> [jon@diana ~]$ javac PdbToXMLConverter2.java
> PdbToXMLConverter2.java:69: invalid method
> declaration; return type required
>     public PdbToXMLConverter(String poInput) {
>            ^
> 1 error

This is because you have renamed the class to
PdbToXMLConverter2, but have not renamed the
constructor to match the class name. Rename this
constructor to match the class name and try again.
Make sure that you use

java PdbToXMLConverter2 lFSl.pdb

OH. The name of a java class and of it's file must
match if it is a public class. So, if you have a class
called Foo, it must be in a file called Foo.java and
will produce a class file Foo.class and will have a
constructor called Foo() and you would run its main
method as java Foo <args>..

If it is in package bar, then the class is bar.Foo,
and it will be in a file bar/Foo.java and will produce
a class file bar/Foo.class and if it has a main method
you run it as java bar.Foo <args>.

Best,

Matthew

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From dwaring@u.washington.edu  Wed Dec 11 00:20:47 2002
From: dwaring@u.washington.edu (David Waring)
Date: Tue, 10 Dec 2002 16:20:47 -0800
Subject: [Biojava-l] Build failing
Message-ID: <HCEOLHNOIDOJLKLGOAFMOEFLCIAA.dwaring@u.washington.edu>

I got the following errors when I tried to build biojava-live

compile:
    [javac] Compiling 799 source files to
V:\dwaring\cvs\biojava-live\ant-build\
classes\main
    [javac]
V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
o\filterxml\XMLFilterWriterConfig.java:198: interface expected here
    [javac]     private static class BlankFilterWriter implements
XMLFilterWrite
r {
    [javac]                                                       ^
    [javac]
V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
o\filterxml\XMLFilterWriterConfig.java:217: interface expected here
    [javac]     private static abstract class PropertyFilterWriter
implements XM
LFilterWriter {
    [javac]
^
    [javac]
V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
o\filterxml\XMLFilterWriterConfig.java:313: interface expected here
    [javac]     private static class AndFilterWriter implements
XMLFilterWriter
{
    [javac]                                                     ^
    [javac]
V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
o\filterxml\XMLFilterWriterConfig.java:340: interface expected here
    [javac]     private static class OrFilterWriter implements
XMLFilterWriter {

    [javac]                                                    ^
    [javac]
V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
o\filterxml\XMLFilterWriterConfig.java:112: cannot resolve symbol
    [javac] symbol  : class IsTopLevel
    [javac] location: interface org.biojava.bio.seq.FeatureFilter
    [javac]                 FeatureFilter.IsTopLevel.class,
    [javac]                              ^
    [javac]
V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
o\filterxml\XMLFilterWriterConfig.java:185:
writeFilter(org.biojava.bio.seq.Feat
ureFilter,org.biojava.utils.xml.XMLWriter) in
org.biojava.bio.seq.io.filterxml.X
MLFilterWriter cannot be applied to
(org.biojava.bio.seq.FeatureFilter,org.bioja
va.utils.xml.XMLWriter,org.biojava.bio.seq.io.filterxml.XMLFilterWriterConfi
g)
    [javac]                 xfw.writeFilter(ff, xw, this);
    [javac]                    ^
    [javac]
V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\progr
am\das\DASMergeFeatureHolder.java:35: cannot resolve symbol
    [javac] symbol  : method getMergeMap  ()
    [javac] location: class
org.biojava.bio.program.das.DASMergeFeatureHolder
    [javac]     Map mm = getMergeMap();
    [javac]                  ^
    [javac]
V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\progr
am\das\DASMergeFeatureHolder.java:48: cannot resolve symbol
    [javac] symbol  : method getMergeMap  ()
    [javac] location: class
org.biojava.bio.program.das.DASMergeFeatureHolder
    [javac]     Map mm = getMergeMap();
    [javac]                  ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -deprecation for details.
    [javac] 8 errors

BUILD FAILED
file:V:/dwaring/cvs/biojava-live/build.xml:281: Compile failed; see the
compiler
 error output for details.

Total time: 1 minute 27 seconds




From matthew_pocock@yahoo.co.uk  Wed Dec 11 01:02:12 2002
From: matthew_pocock@yahoo.co.uk (Matthew Pocock)
Date: Wed, 11 Dec 2002 01:02:12 +0000
Subject: [Biojava-l] Build failing
In-Reply-To: <HCEOLHNOIDOJLKLGOAFMOEFLCIAA.dwaring@u.washington.edu>
References: <HCEOLHNOIDOJLKLGOAFMOEFLCIAA.dwaring@u.washington.edu>
Message-ID: <3DF68E94.6080003@yahoo.co.uk>

Hi David,

Is it possible that you have either a truncated or corrupted version of 
the biojava source tree? I'm sure we've broken the 1k mark for source 
files now. We're getting better at hiding them away though ;-)

Try checking the files out again from clean. That may sort things out.

Matthew

David Waring wrote:
> I got the following errors when I tried to build biojava-live
> 
> compile:
>     [javac] Compiling 799 source files to
> V:\dwaring\cvs\biojava-live\ant-build\
> classes\main
>     [javac]
> V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> o\filterxml\XMLFilterWriterConfig.java:198: interface expected here
>     [javac]     private static class BlankFilterWriter implements
> XMLFilterWrite
> r {
>     [javac]                                                       ^
>     [javac]
> V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> o\filterxml\XMLFilterWriterConfig.java:217: interface expected here
>     [javac]     private static abstract class PropertyFilterWriter
> implements XM
> LFilterWriter {
>     [javac]
> ^
>     [javac]
> V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> o\filterxml\XMLFilterWriterConfig.java:313: interface expected here
>     [javac]     private static class AndFilterWriter implements
> XMLFilterWriter
> {
>     [javac]                                                     ^
>     [javac]
> V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> o\filterxml\XMLFilterWriterConfig.java:340: interface expected here
>     [javac]     private static class OrFilterWriter implements
> XMLFilterWriter {
> 
>     [javac]                                                    ^
>     [javac]
> V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> o\filterxml\XMLFilterWriterConfig.java:112: cannot resolve symbol
>     [javac] symbol  : class IsTopLevel
>     [javac] location: interface org.biojava.bio.seq.FeatureFilter
>     [javac]                 FeatureFilter.IsTopLevel.class,
>     [javac]                              ^
>     [javac]
> V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> o\filterxml\XMLFilterWriterConfig.java:185:
> writeFilter(org.biojava.bio.seq.Feat
> ureFilter,org.biojava.utils.xml.XMLWriter) in
> org.biojava.bio.seq.io.filterxml.X
> MLFilterWriter cannot be applied to
> (org.biojava.bio.seq.FeatureFilter,org.bioja
> va.utils.xml.XMLWriter,org.biojava.bio.seq.io.filterxml.XMLFilterWriterConfi
> g)
>     [javac]                 xfw.writeFilter(ff, xw, this);
>     [javac]                    ^
>     [javac]
> V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\progr
> am\das\DASMergeFeatureHolder.java:35: cannot resolve symbol
>     [javac] symbol  : method getMergeMap  ()
>     [javac] location: class
> org.biojava.bio.program.das.DASMergeFeatureHolder
>     [javac]     Map mm = getMergeMap();
>     [javac]                  ^
>     [javac]
> V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\progr
> am\das\DASMergeFeatureHolder.java:48: cannot resolve symbol
>     [javac] symbol  : method getMergeMap  ()
>     [javac] location: class
> org.biojava.bio.program.das.DASMergeFeatureHolder
>     [javac]     Map mm = getMergeMap();
>     [javac]                  ^
>     [javac] Note: Some input files use or override a deprecated API.
>     [javac] Note: Recompile with -deprecation for details.
>     [javac] 8 errors
> 
> BUILD FAILED
> file:V:/dwaring/cvs/biojava-live/build.xml:281: Compile failed; see the
> compiler
>  error output for details.
> 
> Total time: 1 minute 27 seconds
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 


-- 
BioJava Consulting LTD - Support and training for BioJava
http://www.biojava.co.uk

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From gilmanb@genome.wi.mit.edu  Wed Dec 11 02:05:11 2002
From: gilmanb@genome.wi.mit.edu (Brian Gilman)
Date: Tue, 10 Dec 2002 21:05:11 -0500 (EST)
Subject: [Biojava-l] Build failing
In-Reply-To: <3DF68E94.6080003@yahoo.co.uk>
Message-ID: <Pine.OSF.4.10.10212102059210.16350-100000@darwin.wi.mit.edu>

Wow,

	I'm very excited to hear Matthew endorse web services as a
potential direction for the hackathon. As you already know, I've been
tauting/using/running our department off a web services architecture for
three years now. I'd love help to web services enable Bio-Java for the
rest of the world to use! 

	This is right in line for the goals of the OmniGene project,
MOBY, and openBQS. Correct me if I'm wrong Mark and Martin but, I think
there might be some wonderful opportunities to start webservicesifying the
biojava framework. 

	I guess this is a HUGE hand in the air as a volunteer on that
project. I've also got a lot of experience writing web services in Perl,
Python, C++,C# and javascript (mozilla API). So, bombard me with
questions!! I'm not sure I'll be able to answer all of them but, I'll try
:)  

				Best, 

					-B

-----------------------
Brian Gilman <gilmanb@genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617  252 1069 / fax +1 617 252 1902


On Wed, 11 Dec 2002, Matthew Pocock wrote:

> Hi David,
> 
> Is it possible that you have either a truncated or corrupted version of 
> the biojava source tree? I'm sure we've broken the 1k mark for source 
> files now. We're getting better at hiding them away though ;-)
> 
> Try checking the files out again from clean. That may sort things out.
> 
> Matthew
> 
> David Waring wrote:
> > I got the following errors when I tried to build biojava-live
> > 
> > compile:
> >     [javac] Compiling 799 source files to
> > V:\dwaring\cvs\biojava-live\ant-build\
> > classes\main
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:198: interface expected here
> >     [javac]     private static class BlankFilterWriter implements
> > XMLFilterWrite
> > r {
> >     [javac]                                                       ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:217: interface expected here
> >     [javac]     private static abstract class PropertyFilterWriter
> > implements XM
> > LFilterWriter {
> >     [javac]
> > ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:313: interface expected here
> >     [javac]     private static class AndFilterWriter implements
> > XMLFilterWriter
> > {
> >     [javac]                                                     ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:340: interface expected here
> >     [javac]     private static class OrFilterWriter implements
> > XMLFilterWriter {
> > 
> >     [javac]                                                    ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:112: cannot resolve symbol
> >     [javac] symbol  : class IsTopLevel
> >     [javac] location: interface org.biojava.bio.seq.FeatureFilter
> >     [javac]                 FeatureFilter.IsTopLevel.class,
> >     [javac]                              ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:185:
> > writeFilter(org.biojava.bio.seq.Feat
> > ureFilter,org.biojava.utils.xml.XMLWriter) in
> > org.biojava.bio.seq.io.filterxml.X
> > MLFilterWriter cannot be applied to
> > (org.biojava.bio.seq.FeatureFilter,org.bioja
> > va.utils.xml.XMLWriter,org.biojava.bio.seq.io.filterxml.XMLFilterWriterConfi
> > g)
> >     [javac]                 xfw.writeFilter(ff, xw, this);
> >     [javac]                    ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\progr
> > am\das\DASMergeFeatureHolder.java:35: cannot resolve symbol
> >     [javac] symbol  : method getMergeMap  ()
> >     [javac] location: class
> > org.biojava.bio.program.das.DASMergeFeatureHolder
> >     [javac]     Map mm = getMergeMap();
> >     [javac]                  ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\progr
> > am\das\DASMergeFeatureHolder.java:48: cannot resolve symbol
> >     [javac] symbol  : method getMergeMap  ()
> >     [javac] location: class
> > org.biojava.bio.program.das.DASMergeFeatureHolder
> >     [javac]     Map mm = getMergeMap();
> >     [javac]                  ^
> >     [javac] Note: Some input files use or override a deprecated API.
> >     [javac] Note: Recompile with -deprecation for details.
> >     [javac] 8 errors
> > 
> > BUILD FAILED
> > file:V:/dwaring/cvs/biojava-live/build.xml:281: Compile failed; see the
> > compiler
> >  error output for details.
> > 
> > Total time: 1 minute 27 seconds
> > 
> > 
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> 
> 
> -- 
> BioJava Consulting LTD - Support and training for BioJava
> http://www.biojava.co.uk
> 
> __________________________________________________
> Do You Yahoo!?
> Everything you'll ever need on one web page
> from News and Sport to Email and Music Charts
> http://uk.my.yahoo.com
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 


From zren@amylin.com  Wed Dec 11 16:19:14 2002
From: zren@amylin.com (Ren, Zhen)
Date: Wed, 11 Dec 2002 08:19:14 -0800
Subject: [Biojava-l] SymbolParsers in Alphabet
Message-ID: <C527D913CB1168458AE19E0FECDE58DE0D3660@api-exch-1.amylin.com>

Thank you for the suggestion.  I made that work.  Here is another related question: how can  I make my own custom alphabet handle the ambiguity symbol X like what the predefined protein alphabet does?  Thanks.

Zhen

-----Original Message-----
From: Thomas Down [mailto:td2@sanger.ac.uk]
Sent: Monday, December 09, 2002 3:16 PM
To: Ren, Zhen
Cc: biojava-l@biojava.org
Subject: Re: [Biojava-l] SymbolParsers in Alphabet


On Mon, Dec 09, 2002 at 02:07:51PM -0800, Ren, Zhen wrote:
> Hi, there,
> 
> The interface Alphabet has a method
>     public SymbolTokenization getTokenization(java.lang.String name) throws BioException
> 
> Every alphabet should have a SymbolParser under the name 'token' that uses the symbol token characters to translate a string into a SymbolList. Likewise, there should be a SymbolParser under the name 'name' that uses symbol names to identify symbols.
> 
> I'd like to know how I can have these two SymbolParsers under the names 'token' and 'name' incorporated into an alphabet I intend to create by myself.

Hmmm, "SymbolParser" is an old interface name.  Its functionality
has been subsumed into SymbolTokenization, but a few references to
it survived in the javadoc for a while.  I think these are gone
now, if you get the latest CVS version.

Exactly how tokenizations are handled depends on the Alphabet
implementation.  If you write your own Alphabet, you can, of
coure, write a getTokenization method yourself.

If you're construction a SimpleAlphabet, getTokenization("name") is handled
automatically for you.  To add extra tokenizations, you can do
something like:

     CharacterTokenization toke = new CharacterTokenization(
         myAlphabet,
         false
     );
     toke.bindSymbol(symbol0, '0');
     toke.bindSymbol(symbol1, '1');
     myAlphabet.putTokenization("token", toke);

Hope this helps,

     Thomas.


From td2@sanger.ac.uk  Wed Dec 11 16:47:29 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Wed, 11 Dec 2002 16:47:29 +0000
Subject: [Biojava-l] SymbolParsers in Alphabet
In-Reply-To: <C527D913CB1168458AE19E0FECDE58DE0D3660@api-exch-1.amylin.com>
References: <C527D913CB1168458AE19E0FECDE58DE0D3660@api-exch-1.amylin.com>
Message-ID: <20021211164729.GM186451@jabba.sanger.ac.uk>

On Wed, Dec 11, 2002 at 08:19:14AM -0800, Ren, Zhen wrote:
> Thank you for the suggestion.  I made that work.  Here is another related question: how can  I make my own custom alphabet handle the ambiguity symbol X like what the predefined protein alphabet does?  Thanks.

You can bind a token to any ambiguity symbol:

   Set ambiSet = new HashSet();
   ambiSet.add(symbol1);
   ambiSet.add(symbol2);
   ambiSymbol = myAlphabet.getAmbiguity(ambiSet);
   toke.bindSymbol(ambiSymbol, 'Y');

If all you care about it the symbol which matches *all*
symbols in the alpabet (equivalnet to 'n' in DNA and 'X' in
protein), you can just do:

   toke.bindSymbol(
       AlphabetManager.getAllAmbiguitySymbol(myAlphabet),
       'X'
   );

For non-tiny alphabets, you probably won't want to define
a token for every possible ambiguity symbol.  In recent
CVS versions, if you try to retreive the token for an
unrecognized ambigutiy symbol, it will default to the token
used for the all-ambiguity symbol.

    Thomas.

From zren@amylin.com  Wed Dec 11 17:12:28 2002
From: zren@amylin.com (Ren, Zhen)
Date: Wed, 11 Dec 2002 09:12:28 -0800
Subject: [Biojava-l] SymbolParsers in Alphabet
Message-ID: <C527D913CB1168458AE19E0FECDE58DE8E9CB4@api-exch-1.amylin.com>

Great!  Thanks.

-----Original Message-----
From: Thomas Down [mailto:td2@sanger.ac.uk]
Sent: Wednesday, December 11, 2002 8:47 AM
To: Ren, Zhen
Cc: biojava-l@biojava.org
Subject: Re: [Biojava-l] SymbolParsers in Alphabet


On Wed, Dec 11, 2002 at 08:19:14AM -0800, Ren, Zhen wrote:
> Thank you for the suggestion.  I made that work.  Here is another related question: how can  I make my own custom alphabet handle the ambiguity symbol X like what the predefined protein alphabet does?  Thanks.

You can bind a token to any ambiguity symbol:

   Set ambiSet = new HashSet();
   ambiSet.add(symbol1);
   ambiSet.add(symbol2);
   ambiSymbol = myAlphabet.getAmbiguity(ambiSet);
   toke.bindSymbol(ambiSymbol, 'Y');

If all you care about it the symbol which matches *all*
symbols in the alpabet (equivalnet to 'n' in DNA and 'X' in
protein), you can just do:

   toke.bindSymbol(
       AlphabetManager.getAllAmbiguitySymbol(myAlphabet),
       'X'
   );

For non-tiny alphabets, you probably won't want to define
a token for every possible ambiguity symbol.  In recent
CVS versions, if you try to retreive the token for an
unrecognized ambigutiy symbol, it will default to the token
used for the all-ambiguity symbol.

    Thomas.


From hra@cs.uga.edu  Wed Dec 11 17:41:56 2002
From: hra@cs.uga.edu (Hamid Arabnia)
Date: Wed, 11 Dec 2002 12:41:56 -0500 (EST)
Subject: [Biojava-l] Call For Papers: 2003 Int'l MultiConference in CS + CE + Math - Las Vegas, June 23, 2003
Message-ID: <200212111741.MAA26298@apollo.cs.uga.edu>

                 C A L L   F O R   P A P E R S

    The 2003 International Multiconference in Computer Science
                   and Computer Engineering
                 (15 Joint Int'l Conferences)

            Monte Carlo Resort, Las Vegas, Nevada, USA
                       June 23-26, 2003

Dear Colleagues:

You are invited to submit a draft paper (see instructions below)
and/or a proposal to organize a technical session/workshop.  All
accepted papers will be published in the respective conference
proceedings.  The names of technical session/workshop organizers/chairs
will appear on the cover of the proceedings/books as Associate Editors.

Any help in distributing this announcement would be most appreciated.

The 2003 International Multiconference in Computer Science & Computer
Engineering is composed of the following 15 conferences - each event is
the premier conference for presentation of advances in its respective
subject.  All conferences will be held simultaneously (same location &
dates: June 23-26, 2003, Las Vegas, USA):

1.  The 2003 International Conference on Parallel and Distributed
    Processing Techniques and Applications (PDPTA'03)

2.  The 2003 International Conference on Imaging Science,
    Systems, and Technology (CISST'03)

3.  The 2003 International Conference on Artificial Intelligence
    (IC-AI'03)

4.  The 2003 International Conference on Internet Computing (IC'03)

5.  The 2003 International Conference on Embedded Systems and
    Applications (ESA'03)

6.  The 2003 International Conference on Wireless Networks (ICWN'03)

7.  The 2003 International Conference on Machine Learning; Models,
    Technologies and Applications (MLMTA)

8.  The 2003 International Conference on Mathematics and
    Engineering Techniques in Medicine and Biological Sciences
    (METMBS'03)

9.  The 2003 International Conference on Communications in
    Computing (CIC'03)

10. The 2003 International Conference on Engineering of
    Reconfigurable Systems and Algorithms (ERSA'03)

11. The 2003 International Conference on VLSI (VLSI'03)

12. The 2003 International Conference on Information and
    Knowledge Engineering (IKE'03)

13. The 2003 International Conference on Software Engineering
    Research and Practice (SERP'03)

14. The 2003 International Conference on Security and Management
    (SAM'03)

15. The First International Conference on Web Services (ICWS'03)

(a link to each conference's URL can be found at
http://www.ashland.edu/~iajwa/conferences)

Please regard this announcement as General Guidelines.
You are requested to send your submission to the Multiconference
chair whose address appears below (The Chair may be forwarding
the papers to respective conference chairs/committees).


CONFERENCES CONTACT:

    H. R. Arabnia, Ph.D.
    Chair, The 2003 Int'l Multiconference in CS & CE
    The University of Georgia
    Department of Computer Science
    415 Graduate Studies Research Center
    Athens, Georgia 30602-7404, U.S.A.

    Tel: (706) 542-3480
    Fax: (706) 542-2966
    email: hra@cs.uga.edu


HISTORY:

    The International Multiconference in Computer Science & Computer
    Engineering is a major annual international research event.
    The last Multiconference attracted over 1,550 computer science
    and Engineering researchers from 72 countries.  It is anticipated
    that The 2003 Int'l Multiconference will attract about 2000
    participants.  The 2003 event is composed of 15 (planned) major
    conferences - attendees will have full access to all 15
    conferences' sessions & tracks.


SUBMISSION OF PAPERS:

    Prospective authors are invited to submit three copies
    of their draft paper (about 5 pages - single space, font size
    of 10 to 12) to H. R. Arabnia by the due date (who may be
    forwarding the papers to respective conference chairs/committees).
    E-mail & Fax submissions are also acceptable.

    The length of the Camera-Ready papers (if accepted) will be
    limited to 7 (IEEE style) pages.  Papers must not have been
    previously published or currently submitted for publication
    elsewhere.  The first page of the draft paper should include:
    title of the paper, name, affiliation, postal address, E-mail
    address, telephone number, & Fax number for each author.  The first
    page should also include the name of the author who will be
    presenting the paper (if accepted) & a maximum of 5 keywords.


EVALUATION PROCESS:

    Papers will be evaluated for originality, significance, clarity, &
    soundness.  Each paper will be refereed by two researchers in the
    topical area.  The Camera-Ready papers will be reviewed by one person.


PUBLICATION:

    The conference proceedings will be published by CSREA Press (ISBN)
    in hardcopy/book.  The proceedings will be available at the conference.
    Some accepted papers will also be considered for journal publication
    (soon after the conference).  (In addition to the hardcopy, it is
    also planned to publish the papers on a CD.) All conference
    proceedings published by CSREA Press are considered for inclusion
    in major database indexes that are designed to provide easy access
    to the current literature of the sciences (database examples: ISI
    Thomson Scientific, IEE INSPEC, ...).


ORGANIZERS/SPONSORS:

    A number of university faculty members & their staff in cooperation
    with the Monte Carlo Resort (Conference Division, Las Vegas ), will
    be organizing the conferences.  The conferences will be sponsored by
    World Academy of Sciences & co-sponsored by Computer Science Research,
    Education, & Applications Press (CSREA: USA Federal EIN # 58-2171953)
    together with research centers, international associations,
    international research groups, & developers of high-performance
    machines & systems.  The complete list of sponsors & co-sponsors
    will be available at a later time.
    (Previous conferences' sponsors included: CSREA, the National
    Supercomputing Center for Energy & the Environment - DOE, The
    Int'l Association for Mathematics & Computers in Simulation, The
    Int'l Technology Institute (ITI), Java High Performance Computing
    research group, World Scientific & Engineering Society, Sundance
    Digital Signal Processing Inc., Computer Vision R&A Tech.,
    Hewlett-Packard Inc., Korea Information Processing Society (KIPS),
    Society of Japan (SIGMPS/IPSJ), IEEE, a number of publishers of
    books & journals, ...)


LOCATION OF CONFERENCES:

    The conferences will be held in the Monte Carlo Resort hotel
    Las Vegas, Nevada, USA (with any overflows at other near-by
    hotels).  The Monte Carlo Resort is a mega hotel with excellent
    conference facilities & over 3,000 rooms.  The hotel is minutes
    from the Las Vegas airport with 24-hour shuttle service to & from
    the airport.  This hotel has many vacation & recreational
    attractions, including: waterfalls, casino, spa, pools &
    kiddie pools, sunning decks, Easy River water ride, wave pool
    with cascades, lighted tennis courts, health spa (with workout
    equipment, whirlpool, sauna, ...), arcade virtual reality game
    rooms, nightly shows, snack bars, a number of restaurants,
    shopping area, bars, ...  Many of these attractions are open 24
    hours a day & most are suitable for families & children.  The
    negotiated hotel's room rate for conference attendees is very
    reasonable (79USD + tax) per night (no extra charge for double
    occupancy) for the duration of the conference.
    The hotel is within walking distance from most other
    Las Vegas attractions (major shopping areas, recreational
    destinations, fine dining & night clubs, free street
    shows, ...).


IMPORTANT DATES: (Some tracks have different deadlines - check the
web site)

    Feb.  17, 2003 (Monday):    Draft papers (about 5 pages) due
    March 21, 2003 (Friday):    Notification of acceptance
    April 22, 2003 (Tuesday):   Camera-Ready papers & Prereg. due
    June 23-26, 2003:           All 15 Int'l Conferences

    Proposals to organize technical sessions should be submitted
    as soon as possible.


PROPOSAL FOR ORGANIZING TECHNICAL SESSIONS:

    Each technical session will have at least 6 papers.  The session
    chairs will be responsible for all aspects of their sessions;
    including, soliciting papers, reviewing, selecting, ...  The
    names of session chairs will appear as Associate Editors on the
    cover of the conference proceedings.  After the conference, some
    sessions will be considered for publication in relevant journals
    as Special Issues with the session proposer as the Guest Editor
    of the journal.
    Proposals to organize technical sessions should include the
    following information: name & address (+ E-mail) of proposer,
    title of session, a 100-word description of the topic of the
    session, & a short description on how the session will be
    advertised (in most cases, session proposers solicit papers
    from colleagues & researchers whose work is known to the session
    proposer).  Mail your proposal to H. R. Arabnia; E-mail
    submissions are preferred.


MEMBERS OF PROGRAM & ORGANIZING COMMITTEES:

    The Program Committees are currently being formed.  Those
    interested in joining the Program Committees should email
    H. R. Arabnia (hra@cs.uga.edu) the following information: Name,
    affiliation & position, complete mailing address, email address,
    tel/fax numbers, name of the conference offering to help with, a
    short biography together with research interests.


EXHIBITION & ROBOTICS COMPETITION:

    An exhibition is planned for the duration of the conferences.
    Interested parties should contact H. R. Arabnia (address is
    given below).  All exhibitors will be considered to be the
    co-sponsors of the conferences.

    There will also be a Robotics Competition (refer to the following
    url for regulations and more information:
    www.cs.uga.edu/~potter/robotics/RoboticsCompetition.htm


TOPICAL SCOPE FOR EACH CONFERENCE APPEARS BELOW (the list of topics
    that appear below should be regarded as a partial list of topics.
    each conference considers papers in ALL ASPECTS of its domain.)

SCOPE OF PDPTA'03 (Topics of interest include, but are not limited to):
    (The 2003 Int'l Conference on Parallel & Distributed Processing
    Techniques and Applications)

  O  Parallel/Distributed applications
  O  Parallel/Distributed architectures
  O  Building block processors
  O  Networks & Interconnection networks
  O  Reliability & fault-tolerance
  O  Performance analysis, evaluation, prediction, ...
  O  Real-time & embedded systems
  O  Parallel/Distributed algorithms
  O  Mobile computation & communication
  O  Object Oriented Technology & related issues
  O  Multimedia Communications, Systems, & Applications
  O  Software tools & environments for parallel & distributed platforms
  O  High-performance computing in Computational Science
  O  Information & data fusion
  O  Petri Nets: theory, analysis, tools & applications
  O  Web-based simulation & computing
  O  Education: parallel & distributed processing in
     computer science curriculum
  O  Recent history (last decade) of parallel/distributed
     processing & what to expect in the next decade: New Horizons
  O  Other aspects & applications relating to high-performance
     computations


SCOPE OF CISST'03 (Topics of interest include, but are not limited to):
    (The 2003 Int'l Conference on Imaging Science, Systems, & Technology)

  O  Image generation, acquisition, & processing
  O  Image display techniques
  O  Image data structures & databases
  O  Convergence of imaging media (video & computer)
  O  Virtual reality
  O  Image compression, coding, & encryption
  O  Multimedia / Applications
  O  Tools for multimedia production & services
  O  Digital imaging for film & television
  O  Visualization
  O  Scene & object modeling
  O  Knowledge acquisition
  O  Visual inspection
  O  Document image understanding
  O  Image algebra
  O  Optical image processing systems
  O  Mathematical morphology
  O  Architecture of imaging & vision systems (including
     parallel architectures & algorithms)
  O  Neural network techniques & fuzzy logic
  O  Performance analysis & evaluation
  O  Software tools & environments for imaging
  O  Animation
  O  Geometric modeling & Fractals
  O  CAD/CAM systems
  O  Rendering techniques
  O  Applications including: medicine, robotic, GIS,
     remote sensing, industrial inspection (or machine vision),
     nondestructive evaluation (or NDE), ...
  O  Multi-resolution & multi-spectral image processing
  O  Image sequence processing
  O  Information fusion
  O  Other aspects & applications relating to imaging science


SCOPE OF IC-AI'03 (Topics of interest include, but are not limited to):
   (The 2003 Int'l Conference on Artificial Intelligence)

  O.  Intelligent Information Systems
  O.  Intelligent Software Engineering
  O.  Intelligent Agents
  O.  Intelligent Networks
  O.  Intelligent Databases
  O.  Brain Models
  O.  Evolutionary Algorithms
  O.  Data mining
  O.  Reasoning Strategies
  O.  Automated Problem Solving
  O.  Distributed AI Algorithms & Techniques
  O.  Distributed AI Systems & Architectures
  O.  Expert Systems
  O.  Fuzzy Logic
  O.  Genetic Algorithms
  O.  Heuristic Searching
  O.  Knowledge Acquisition
  O.  Knowledge Discovery
  O.  Knowledge Representation
  O.  Knowledge-Intensive Problem Solving Techniques
  O.  Languages & Programming Techniques for AI
  O.  Software Tools for AI
  O.  Natural Language Processing
  O.  Neural Networks & Applications
  O.  Multisource Information Fusion: Theory & Applications
  O.  Multisource-Multisensor Data Fusion
  O.  Learning & Adaptive Sensor Fusion
  O.  Multisensor Data Fusion Using Neural & Fuzzy Techniques
  O.  Integration of AI with other Technologies
  O.  Evaluation of AI Tools
  O.  Social Impact of AI
  O.  Applications: Computer Vision, Signal Processing, Military,
      Surveillance, Robotics, Medicine, Pattern Recognition,
      Face Recognition, Finger Print Recognition, Finance & Marketing,
      Stock Market, Education, Emerging Applications


SCOPE OF IC'03 (Topics of interest include, but are not limited to):
    (The 2003 Int'l Conference on Internet Computing)

  O  Internet Security 
  O  Internet Applications & Appliances 
  O  Performance Evaluation of the Internet 
  O  Resource Management & Location 
  O  Design & Analysis of Internet Protocols 
  O  Web based computing 
  O  Network Management 
  O  Network Architectures 
  O  Network Computing 
  O  Network Operating Systems 
  O  Quality of Service 
  O  Wide Area Consistency 
  O  Electronic Commerce 
  O  The WWW & Intranets 
  O  Metacomputing 
  O  Grid based Computing & Tools 
  O  Languages for Distributed Programming 
  O  Cooperative Applications 
  O  Tele-Medical & other applications 
  O  Internet Telephony
  O  Mobile Computing
  O  Educational Applications
  O  Digital Libraries/Digital Image Collections
  O  Web Interfaces to Databases
  O  User-interface/Multimedia/Video/Audio/User Interaction
  O  Markup Languages/HTML/XML/VRML
  O  Java Applications on Internet
  O  Alternative Web lifestyles, role-playing, chat, ...
  O  Caching Algorithms for the Internet
  O  Traffic Models & Statistics
  O  Server Space/Web Server Performance
  O  Web Monitoring
  O  Web Documents Management
  O  Web Site Design & Coordination
  O  Other aspects & applications relating to internet-based computing


SCOPE OF ESA'03 (Topics of interest include, but are not limited to):
    (The 2003 Int'l Conference on Embedded Systems and Applications)

  O  Object Oriented Technologies for Embedded Systems
  O  Assemblers & Cross Assemblers
  O  Bluetooth & Embedded Systems
  O  Languages for Embedded Systems
  O  Memory Management Issues in Embedded Systems
  O  Communication Tools
  O  System-on-a-Chip Technologies
  O  Embedded Programming Issues
  O  Designing for Low-Power Operations
  O  Development Tools
  O  Distributed Real-Time Systems
  O  Embedded Processors
  O  Next Generation of Handheld Devices
  O  Embedded Programming Standards
  O  Testing Techniques
  O  Embedded Microcontrollers
  O  Emulators & Simulators
  O  Flash Memory Chips
  O  Managing Embedded Projects
  O  Embedded Engineering
  O  Multitasking Design for Embedded Systems
  O  Embedded Internet Tools
  O  Optimization Issues
  O  Power Management Circuits
  O  Real-Time Kernels
  O  Real-Time Operating Systems
  O  Safety Critical Systems
  O  Signal Processors
  O  System Design Tools
  O  Task Scheduling Techniques
  O  Compilers
  O  DSPs
  O  Debuggers


SCOPE OF ICWN'03 (Topics of interest include, but are not limited to):
   (The 2003 Int'l Conference on Wireless Networks)

  O  Mobile wireless QoS, radio resource management
  O  Mobile wireless Internet, IPv6
  O  Heterogeneous wireless networks, radio access networks
  O  OFDM
  O  W-CDMA, cdma2000, TD-SCDMA
  O  MIMO, adaptive antenna
  O  Software-defined radio, reconfigurable radio networks
  O  Wireless security
  O  Wireless applications, mobile e-commerce, wireless multimedia
  O  Modeling, simulation, and measurement of wireless systems
  O  Satellite-based systems
  O  Broadcast networks
  O  High altitude platform
  O  GPS, location-based service
  O  Mobile agents
  O  Wireless & mobile applications
  O  Multiple access
  O  Routing, multicasting, ...
  O  Resource management, wireless QoS
  O  Mobile Internet
  O  Transport-layer issues
  O  Wireless security
  O  Wireless network architectures
  O  Mobile computing
  O  Modeling, simulation, & measurement of wireless systems/networks
  O  Ad hoc networks, sensor networks, ...
  O  4G, 3.5G, and 3G wireless systems
  O  Personal area networks, body wireless networks, Bluetooth
  O  Wireless sensor networks
  O  Coding & modulation
  O  Multi-user detection
  O  Power management & control, low-power protocols
  O  OFDM
  O  Wireless IP networks, interworking
  O  Wireless multimedia, QoS adaptation
  O  WAP, mobile e-commerce
  O  Location-based service, GPS
  O  Distributed algorithms for wireless networks


SCOPE OF MLMTA'03 (Topics of interest include, but are not limited to):
   (The 2003 Int'l Conference on Machine Learning; Models, Technologies
   & Applications)

  O  Artificial Neural Networks & Learning
  O  Fuzzy Logic
  O  Fusion & Learning
  O  Information Retrieval & Data Mining
  O  Inductive Learning & Applications
  O  Knowledge Representation & Management
  O  Knowledge Acquisition & Discovery Techniques
  O  Machine Learning in Problem Solving
  O  Statistical Methods in Learning
  O  Evolutionary Algorithms
  O  Bayesian-Based Methodologies
  O  Reinforcement Learning Methods
  O  Grammatical Inference
  O  Learning Models
  O  Multi-Agent Learning
  O  Cognitive Modeling
  O  Hybrid Techniques
  O  Hierarchical Learning Models
  O  Collaborative Filtering
  O  Case-Based Reasoning
  O  Semantic Indexing
  O  Natural Language Processing
  O  Machine Translation
  O  Markov Decision Processes (including Semi-Markov DM)
  O  ODE Methods & Machine Learning
  O  Multi-Criteria Reinforcement Learning
  O  Temporal Abstractions
  O  Relational Learning Models
  O  Feature Selection & Classification
  O  Speedup Learning Techniques
  O  Computational Needs of Learning Models
  O  Learning by Examples
  O  Formal Learning Methods
  O  Graph-Based Learning
  O  Theory Refinement Methodologies
  O  Probabilistic Reasoning
  O  Decision Trees
  O  Learning Based on Adaptive Techniques
  O  Learning Topological Maps
  O  Verification Models
  O  Mobile Robotics
  O  Learning in Planning
  O  Query Learning
  O  Active Learning
  O  Memory-Based Learning
  O  Instance-Based Learning
  O  Self-Adaptation Techniques
  O  Requirements Models
  O  Machine Learning & Software Engineering
  O  Game Playing (Chess, ...)
  O  Performance Analysis
  O  Transformation-Based Learning
  O  Simulated Annealing & Learning
  O  Life-Long Learning
  O  Q-Learning
  O  Predictive Learning Models
  O  Text Categorization & Classification
  O  Machine Learning Applications (Medicine, Games, Biology,
     Industrial Applications, Robotics, Security & Terrorism
     Prevention, ...)


SCOPE OF METMBS'03 (Topics of interest include, but are not limited to):
   (The 2003 Int'l Conference on Mathematics & Engineering Techniques in
   Medicine & Biological Sciences)

  O  Bioinformatics
  O  Cheminformatics
  O  Data mining in medicine & biological sciences
  O  Pattern recognition in medicine & biological sciences
  O  Signal processing in medicine & biological sciences
  O  Image processing in medicine & biological sciences
  O  Medical decision-making
  O  Medical Physics
  O  Biomedical Engineering
  O  Biomedical Electronics
  O  Biosignal interpretation
  O  Any application of computers in Medicine & biological sciences
     (protein structure-function analysis, drug & protein design,
     molecular modeling & simulation, ...)
  O  Application of information technology in biomedicine
     (e.g. medical database management, information retrieval &
     use of computers in hospitals)
  O  Application of Computational Intelligence (artificial neural
     networks, fuzzy logic, & evolutionary computing) in medicine
     & biological sciences
  O  Medical & bio-computing
  O  High-performance computing as applied to natural & medical sciences
  O  Computer-based medical systems (automation in medicine, ...)
  O  Recent history (last ten years) of Mathematics & engineering
     techniques in medicine & biological sciences, & what to expect
     during the next decade; New horizons. Review articles ...
  O  Other aspects & applications relating to technological
     advancements in medicine & biological sciences


SCOPE OF CIC'03 (Topics of interest include, but are not limited to):
    (The 2003 Int'l Conference on Communications in Computing)

  O  High Performance Applications (e.g. scientific, commercial, ...)
  O  Distributed Systems & Advanced Applications (e.g. multimedia,
     cooperative systems)
  O  Grid computing
  O  Scalable & Interoperable Systems & Associated Standards
  O  Software Systems (e.g. operating system support, middleware, ...)
  O  Architecture (e.g. VLSI, SIMD, MIMD, vector, systolic,
     reconfigurable, ...)
  O  Interconnection networks (e.g. bus-based, optical)
  O  ATM based networks
  O  Communications (e.g. routing, wireless, mobile)
  O  Visualization (e.g. scientific visualization, debugging &
     load balancing tools)
  O  Photonics & Optical Computing
  O  Performance Issues (e.g. benchmarks, performance measurement,
     evaluation & prediction)
  O  Modeling & Simulation of High Performance Systems
  O  Advanced Compilation Techniques (e.g. parallelizing compilers)
  O  Programming Languages for Parallel & other High Performance
     Computing
  O  Parallel/Distributed/Vector Algorithms
  O  Reliability & Fault Tolerance
  O  Embedded & Real Time Systems
  O  Digital Signal Processing
  O  Neural Computing, Genetic Algorithms
  O  Issues in High Performance Computing (e.g. evolving paradigms,
  O  Internet & web based processing, E-commerce, telecommunication
     network, cluster-based computing

SCOPE OF ERSA'03 (Topics of interest include, but are not limited to):
    (The 2003 Int'l Conference on Engineering of Reconfigurable Systems
    &  Algorithms)

  O  Theory, Mapping & Parallelization:
     Theoretical models of computing in space-time & adaptive
     computing. Mapping algorithms into hardware & synthesis
     of regular arrays. Parallelization & (space-time) partitioning
     of algorithms. System architectures using configurable computing
     platform. Newly developed algorithms for efficient
     implementation on reconfigurable systems.
  O  Software, CAD & Operating Systems:
     CAD, specification, partitioning & verification. Hardware
     compilation, hardware/software codesign, developing correct
     circuits. High & low-level languages & compilers, design
     environments. Operating systems & run-time reconfiguring.
     IP-based & object oriented models & mapping methods.
  O  Adaptive Hardware Architectures:
     Adaptive & dynamically reconfigurable systems. Reconfigurable
     processor architectures. Complex systems using reconfigurable
     processors. Application-tailored reconfigurable Systems-on-Chip.
     Low power systems on reconfigurable platform.
  O  Applications:
     Wireless communication systems. Multimedia & virtual reality.
     Automotive industry. Security systems. Classical image &
     signal processing.
  O  Focus Sessions:
     High-level Synthesis of Reconfigurable Systems.
     Operating System for Reconfigurable Hardware.
     Java-based Environment for Reconfigurable Systems.
     Configurable Computing Architectures & Hardware.
     Configurable Systems-on-Chip.
     Emerging Devices for Reconfigurable Systems.
     Low Power Systems Using FPGAs.
     Reconfigurable Floating Point Processing.
     Software Defined Radio.
     Custom Computing Machines for Image Processing.


SCOPE OF VLSI'03 (Topics of interest include, but are not limited to):
   (The 2003 Int'l Conference on VLSI)

  O  Quantum Computing
  O  Nanoelectronics
  O  Molecular & Biological Computing
  O  MEMS
  O  Circuits & Systems
  O  Novel Design & Methodologies
  O  System-on-a-Chip: Design & Methodology
  O  Low Power VLSI System Design
  O  Complexity Issues
  O  Simulation Tools
  O  Algorithm Design Approaches (AI, Genetic, ...)
  O  High-Level Design Methodologies
  O  ASIC Architectures
  O  Reconfigurable Systems Design
  O  Novel Devices & Circuits
  O  Emerging Trends
  O  High-Performance Circuits
  O  Reusable Architectures
  O  Test & Verification
  O  Synthesis
  O  Mixed-Signal Design & Analysis
  O  Electrical/Packaging Designs & Co-Designs
  O  Applications (all applications will be considered)


SCOPE OF IKE'03 (Topics of interest include, but are not limited to):
    (The 2003 Int'l Conference on Information and Knowledge Engineering)

  O  Client-Server Architectures
  O  Information & Knowledge Engineering
  O  Mobile Agents
  O  Web-Based Design & Development
  O  Knowledge & Information Management Techniques
  O  Data Mining Techniques
  O  Database Engineering & Systems
  O  Knowledge Delivery Methods
  O  Data Security
  O  Knowledge Life Cycle
  O  Business Architectures
  O  Formal & Visual Specification Languages
  O  Software Tools & Support
  O  Performance Evaluation Techniques
  O  Knowledge-Based Systems
  O  Clustering Techniques
  O  Web Technology & Systems
  O  Dataweb Models & Systems
  O  Data Warehouses
  O  Workflow Management
  O  Knowledge & Information Extraction & Discovery Techniques
  O  Service Recovery
  O  Large-Scale Information Processing Methods
  O  Data & Knowledge Processing
  O  Database Engineering & Systems (Distributed, Video, ...)
  O  Information Quality (Quality Metrics)
  O  E-Libraries (Digital Libraries)
  O  Intelligent Knowledge-Based Systems
  O  Agent-Based Techniques & Systems
  O  Content Management
  O  Information Reliability & Security
  O  Hardware Architectures
  O  Modeling & Simulation
  O  Decision Support Systems
  O  Expert Systems
  O  Aspect-Oriented Programming
  O  Re-usability of Software/Knowledge/Information
  O  Privacy Issues
  O  Interoperability Issues
  O  Object-Oriented Modeling & Systems
  O  Knowledge Classification Tools
  O  Case-Based Reasoning
  O  Bayesian Techniques
  O  Managing Copyright Laws
  O  Digital Watermarking
  O  Data/Information/Knowledge Models
  O  Digital Typography
  O  Electronic Publishing
  O  Data Fusion
  O  Applications (Image Processing, OCR, Artistic Imaging,
     e-Commerce, Multimedia, Business, GIS, Banking, ...)


SCOPE OF SERP'03 (Topics of interest include, but are not limited to):
   (The 2003 Int'l Conference on Software Engineering Research and Practice)

  O  Software architectures
  O  Object-Oriented technology
  O  Measurement, metrics & analysis
  O  Survivable systems
  O  Requirements engineering
  O  Reverse engineering
  O  Software domain modeling
  O  Software process modeling
  O  Workflow - Computer Supported Cooperative Work (CSCW)
  O  Project management issues
  O  Distributed & parallel systems
  O  Legal issues & standards
  O  Configuration management (issues & tools)
  O  Automated software specification
  O  Automated software design & synthesis
  O  Theoretic approaches (formal methods, graph, ...)
  O  Domain modeling & meta-modeling
  O  Evolution & maintenance
  O  Knowledge acquisition
  O  Reflection & metadata methodologies
  O  Artificial intelligence approaches to Software Engineering
  O  Automated software engineering
  O  Component-based engineering
  O  Data mining
  O  Interoperability
  O  Intelligent CASE tools
  O  Multimedia in software engineering
  O  Hypermedia
  O  Software reuse
  O  Verification, validation & quality assurance
  O  Performance critical systems
  O  Engineering practices
  O  Programming languages
  O  Program understanding issues
  O  Education (software engineering curriculum design)
  O  Software engineering versus Systems engineering
  O  Software documentation
  O  Technology adoption
  O  Human-Computer Interaction (HCI)
  O  Architecture tradeoff analysis
  O  Novel software tools & environments


SCOPE OF SAM'03 (Topics of interest include, but are not limited to):
    (The 2003 Int'l Conference on Security and Management)

  O  Security Protocols
  O  Mobility Management
  O  Security Algorithms
  O  Location Management
  O  QoS Management
  O  Key Management Techniques
  O  Security in E-commerce & M-commerce
  O  Security Policies
  O  Resource Management
  O  Mobile Network Security
  O  Channel Management
  O  AAA
  O  Encryption
  O  Security in Mobile IPv4/IPv6
  O  VPN
  O  Firewall
  O  IDS (Intrusion Detection System)
  O  Digital contents copyright protection techniques
  O  Watermarking
  O  Secure OS
  O  Honeypot
  O  Virus Issues (Detection, Prevention, ...)
  O  Tracing Techniques in Internet
  O  Active Networks
  O  Security in CDN (Contents Distribution Networks)
  O  Hacking Techniques & Related Issues
  O  Security in GRID
  O  Biological Security Technologies
  O  Surveillance Technologies
  O  High-Tech Systems at Airports
  O  Face Recognition Systems
  O  Signature Recognition Systems
  O  Network Management
  O  System Management
  O  Network Security Management
  O  Management in Network Equipments
  O  SAN (Storage Area Networks) Management
  O  GRID Middleware
  O  GRID Applications
  O  GRID Networks
  O  Security for Protocol Management
  O  Management Protocol (SNMP, CMIP, etc)


SCOPE OF ICWS'03 (Topics of interest include, but are not limited to):
    (The The First International Conference on Web Services)

  O  Web Services architecture
  O  Web Services security
  O  Frameworks for building Web Service applications
  O  Composite Web Service creation and enabling infrastructures
  O  Web Services discovery
  O  Resource management for web services
  O  Solution Management for Web Services
  O  Dynamic invocation mechanisms for Web Services
  O  Quality of service for Web Services
  O  Web Services modeling
  O  UDDI enhancements
  O  SOAP enhancements
  O  Case studies for Web Services
  O  E-Commerce applications using Web Services
  O  Grid based Web Services applications (e.g. OGSA)
  O  Business process integration and management using Web Services
  O  Multimedia applications using Web Services
  O  Communication applications using Web Services
  O  Interactive TV applications using Web Services

From dwaring@u.washington.edu  Wed Dec 11 18:42:46 2002
From: dwaring@u.washington.edu (David Waring)
Date: Wed, 11 Dec 2002 10:42:46 -0800
Subject: [Biojava-l] Build failing
In-Reply-To: <200212110103.23111.david.huen@ntlworld.com>
Message-ID: <HCEOLHNOIDOJLKLGOAFMMEGACIAA.dwaring@u.washington.edu>

Thanks ant clean worked!

> -----Original Message-----
> From: David Huen [mailto:david.huen@ntlworld.com]
> Sent: Tuesday, December 10, 2002 5:03 PM
> To: David Waring
> Subject: Re: [Biojava-l] Build failing
> 
> 
> On Wednesday 11 Dec 2002 12:20 am, David Waring wrote:
> 
> I've just done an update which got me these files but mine 
> compiles fine.  
> You might consider a cvs update -d and an ant clean before recompiling 
> perhaps?
> 
> Regards,
> David
> 
> > I got the following errors when I tried to build biojava-live
> >
> > compile:
> >     [javac] Compiling 799 source files to
> > V:\dwaring\cvs\biojava-live\ant-build\
> > classes\main
> 
> You seem to be copying rather fewer files than me here: i have 
> 936 at this 
> point.  Mine is slightly customised but not to this extent.
> 
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:198: interface expected here
> >     [javac]     private static class BlankFilterWriter implements
> > XMLFilterWrite
> > r {
> >     [javac]                                                       ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:217: interface expected here
> >     [javac]     private static abstract class PropertyFilterWriter
> > implements XM
> > LFilterWriter {
> >     [javac]
> > ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:313: interface expected here
> >     [javac]     private static class AndFilterWriter implements
> > XMLFilterWriter
> > {
> >     [javac]                                                     ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:340: interface expected here
> >     [javac]     private static class OrFilterWriter implements
> > XMLFilterWriter {
> >
> >     [javac]                                                    ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:112: cannot resolve symbol
> >     [javac] symbol  : class IsTopLevel
> >     [javac] location: interface org.biojava.bio.seq.FeatureFilter
> >     [javac]                 FeatureFilter.IsTopLevel.class,
> >     [javac]                              ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:185:
> > writeFilter(org.biojava.bio.seq.Feat
> > ureFilter,org.biojava.utils.xml.XMLWriter) in
> > org.biojava.bio.seq.io.filterxml.X
> > MLFilterWriter cannot be applied to
> > (org.biojava.bio.seq.FeatureFilter,org.bioja
> > 
> va.utils.xml.XMLWriter,org.biojava.bio.seq.io.filterxml.XMLFilterWriterCo
> >nfi g)
> >     [javac]                 xfw.writeFilter(ff, xw, this);
> >     [javac]                    ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\progr
> > am\das\DASMergeFeatureHolder.java:35: cannot resolve symbol
> >     [javac] symbol  : method getMergeMap  ()
> >     [javac] location: class
> > org.biojava.bio.program.das.DASMergeFeatureHolder
> >     [javac]     Map mm = getMergeMap();
> >     [javac]                  ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\progr
> > am\das\DASMergeFeatureHolder.java:48: cannot resolve symbol
> >     [javac] symbol  : method getMergeMap  ()
> >     [javac] location: class
> > org.biojava.bio.program.das.DASMergeFeatureHolder
> >     [javac]     Map mm = getMergeMap();
> >     [javac]                  ^
> >     [javac] Note: Some input files use or override a deprecated API.
> >     [javac] Note: Recompile with -deprecation for details.
> >     [javac] 8 errors
> >
> > BUILD FAILED
> > file:V:/dwaring/cvs/biojava-live/build.xml:281: Compile failed; see the
> > compiler
> >  error output for details.
> >
> > Total time: 1 minute 27 seconds
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> 

From andreas.matern@lbri.lionbioscience.com  Wed Dec 11 23:35:06 2002
From: andreas.matern@lbri.lionbioscience.com (Andreas Matern)
Date: Wed, 11 Dec 2002 18:35:06 -0500
Subject: [Biojava-l] Newbie question: species info from EMBL?
References: BRD_12351110
Message-ID: <3DF7CBAA.4040107@lbri.lionbioscience.com>

I should know better, but it's been a while since I've used biojava...

I need to parse an EMBL file, pulling out all the FASTA for organisms of 
  interest.

in bioperl I would do something like:

$in  = Bio::SeqIO->new(-file => "$file" , '-format' => 'EMBL');
$out = Bio::SeqIO->new(-file=> ">$file.out", '-format' => 'Fasta');
while ( $seq = $in->next_seq() ) {
   $acc = $seq->accession_number;
   $species = $seq->species();
   $species = $species->binomial();
	//there exists %myfavoritespecies() somewhere...
   if (exists($myfavoritespecies{$species})) {
	$seq->display_id($acc);
	$out->write_seq($seq);
   }
}

in biojava it's something like:  (TOTALLY stolen from bioconf.otago.ac.nz)

public class TestEMBLParsing {
     public static void main (String[] args) {
         BufferedReader br = null;

         try {
             br = new BufferedReader(new FileReader(args[0]));
         } catch (FileNotFoundException e) {
             e.printStackTrace();
         }
         // read the embl file
         SequenceIterator sequences = SeqIOTools.readEmbl(br);
         while (sequences.hasNext()) {
             try {
                 Sequence seq = sequences.nextSequence();
                 String accession = seq.getName();
                 String fasta = seq.seqString();
                 // how do I check to see if its my species of interest?
		// how do I create a FASTA output stream?
                 System.out.println(accession); // for testing
                 System.out.println(fasta); // for testing
             } catch (NoSuchElementException e) {
                 e.printStackTrace();
             } catch (BioException e) {
                 e.printStackTrace();
             }
         }
     }
}


Thanks so much, sorry if this has been posted somewhere... just couldn't 
find it looking around the website...

-Andreas



--------------
Andreas Matern
Bioinformatician
Bioinformatics - Research and Development
Lion Bioscience Research Inc.
141 Portland Street, 10th floor
Cambridge, MA 02139  USA
Phone: 617-245-5483
Fax: 617-245-5499
amatern@lbri.lionbioscience.com
www.lionbioscience.com


From mark.schreiber@agresearch.co.nz  Thu Dec 12 04:13:47 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Thu, 12 Dec 2002 17:13:47 +1300
Subject: [Biojava-l] Updates to Biojava in Anger
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650126D2B2@inbox.agresearch.co.nz>

Hi -

I have added some new tutorials to biojava in anger covering writing
GenBanks/EMBL as Fasta, Listing the Annotations of a Sequence and
Filtering sequences based on Annotation.

See http://bioconf.otago.ac.nz/biojava/

As usual any feedback is welcome.

Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
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From monoranjang@yahoo.co.in  Thu Dec 12 04:33:40 2002
From: monoranjang@yahoo.co.in (=?iso-8859-1?q?Monoranjan=20Gorai?=)
Date: Thu, 12 Dec 2002 04:33:40 +0000 (GMT)
Subject: [Biojava-l] Book Names For Biojava
Message-ID: <20021212043340.11631.qmail@web8006.mail.in.yahoo.com>

Hi,
 Please give me some name of books which I can use to
learn biojava in depth.

                Regards
                Monoranjan

________________________________________________________________________
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       visit http://in.tv.yahoo.com

From mark.schreiber@agresearch.co.nz  Thu Dec 12 20:11:21 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Fri, 13 Dec 2002 09:11:21 +1300
Subject: [Biojava-l] Book Names For Biojava
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650126D2DD@inbox.agresearch.co.nz>

Hi -

At the moment there are no books on biojava specifically (although there
is one being written it probably won't be done for a while). For online
documentation and tutorials take a look at
http://www.biojava.org/tutorials/index.html or
http://bioconf.otago.ac.nz/biojava/.

You can also read the API documentation. To get the most upto date (and
best) docs it's probably best to download biojava-live from cvs and get
the javadoc from there.

- Mark


> -----Original Message-----
> From: Monoranjan Gorai [mailto:monoranjang@yahoo.co.in] 
> Sent: Thursday, 12 December 2002 5:34 p.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Book Names For Biojava
> 
> 
> Hi,
>  Please give me some name of books which I can use to
> learn biojava in depth.
> 
>                 Regards
>                 Monoranjan
> 
> ______________________________________________________________
> __________
> Missed your favourite TV serial last night? Try the new, Yahoo! TV.
>        visit http://in.tv.yahoo.com 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
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From is87002@cis.nctu.edu.tw  Sun Dec 15 15:18:47 2002
From: is87002@cis.nctu.edu.tw (ChengTao Chu)
Date: Sun, 15 Dec 2002 23:18:47 +0800
Subject: [Biojava-l] I can't execute the sample in the BioJava tutorial
Message-ID: <3DFC9D57.8050406@cis.nctu.edu.tw>

Hi-

I got the source code through the cvs available in biojava and built it 
by ant.
However there are some problems compiling the Roulet example in 
http://www.biojava.org/tutorials/events2.html.
First, there is no method named getToken() in org.biojava.bio.symbol.Symbol.
Second, there is no method named generateChangeSupport in 
org.biojava.bio.dist.AbstractDistribution.
Did i get the wrong version of biojava??

Thanks a lot.

- ChengTao


From mark.schreiber@agresearch.co.nz  Mon Dec 16 02:50:18 2002
From: mark.schreiber@agresearch.co.nz (Schreiber, Mark)
Date: Mon, 16 Dec 2002 15:50:18 +1300
Subject: [Biojava-l] Bjia updates
Message-ID: <AF026AF0FF4B054590228FD1F1DE51650126D589@inbox.agresearch.co.nz>

Hi -

I went a bit mad on the weekend and added some more tutorials to
'Biojava in Anger' (OK so I have no life). There are now 26 'recipes'.
Major new topics are Alphabets & Symbols and Distributions.

Point your browser to

http://bioconf.otago.ac.nz/biojava/

- Mark


Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From leesuyee@yahoo.com  Mon Dec 16 06:37:05 2002
From: leesuyee@yahoo.com (suyee)
Date: Sun, 15 Dec 2002 22:37:05 -0800 (PST)
Subject: [Biojava-l] ClustalW enquiry
Message-ID: <20021216063705.58666.qmail@web14202.mail.yahoo.com>

Hi,    
  I am Su Yee, a polytechnic student from Singapore. Currently,
i am doingon a project on ClustalW.
  can anybody tell me how to use Java call the clustalw.exe and
pass in all the parameters needed as i dont have enough time to
convert all the clustalw C code into Java Language.
   Besides that, i still unclear with the pairwise alignment -
fast/approximate part, is there any tutorial/ website i can
refer to.
   Ur feedback is value to me, Waiting for ur answer.  
   Thanks a lot.Lee Su Yee

__________________________________________________
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From glorja_kovac@latinmail.com  Mon Dec 16 13:20:56 2002
From: glorja_kovac@latinmail.com (glorja kovac)
Date: Mon, 16 Dec 2002 08:20:56 -0500
Subject: [Biojava-l] CAN YOU ASSIST ME?
Message-ID: <20021216132052.5CC913BF70@smtp.latinmail.com>

Hi 
My name is Glorja Kovac, daughter of late Miodrag Kovac, former Yugoslav Minister of Health. My father died under mysterious circumstances and immediately after his death the government seized our properties and froze our account. I was under house arrest for almost a year I was released after so much pressure from the British and u.s.a government. I discovered in my fathers memo that he deposited a large sum of money about US40.3 Million Dollars in a secured location outside my country (location will be given to you in due time). Because of the suspicious circumstances surrounding his death I can not contact any of my fathers friends to assist me in recovering this fund since I do no longer trust anybody. Presently, I have been able to get all the particulars that will enable me establish claim to this fund but I cannot do this alone without the assistance of an outsider who does not have any relationship with my country. It will be impossible for me to divulge all the need! 
ed information concerning these fu 
nds to you now until 

I am sure I can trust you adequately. I have contacted you hoping that I can trust and rely on you. Your assistance will be highly financially compensated and I am willing to negotiate with you whatever compensation you want. I will need your assistance in securing the release of these funds as it will be risky for me to present myself as the owner. If you are willing to assist me I will be most glad, however should you not be in a position to assist I will appreciate if you do not communicate the contents of this letter to any third party. Any action in this direction will be destructive to my person. Please you can reply me through this my private e-mail box: glorja_kovac@wowmail.com 

Yours submitfully, 

Glorja Kovac 







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From fpepin@cs.mcgill.ca  Mon Dec 16 15:24:43 2002
From: fpepin@cs.mcgill.ca (Francois Pepin)
Date: Mon, 16 Dec 2002 10:24:43 -0500
Subject: [Biojava-l] ClustalW enquiry
In-Reply-To: <20021216063705.58666.qmail@web14202.mail.yahoo.com>
Message-ID: <000301c2a517$42fa0e70$dc8b6620@hermes>

I haven't had the time to check all of biojava for that, but I have code
to call external applications here.

Or you can look at the Runtime class (more specifically Runtime.exec()),
that's the java command to call outside stuff.

Francois

-----Original Message-----
From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]
On Behalf Of suyee
Sent: 16 decembre, 2002 01:37
To: biojava-l@biojava.org
Subject: [Biojava-l] ClustalW enquiry


Hi,    
  I am Su Yee, a polytechnic student from Singapore. Currently, i am
doingon a project on ClustalW.
  can anybody tell me how to use Java call the clustalw.exe and pass in
all the parameters needed as i dont have enough time to convert all the
clustalw C code into Java Language.
   Besides that, i still unclear with the pairwise alignment -
fast/approximate part, is there any tutorial/ website i can refer to.
   Ur feedback is value to me, Waiting for ur answer.  
   Thanks a lot.Lee Su Yee

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From graemeca@bioinformatics.ubc.ca  Mon Dec 16 19:47:08 2002
From: graemeca@bioinformatics.ubc.ca (Graeme Campbell)
Date: Mon, 16 Dec 2002 11:47:08 -0800
Subject: [Biojava-l] Protease and Digest classes
Message-ID: <3DFE2DBC.80109@bioinformatics.ubc.ca>

Hi there,

I've been trying to create a list of peptides from a theoretical trypsin 
digest using BioJava.  I'm using the Protease and Digest classes, but 
for some reason there is no cleavage between R and Q residues (and 
possibly between K and Q), even though Protease.TRYPSIN is defined in 
ProteaseManager.xml as cleaving after R and K, but not before P. Here is 
the code I'm using:

Digest d = new Digest();
d.setMaxMissedCleavages(0);
Protease trypsin = Protease.getProteaseByName(Protease.TRYPSIN);
d.setProtese(trypsin);
d.setSequence(s);
try {
     d.addDigestFeatures();
}
catch (Exception e) {

}

When I attempt to create my own Protease with the same constraints 
(after K,R not before P) I get the same results.

Protease trypsin = new Protease("RK", true, "P");

However, if I create a protease with no cleavage exceptions it cleaves 
between R and Q.

Protease trypsin = new Protease("RK", true, "");

Can anyone tell me what is going wrong?

Thanks,

Graeme


From jurgen@bmrb.wisc.edu  Mon Dec 16 23:30:29 2002
From: jurgen@bmrb.wisc.edu (Jurgen F. Doreleijers)
Date: Mon, 16 Dec 2002 17:30:29 -0600
Subject: [Biojava-l] Half html code taken into xml by BlastLikeToXMLConverter
Message-ID: <FGEBLGMMDOCOJENCLANJEEFPCNAA.jurgen@bmrb.wisc.edu>

Hi,

I enjoyed using the biojava.org api for parsing the blast output. I discover
that sometimes there's html markup in the blast output e.g. in entry
ref|NP_012821.1. The problem is that the markup is included when
BlastLikeToXMLConverter converts the data to xml. The markup tags don't
always match because of truncation in the blast output and that invalidates
the xml files.

Question: is there a way to filter the markup out upon parsing? Or do I need
to do a pre-run deleting any markup?

Thanks,
Jurgen

---
Jurgen F. Doreleijers, Ph.D.
CESG/BMRB, Univ. of Wisconsin-Madison, WI, USA
mailto:jurgen@bmrb.wisc.edu




From c.watt@cranfield.ac.uk  Tue Dec 17 14:29:32 2002
From: c.watt@cranfield.ac.uk (Colin Watt)
Date: Tue, 17 Dec 2002 14:29:32 -0000
Subject: [Biojava-l] (no subject)
Message-ID: <14C3BE4305F23C41B52D29083764DB8303EDC8@mailhub.silsoe.cranfield.ac.uk>


Regards
Colin

From Markus.Roth@tg.fh-giessen.de  Fri Dec 20 13:45:34 2002
From: Markus.Roth@tg.fh-giessen.de (Markus Roth)
Date: Fri, 20 Dec 2002 14:45:34 +0100
Subject: [Biojava-l] BlastLikeAlignment with BlastLikeSearchBuilder or SeqSimilarityAdapter
Message-ID: <200212201445.34534.markus.roth@tg.fh-giessen.de>

hi there,
I've been trying to create SeqSimilaritySearchResults from SAX
with the BlastLikeSearchBuilder. Is there any possibility to get
the MatchConsensus from the Alignment ?
or is there nothing about the Consensus in the SeqSimilaritySearchHit 
(SeqSimilaritySearchSubHit) ?
I found something like this in  Blast2HTMLHandler --> BlastLikeAlignment,
how can I get this with the SeqSimilarityAdapter ?

regards
Max


From td2@sanger.ac.uk  Fri Dec 20 16:34:10 2002
From: td2@sanger.ac.uk (Thomas Down)
Date: Fri, 20 Dec 2002 16:34:10 +0000
Subject: [Biojava-l] biojava-ensembl 1.3.9 released
Message-ID: <20021220163410.GD247684@jabba.sanger.ac.uk>

Hi...

I've just put together a new release of the biojava-ensembl
code, which works with the latest BioJava code, and current
(schemaVersion 9) Ensembl databases (earlier database versions
are still supported).

For those who haven't seen it before, biojava-ensembl offers
full read-only access to the sequence, assembly, and annotation
data stored in Ensembl core databases, using standard BioJava
interfaces.  Note that all this is separate from the ensj
codebase, which provides an Ensembl-specific API rather than
using BioJava interfaces.

For those who have used it before, there are have been
a number of recent changes which make it worth upgrading:

   - The previously separate `ensembl' module has been merged
     into biojava-ensembl

   - There have been many, many, architectural changes under
     the hood to improve performance and avoid excessive memory
     usage.

   - The SequenceDB.filter method from BioJava 1.3 is supported.
     This can be used for problems such as finding a transcript
     feature by ID, or finding where a particular clone appears
     in the assembly.

   - Sequences publish informative feature-schemas.

   - The assembly has been collapsed from three levels
     down to two -- FPC contigs are no longer exposed as
     first-class sequences.

biojava-ensembl is available from

   http://www.biojava.org/download/biojava-ensembl/

or from BioJava CVS (checkout biojava-ensembl).

Let me know if there are any problems with this release,

     Thomas.

From staff@yoppit.com  Fri Dec 20 18:58:34 2002
From: staff@yoppit.com (Nina)
Date: Fri, 20 Dec 2002 13:58:34 -0500 (EST)
Subject: [Biojava-l] Buy a  new car at 1% over invoice!
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From leesuyee@yahoo.com  Sat Dec 21 22:16:10 2002
From: leesuyee@yahoo.com (suyee)
Date: Sat, 21 Dec 2002 14:16:10 -0800 (PST)
Subject: [Biojava-l] ClustalW
Message-ID: <20021221221610.99642.qmail@web14206.mail.yahoo.com>

sorry to disturb again . 

can anybody tell me wat does line 390 of function forward_pass
() under "palign.c" (Clustalw source code) do? wat is "hh"?
      hh = p + matrix[(int)ia[i]][(int)ib[j]];


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From rwarren@bcgsc.bc.ca  Tue Dec 24 20:17:27 2002
From: rwarren@bcgsc.bc.ca (Rene Warren)
Date: Tue, 24 Dec 2002 12:17:27 -0800
Subject: [Biojava-l] BlastLikeSAXParser and Blastall version
Message-ID: <3E08C0D7.5020601@bcgsc.bc.ca>

Hi,

I have used the BlastLikeSAXParser class and I seem to have set up 
everything correctly.  However, it catches this exception and I find it 
quite strange considering that I'm using an older version of blastall 
(2000).  I also tried a blast output from blastall v 2.2.2 (current) 
without success.  The same is observed when blastn is used.



sax exception:org.xml.sax.SAXException: Program ncbi-blastp Version 
2.0.14 is not supported by the biojava blast-like parsing framework
/




Do you have any thoughts, comments or ideas regarding this?

Also, I have used the SAX XMLparser to parse a blast output in xml 
format.  Do you guys know if NCBI is complient to the XML format, 
because that doesn't seem to work either.

Thank you very much for your time and consideration,

Sincerely,

Rene Warren
Computational Biologist
BC Genome Sciences Centre


From jon portuondo murguiondo <jon.portuondo01@campus.upf.es>  Fri Dec 27 17:50:32 2002
From: jon portuondo murguiondo <jon.portuondo01@campus.upf.es> (jon portuondo murguiondo)
Date: Fri, 27 Dec 2002 17:50:32
Subject: [Biojava-l] Once more time
Message-ID: <1041007832.5981@mail.infomail.es>

Mensaje con FORMATO mime.
-------5981-----INFOMAIL-----
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Content-Transfer-Encoding: 8bit

Hi! I have tried all the options you proposed me, and none worked at all. SOS! 

I read the tutorial, very interesting.
 http://java.sun.com/docs/books/tutorial/java/interpack/packages.html

I tried to put the .class in this directory 
(relative to my CLASSPATH) 
 :/org/biojava/bio/program/PdbToXMLConverter.class 
 But it does'nt solve the problem. 

 If I put the .class in the directory where I run the 
 program, the error is the same. 

 On the other hand, if the .class is ONLY in the 
 package directory (the org/biojava....), I mean if I 
 remove the .class from the current directory, the 
 problem is: 
 
 [jon@diana ~]$ java PdbToXMLConverter 1FS1.pdb 
 Exception in thread "main" 
 java.lang.NoClassDefFoundError: PdbToXMLConverter 
 [jon@diana ~]$ 
 
In this configuration, if I type: 
 
[jon@diana program]$ java org.biojava.bio.program.PdbToXMLConverter /home/jon/1FS1.pdb
Exception in thread "main" java.lang.NoSuchMethodError: main

 I tried removing the package line "package 
org.biojava.bio.program" of the .java, but the error was the same than the previous one.

This is my extra-large CLASSPATH:
CLASSPATH=/home/jon:/home/jon/java/llibreries/biojava-20020823.jar:/home/jon/java/llibreries/xerces.jar:/home/jon/java/llibreries/bytecode-0.91.jar:/home/jon/java/llibreries/jakarta-regexp.jar:/home/jon/java/llibreries/xml.jar:/usr/java/j2re1.4.1_01/lib/javaplugin.jar/home/jon/java/biojava-live/src.

I suppose there are too much directories in the CLASSPATH but I'm trying all possibilities I can imagine.

I have downloaded the source of the library biojava-20020823 (that is in a .tar.gz file in that direction: http://biojava.org/download/source/
Inside this document I don't find the package java.lang...
If I compile the PdbToXmlConverter.java that is inside biojava-20020823.tar.gz, the problem is exactly the same that the previous one(I say that because you can download that file and try to make it run). 
I remember you I work in Linux with j2re1.4.1_01 and j2sdk1.
.4.1_01. 

The questions are:
Where is java.lang package? 
Is that in the biojava-20020823.jar library? 
Could be any problem with the version number? 
HOW CAN I SOLVE THE PROBLEM?
Thanks for all!

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From: =?iso-8859-1?q?Matthew=20Pocock?= <matthew_pocock@yahoo.co.uk>
Subject: Re: [Biojava-l] It's me once again
To: jon portuondo murguiondo <jon.portuondo01@campus.upf.es>,
       biojava-l@biojava.org
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Date: Tue, 10 Dec 2002 17:16:01 +0000 (GMT)
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Hi,

Try reading through this tutorial. It should help fill
the gaps.

http://java.sun.com/docs/books/tutorial/java/interpack/packages.html

> I tried to put the .class in this directory
> (relative to my CLASSPATH)
> :/org/biojava/bio/program/PdbToXMLConverter.class
> But it does'nt solve the problem.
> If I put the .class in the directory where I run the
> program, the error is the same.
> On the other hand, if the .class is ONLY in the
> package directory (the org/biojava....), I mean if I
> remove the .class from the current directory, the
> problem is: 
> 
> [jon@diana ~]$ java PdbToXMLConverter 1FS1.pdb
> Exception in thread "main"
> java.lang.NoClassDefFoundError: PdbToXMLConverter
> [jon@diana ~]$

In this configuration, you would need to type:

java org.biojava.bio.program.PdbToXMLConverter
lFSl.pdb

Notice that the package prefix to the class matches
the package of the classes package & it's location.

> 
> I tried removing the package line "package
> org.biojava.bio.program" but the following error
> ocurred while compiling:
> 
> [jon@diana ~]$ javac PdbToXMLConverter2.java
> PdbToXMLConverter2.java:69: invalid method
> declaration; return type required
>     public PdbToXMLConverter(String poInput) {
>            ^
> 1 error

This is because you have renamed the class to
PdbToXMLConverter2, but have not renamed the
constructor to match the class name. Rename this
constructor to match the class name and try again.
Make sure that you use

java PdbToXMLConverter2 lFSl.pdb

OH. The name of a java class and of it's file must
match if it is a public class. So, if you have a class
called Foo, it must be in a file called Foo.java and
will produce a class file Foo.class and will have a
constructor called Foo() and you would run its main
method as java Foo <args>..

If it is in package bar, then the class is bar.Foo,
and it will be in a file bar/Foo.java and will produce
a class file bar/Foo.class and if it has a main method
you run it as java bar.Foo <args>.

Best,

Matthew

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From jon portuondo murguiondo <jon.portuondo01@campus.upf.es>  Fri Dec 27 20:00:02 2002
From: jon portuondo murguiondo <jon.portuondo01@campus.upf.es> (jon portuondo murguiondo)
Date: Fri, 27 Dec 2002 20:00:02
Subject: [Biojava-l] PdbToXMLConverter with PDBConverter
Message-ID: <1041015602.23505@mail.infomail.es>

Hello, I have the first output! The problem I had was that PdbToXMLConverter doesn't have main method. 
This is the program that Matthew gave me, called PDBConverter.java:

----------------------------------------------------------------------------------------------------
package org.biojava.bio.program;
import java.io.*; 
  import org.biojava.bio.program.*; 
  public class PDBConverter { 
  public static void main(String[] args) 
  throws Exception { 
  StringBuffer sbuf = new StringBuffer(); 
  BufferedReader in = new BufferedReader( 
  new FileReader( 
  new File(args[0]) ) ); 
  for( 
  String line = in.readLine(); 
  line != null; 
  line = in.readLine() 
  ) { 
  sbuf.append(line); 
                } 
  PdbToXMLConverter converter = 
  new PdbToXMLConverter(sbuf.toString()); 
  converter.convert(); 
        } 
  } 

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

With this program I finally get an output from PdbToXMLConverter, but it is really odd:

------------------------------------------------------------------------------------------------
<?xml version="1.0"?>
no protocol: HEADER    LIGASE                                  08-SEP-00   1FS1              TITLE     INSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE STRUCTURE OF             TITLE    2 THE SKP1-SKP2 COMPLEX                                                COMPND    MOL_ID: 1;                                                            COMPND   2 MOLECULE: CYCLIN A/CDK2-ASSOCIATED P19;                              COMPND   3 CHAIN: A, C;                                                         COMPND   4 FRAGMENT: RESIDUES 101-153;                                          COMPND   5 SYNONYM: SKP2 F-BOX;                                                 COMPND   6 ENGINEERED: YES;                                                     COMPND   7 MOL_ID: 2;                                                           COMPND   8 MOLECULE: CYCLIN A/CDK2-ASSOCIATED P45;                              COMPND   9 CHAIN: B, D;                                                         COMPND  10 FRAGMENT: RESIDUES 1-147;              
                              COMPND  11 SYNONYM: SKP1;                                                       COMPND  12 ENGINEERED: YES                                                      SOURCE    MOL_ID: 1;                                                            SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   SOURCE   3 ORGANISM_COMMON: HUMAN;                                              SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 SOURCE   5 EXPRESSION_SYSTEM_COMMON: BACTERIA;                                  SOURCE   6 MOL_ID: 2;                                                           SOURCE   7 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   SOURCE ---------------------------------------------------------------------------------------------------
There is no change of line and I am sure that would be more defects on that expected XML.

To get it run I typed:
java org.biojava.bio.program.PDBConverter /home/jon/1FS1.pdb

I would like to understand why the output is so odd and how can I get the expected structured XML.
Thanks for all!

From leesuyee@yahoo.com  Sun Dec 29 05:36:20 2002
From: leesuyee@yahoo.com (suyee)
Date: Sat, 28 Dec 2002 21:36:20 -0800 (PST)
Subject: [Biojava-l] help
Message-ID: <20021229053620.87433.qmail@web14202.mail.yahoo.com>

can anyone help me in this..

may i know how to use "log" in Java. 
For example, this is the part that i need to use log algorithm: 
 
     g = (min + log((double)min)) ;

thanks

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From dr.baiju@asianetglobal.com  Tue Dec 31 06:37:55 2002
From: dr.baiju@asianetglobal.com (Dr.Baiju gangadharan)
Date: Mon, 30 Dec 2002 22:37:55 -0800 (PST)
Subject: [Biojava-l] enquiry
Message-ID: <20021231063755.BB74A11E61@sitemail.everyone.net>

Dear  sir,
   which  language  you  think  as  most  important for  bioinformatics  applications.

    sincerely,

                                  Dr.Baiju.G.






                                .............

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