From dlampkin at xencor.com  Mon Jan  5 13:02:38 2004
From: dlampkin at xencor.com (DeAngelo Lampkin)
Date: Mon Jan  5 13:09:46 2004
Subject: [Biojava-l] Blast Version
Message-ID: <DE23C121F2BBDA42BAF0BBD109F59D2D67AA5B@baldy.xencor.com>

Hi George,

I've seen this before.  Check out the following link for the solution.  Basically you have to set the parser to lazy.

http://www.biojava.org/pipermail/biojava-l/2003-July/003990.html

DeAngelo

-----Original Message-----
From: biojava-l-bounces@portal.open-bio.org
[mailto:biojava-l-bounces@portal.open-bio.org]On Behalf Of Y D Sun
Sent: Tuesday, December 23, 2003 9:38 AM
To: biojava-l@biojava.org
Subject: [Biojava-l] Blast Version


Hi,

What blast version does BlastLikeSAXParser support? I encounter the
following error when running the sample code of BLAST Result Parser in
Biojava In Anger to parse blast 2.2.5 output:

org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.5 is not
supported by the biojava blast-like parsing framework
        at
org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXPar
ser.java:241)
        at
org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.
java:160)

Thanks.

George

_______________________________________________
Biojava-l mailing list  -  Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l

From srinandakumar at yahoo.com  Tue Jan  6 06:33:55 2004
From: srinandakumar at yahoo.com (nandakumar sridharan)
Date: Tue Jan  6 08:41:57 2004
Subject: [Biojava-l] biojava doubts and problems
Message-ID: <20040106113355.80521.qmail@web60501.mail.yahoo.com>

any reference books available for the biojava docs and tutorials.
GCContent .java gives exception "usage: java GCContent filename.fa" how to solve it


---------------------------------
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From david.huen at ntlworld.com  Tue Jan  6 08:56:45 2004
From: david.huen at ntlworld.com (David Huen)
Date: Tue Jan  6 09:03:51 2004
Subject: [Biojava-l] biojava doubts and problems
In-Reply-To: <20040106113355.80521.qmail@web60501.mail.yahoo.com>
References: <20040106113355.80521.qmail@web60501.mail.yahoo.com>
Message-ID: <200401061356.46203.david.huen@ntlworld.com>

On Tuesday 06 Jan 2004 11:33 am, nandakumar sridharan wrote:
> any reference books available for the biojava docs and tutorials.

Please look at www.biojava.org for some material.  Follow the link there to 
"Biojava In Anger" for further useful cookbook style materials.

> GCContent .java gives exception "usage: java GCContent filename.fa" how
> to solve it
>
The above is not an exception but a Unix-style way of telling you that the 
command line format for invoking the code.

In this case, it appears to be saying you need to provide it a file in FASTA 
format:-
java GCContent <name of some file in FASTA format goes here!>

Regards,
David Huen

From benjamins at Biomax.de  Wed Jan  7 03:47:11 2004
From: benjamins at Biomax.de (Benjamin Schuster-Boeckler)
Date: Wed Jan  7 03:54:14 2004
Subject: [Biojava-l] Is there a way to determine the query within a
	FeatureFilter?
Message-ID: <3FFBC78F.4090900@Biomax.de>

As I understood the principle, a FeatureFilter will be used to test one 
Feature after the other through it's accept(Feature f) method. Now my 
problem is that this is _far_ too slow. I need to check millions of 
Features of which only a few will be selected. So what I want to do is 
to get the "rule" that the FeatureFilter uses and translate it into a 
SQL query so I can get the right Features from the database straight 
away. Unfortunately, I don't see a way how this could be possible.

Thanks in advance, Greetings,

Bejamin Schuster-B?ckler


From benjamins at Biomax.de  Wed Jan  7 04:25:23 2004
From: benjamins at Biomax.de (Benjamin Schuster-Boeckler)
Date: Wed Jan  7 04:32:26 2004
Subject: [Biojava-l] Is there a way to determine the query within
	a	FeatureFilter?
In-Reply-To: <3FFBC78F.4090900@Biomax.de>
References: <3FFBC78F.4090900@Biomax.de>
Message-ID: <3FFBD083.5080501@Biomax.de>

Benjamin Schuster-Boeckler wrote:

> As I understood the principle, a FeatureFilter will be used to test 
> one Feature after the other through it's accept(Feature f) method. Now 
> my problem is that this is _far_ too slow. I need to check millions of 
> Features of which only a few will be selected. So what I want to do is 
> to get the "rule" that the FeatureFilter uses and translate it into a 
> SQL query so I can get the right Features from the database straight 
> away. Unfortunately, I don't see a way how this could be possible. 

Ah, toString() could do it, am I right? I think it returns a neat 
pattern that I could parse token for token...


From thomas at derkholm.net  Wed Jan  7 08:45:08 2004
From: thomas at derkholm.net (Thomas Down)
Date: Wed Jan  7 08:02:39 2004
Subject: [Biojava-l] Is there a way to determine the query within
	a	FeatureFilter?
In-Reply-To: <3FFBD083.5080501@Biomax.de>
References: <3FFBC78F.4090900@Biomax.de> <3FFBD083.5080501@Biomax.de>
Message-ID: <20040107134508.GC23814@firechild>

Once upon a time, Benjamin Schuster-Boeckler wrote:
> Benjamin Schuster-Boeckler wrote:
> 
> >As I understood the principle, a FeatureFilter will be used to test 
> >one Feature after the other through it's accept(Feature f) method. Now 
> >my problem is that this is _far_ too slow. I need to check millions of 
> >Features of which only a few will be selected. So what I want to do is 
> >to get the "rule" that the FeatureFilter uses and translate it into a 
> >SQL query so I can get the right Features from the database straight 
> >away. Unfortunately, I don't see a way how this could be possible. 
> 
> Ah, toString() could do it, am I right? I think it returns a neat 
> pattern that I could parse token for token...

You certainly could do this if you wanted to.  However, I would
generally advise against it.  If you look at all the FeatureFilter
implementations in BioJava, you'll find that they all have accessor
methods for getting at their parameters.  So while it's possible
to convert a filter to text then parse it again, you'd do better
by looking at filters as parse-trees, ready to analyse directly.

You'll find code which manipulates FeatureFilters in this way
throughout the BioJava code base.  One bit which might be
particularly relevant to you is the (private) method sqlizeFilter
in BioSQLSequenceDB.  It's pretty simplistic, but might give you
some ideas.

One thing to remember is that you don't have to translate
every part of a complex filter to SQL -- just do the easy/
important bits, then use the FeatureFilter.accept methods
to apply the parts of the filter your translater doesn't
understand, and you should still get correct results with
good performance.

In the past, David Huen has talked about some more general
solutions for FeatureFilter -> SQL translation, so he might
want to add something here,

     Thomas.
From benjamins at Biomax.de  Fri Jan  9 05:30:05 2004
From: benjamins at Biomax.de (Benjamin Schuster-Boeckler)
Date: Fri Jan  9 05:37:04 2004
Subject: [Biojava-l] I get an IndexOutOfBoundsException with visitFilter in
	WalkerFactory
Message-ID: <3FFE82AD.7030000@Biomax.de>

Hy.

I'm trying to handle the nodes of the filter tree with the visitFilter 
method now. To do so, I wrote a FilterHandler class that looks like:

--------------------------- snip -----------------------------
public final class FilterHandler implements 
org.biojava.utils.walker.Visitor {

    public String and( FeatureFilter.And ffa, String ch1, String ch2 ) {
        return ch1 + " AND " + ch2;
    }

    public String or( FeatureFilter.Or ffo, String ch1, String ch2 ) {
        return ch1 + " OR " + ch2;
    }

    public String not( FeatureFilter.Not ffn, String ch1 ) {
         return "NOT " + ch1;
    }

    public String byAncestor( FeatureFilter.ByAncestor ffb, String ch1) {
        return "BYANCESTOR" + ch1;
    }

    public String byClass( FeatureFilter.ByClass ffc ) {
        return ffc.getTestClass().getName();
    }

    public String byType( FeatureFilter.ByType fft ) {
       return fft.getType();
    }

    public String overlapsLocation( FeatureFilter.OverlapsLocation ffo ) {
       return "["+ffo.getLocation().getMin()+", 
"+ffo.getLocation().getMax()+"]";
    }
}
--------------------------- snap -----------------------------

Of course, this is just a test yet, so later these methods should do 
something more useful ;-) Now, what I get is

--------------------------- snip -----------------------------

java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
	at java.util.ArrayList.RangeCheck(ArrayList.java:507)
	at java.util.ArrayList.get(ArrayList.java:324)
	at org.biojava.utils.walker.WalkerFactory.generateWalker(WalkerFactory.java:299)
	at org.biojava.utils.walker.WalkerFactory.getWalker(WalkerFactory.java:61)
	at org.biojava.bio.seq.FilterUtils.visitFilter(FilterUtils.java:988)

	at com.biomax.pedant3.das.ContigSequence.filter(ContigSequence.java:132)

--------------------------- snap -----------------------------

the filter that was passed to visitFilter was

Not(ByAncestor(ByClass(org.biojava.bio.seq.ComponentFeature))) <- 
gathered by toString()

but from debugging I found out that the error happened while evaluating 
the "and" method in WalkerFactory.getWalker. In line 299, the getWalker 
method tries to get as many elements out of the vector "wrappedLVs" as 
there are parameters to the handler-method, but wrappedLVs only has 1 
element, which is null I think. How can this be?!

Greetings, Benjamin



From benjamins at Biomax.de  Fri Jan  9 05:37:47 2004
From: benjamins at Biomax.de (Benjamin Schuster-Boeckler)
Date: Fri Jan  9 05:44:47 2004
Subject: [Biojava-l] I get an IndexOutOfBoundsException with visitFilter
	in	WalkerFactory
In-Reply-To: <3FFE82AD.7030000@Biomax.de>
References: <3FFE82AD.7030000@Biomax.de>
Message-ID: <3FFE847B.4050900@Biomax.de>

Benjamin Schuster-Boeckler wrote:

>
> but from debugging I found out that the error happened while 
> evaluating the "and" method in WalkerFactory.getWalker. In line 299, 
> the getWalker method tries to get as many elements out of the vector 
> "wrappedLVs" as there are parameters to the handler-method, but 
> wrappedLVs only has 1 element, which is null I think. How can this be?! 

Of course, it's generateWalker instead of getWalker!

Best regards, Ben


From daviddebeule at pandora.be  Sat Jan 10 11:38:53 2004
From: daviddebeule at pandora.be (david de beule)
Date: Sat Jan 10 11:45:53 2004
Subject: [Biojava-l] seqString() produces stacktrace
Message-ID: <001f01c3d798$3bedb1e0$f416a451@davidpc>

Hi all,

This piece of code:

Alphabet dna1 = DNATools.getDNA();
   SymbolTokenization dnaToke1 = dna1.getTokenization("token");
   SymbolList symbolList = new SimpleSymbolList(dnaToke1, "ACTGGACCTAAGG");
   Sequence sequence = new SimpleSequence(symbolList, "test", "test", null);
   SimpleGappedSequence gappedSequence = new SimpleGappedSequence(sequence);

   gappedSequence.addGapsInView(4, 4);
   gappedSequence.removeGap(7);
   gappedSequence.removeGaps(4, 3);
   gappedSequence.addGapsInView(7, 2);
   gappedSequence.addGapsInView(9, 3);
   gappedSequence.addGapsInView(12, 2);
   gappedSequence.addGapsInView(14, 3);
   gappedSequence.addGapsInView(17, 2);
   gappedSequence.removeGap(18);
   gappedSequence.removeGaps(11, 6);

   System.out.println(gappedSequence.seqString());

breaks on the seqString() call and gives produces the following stacktrace:

java.lang.ArrayIndexOutOfBoundsException: 13
 at
org.biojava.bio.symbol.SimpleSymbolList.symbolAt(SimpleSymbolList.java:271)
 at
org.biojava.bio.seq.impl.SimpleSequence.symbolAt(SimpleSequence.java:120)
 at
org.biojava.bio.symbol.SimpleGappedSymbolList.symbolAt(SimpleGappedSymbolLis
t.java:508)
 at
org.biojava.bio.symbol.AbstractSymbolList$SymbolIterator.next(AbstractSymbol
List.java:201)
 at
org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbolList(CharacterTok
enization.java:211)
 at
org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenize
SymbolList(AlphabetManager.java:1383)
 at
org.biojava.bio.symbol.AbstractSymbolList.seqString(AbstractSymbolList.java:
102)

Can this be a bug ?
Any help would be appreciated,

David De Beule



From getksn at rediffmail.com  Sat Jan 10 10:00:36 2004
From: getksn at rediffmail.com (karla suri nath)
Date: Sat Jan 10 11:56:03 2004
Subject: [Biojava-l] wanted info !
Message-ID: <20040110150036.15072.qmail@webmail8.rediffmail.com>

Hello,

   can you please helpme by sending the info regarding development of an application of my own which will help chemists to develop an application to draw chemical structures and as well reade the structure that is drawn.
From mark.schreiber at group.novartis.com  Sun Jan 11 19:57:06 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Sun Jan 11 20:01:05 2004
Subject: [Biojava-l] wanted info !
Message-ID: <OFF4C42323.200F3721-ON48256E19.00050AC4-48256E19.0004F37E@EU.novartis.net>

Hi -

BioJava currently doesn't have support for chemical drawing. I would 
reccomend looking at the Java3D API from sun which has great support for 
drawing things like molecules in 3D.

Of course if you want to contribute some chem drawing code it would be 
most appreciated.

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
1 Science Park Road
#04-14 The Capricorn
Singapore 117528

phone +65 6722 2973
fax  +65 6722 2910





"karla suri nath" <getksn@rediffmail.com>
Sent by: biojava-l-bounces@portal.open-bio.org
01/10/2004 11:00 PM
Please respond to karla suri nath

 
        To:     biojava-l@biojava.org
        cc: 
        Subject:        [Biojava-l] wanted info !


Hello,

   can you please helpme by sending the info regarding development of an 
application of my own which will help chemists to develop an application 
to draw chemical structures and as well reade the structure that is 
drawn._______________________________________________
Biojava-l mailing list  -  Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l



From mark.schreiber at group.novartis.com  Sun Jan 11 21:57:40 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Sun Jan 11 22:01:38 2004
Subject: [Biojava-l] seqString() produces stacktrace
Message-ID: <OF16B82938.1DD9019B-ON48256E19.000FB209-48256E19.000FFD16@EU.novartis.net>

I've done some investigations and the offending line is:


gappedSequence.removeGaps(11, 6);

This seems to be a real bug (at least in BJ1.3.1). Confusingly if you 
change the 6 to any other legal value everything works as expected. 
Matthew do you know whats going on here??

- Mark


Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
1 Science Park Road
#04-14 The Capricorn
Singapore 117528

phone +65 6722 2973
fax  +65 6722 2910





"david de beule" <daviddebeule@pandora.be>
Sent by: biojava-l-bounces@portal.open-bio.org
01/11/2004 12:38 AM

 
        To:     <biojava-l@biojava.org>
        cc: 
        Subject:        [Biojava-l] seqString() produces stacktrace


Hi all,

This piece of code:

Alphabet dna1 = DNATools.getDNA();
   SymbolTokenization dnaToke1 = dna1.getTokenization("token");
   SymbolList symbolList = new SimpleSymbolList(dnaToke1, 
"ACTGGACCTAAGG");
   Sequence sequence = new SimpleSequence(symbolList, "test", "test", 
null);
   SimpleGappedSequence gappedSequence = new 
SimpleGappedSequence(sequence);

   gappedSequence.addGapsInView(4, 4);
   gappedSequence.removeGap(7);
   gappedSequence.removeGaps(4, 3);
   gappedSequence.addGapsInView(7, 2);
   gappedSequence.addGapsInView(9, 3);
   gappedSequence.addGapsInView(12, 2);
   gappedSequence.addGapsInView(14, 3);
   gappedSequence.addGapsInView(17, 2);
   gappedSequence.removeGap(18);
   gappedSequence.removeGaps(11, 6);

   System.out.println(gappedSequence.seqString());

breaks on the seqString() call and gives produces the following 
stacktrace:

java.lang.ArrayIndexOutOfBoundsException: 13
 at
org.biojava.bio.symbol.SimpleSymbolList.symbolAt(SimpleSymbolList.java:271)
 at
org.biojava.bio.seq.impl.SimpleSequence.symbolAt(SimpleSequence.java:120)
 at
org.biojava.bio.symbol.SimpleGappedSymbolList.symbolAt(SimpleGappedSymbolLis
t.java:508)
 at
org.biojava.bio.symbol.AbstractSymbolList$SymbolIterator.next(AbstractSymbol
List.java:201)
 at
org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbolList(CharacterTok
enization.java:211)
 at
org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenize
SymbolList(AlphabetManager.java:1383)
 at
org.biojava.bio.symbol.AbstractSymbolList.seqString(AbstractSymbolList.java:
102)

Can this be a bug ?
Any help would be appreciated,

David De Beule



_______________________________________________
Biojava-l mailing list  -  Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l



From matthew_pocock at yahoo.co.uk  Mon Jan 12 12:41:10 2004
From: matthew_pocock at yahoo.co.uk (Matthew Pocock)
Date: Mon Jan 12 12:52:18 2004
Subject: [Biojava-l] seqString() produces stacktrace
In-Reply-To: <OF16B82938.1DD9019B-ON48256E19.000FB209-48256E19.000FFD16@EU.novartis.net>
References: <OF16B82938.1DD9019B-ON48256E19.000FB209-48256E19.000FFD16@EU.novartis.net>
Message-ID: <4002DC36.3020106@yahoo.co.uk>

I've fixed the symptom - aprox line 285 of SimpleGappedSymbolList we 
where renumbering the ungapped blocks before measuring the number of 
gaps in the block of gaps being edited. I've added lots more error 
checking code to this class. Code in CVS.

Does this now give the result you expected, or have I introduced a bug 
in removing the error?

Matthew

mark.schreiber@group.novartis.com wrote:

>I've done some investigations and the offending line is:
>
>
>gappedSequence.removeGaps(11, 6);
>
>This seems to be a real bug (at least in BJ1.3.1). Confusingly if you 
>change the 6 to any other legal value everything works as expected. 
>Matthew do you know whats going on here??
>
>- Mark
>
>
>Mark Schreiber
>Principal Scientist (Bioinformatics)
>
>Novartis Institute for Tropical Diseases (NITD)
>1 Science Park Road
>#04-14 The Capricorn
>Singapore 117528
>
>phone +65 6722 2973
>fax  +65 6722 2910
>
>
>
>
>
>"david de beule" <daviddebeule@pandora.be>
>Sent by: biojava-l-bounces@portal.open-bio.org
>01/11/2004 12:38 AM
>
> 
>        To:     <biojava-l@biojava.org>
>        cc: 
>        Subject:        [Biojava-l] seqString() produces stacktrace
>
>
>Hi all,
>
>This piece of code:
>
>Alphabet dna1 = DNATools.getDNA();
>   SymbolTokenization dnaToke1 = dna1.getTokenization("token");
>   SymbolList symbolList = new SimpleSymbolList(dnaToke1, 
>"ACTGGACCTAAGG");
>   Sequence sequence = new SimpleSequence(symbolList, "test", "test", 
>null);
>   SimpleGappedSequence gappedSequence = new 
>SimpleGappedSequence(sequence);
>
>   gappedSequence.addGapsInView(4, 4);
>   gappedSequence.removeGap(7);
>   gappedSequence.removeGaps(4, 3);
>   gappedSequence.addGapsInView(7, 2);
>   gappedSequence.addGapsInView(9, 3);
>   gappedSequence.addGapsInView(12, 2);
>   gappedSequence.addGapsInView(14, 3);
>   gappedSequence.addGapsInView(17, 2);
>   gappedSequence.removeGap(18);
>   gappedSequence.removeGaps(11, 6);
>
>   System.out.println(gappedSequence.seqString());
>
>breaks on the seqString() call and gives produces the following 
>stacktrace:
>
>java.lang.ArrayIndexOutOfBoundsException: 13
> at
>org.biojava.bio.symbol.SimpleSymbolList.symbolAt(SimpleSymbolList.java:271)
> at
>org.biojava.bio.seq.impl.SimpleSequence.symbolAt(SimpleSequence.java:120)
> at
>org.biojava.bio.symbol.SimpleGappedSymbolList.symbolAt(SimpleGappedSymbolLis
>t.java:508)
> at
>org.biojava.bio.symbol.AbstractSymbolList$SymbolIterator.next(AbstractSymbol
>List.java:201)
> at
>org.biojava.bio.seq.io.CharacterTokenization.tokenizeSymbolList(CharacterTok
>enization.java:211)
> at
>org.biojava.bio.symbol.AlphabetManager$WellKnownTokenizationWrapper.tokenize
>SymbolList(AlphabetManager.java:1383)
> at
>org.biojava.bio.symbol.AbstractSymbolList.seqString(AbstractSymbolList.java:
>102)
>
>Can this be a bug ?
>Any help would be appreciated,
>
>David De Beule
>
>
>
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l@biojava.org
>http://biojava.org/mailman/listinfo/biojava-l
>
>
>
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l@biojava.org
>http://biojava.org/mailman/listinfo/biojava-l
>
>  
>


From matthew_pocock at yahoo.co.uk  Mon Jan 12 12:47:00 2004
From: matthew_pocock at yahoo.co.uk (Matthew Pocock)
Date: Mon Jan 12 12:58:07 2004
Subject: [Biojava-l] Is there a way to determine the query
	within	a	FeatureFilter?
In-Reply-To: <20040107134508.GC23814@firechild>
References: <3FFBC78F.4090900@Biomax.de> <3FFBD083.5080501@Biomax.de>
	<20040107134508.GC23814@firechild>
Message-ID: <4002DD94.4060109@yahoo.co.uk>

In additon to what Thomas said, you may also want to look at the 
org.biojava.utils.walker package and its use in the FilterUtils code 
(arround line 986). This is a framework we developed to make it trivial 
to walk a fiter expression, possibly building an sql query as you go.

Matthew

Thomas Down wrote:

>Once upon a time, Benjamin Schuster-Boeckler wrote:
>  
>
>>Benjamin Schuster-Boeckler wrote:
>>
>>    
>>
>>>As I understood the principle, a FeatureFilter will be used to test 
>>>one Feature after the other through it's accept(Feature f) method. Now 
>>>my problem is that this is _far_ too slow. I need to check millions of 
>>>Features of which only a few will be selected. So what I want to do is 
>>>to get the "rule" that the FeatureFilter uses and translate it into a 
>>>SQL query so I can get the right Features from the database straight 
>>>away. Unfortunately, I don't see a way how this could be possible. 
>>>      
>>>
>>Ah, toString() could do it, am I right? I think it returns a neat 
>>pattern that I could parse token for token...
>>    
>>
>
>You certainly could do this if you wanted to.  However, I would
>generally advise against it.  If you look at all the FeatureFilter
>implementations in BioJava, you'll find that they all have accessor
>methods for getting at their parameters.  So while it's possible
>to convert a filter to text then parse it again, you'd do better
>by looking at filters as parse-trees, ready to analyse directly.
>
>You'll find code which manipulates FeatureFilters in this way
>throughout the BioJava code base.  One bit which might be
>particularly relevant to you is the (private) method sqlizeFilter
>in BioSQLSequenceDB.  It's pretty simplistic, but might give you
>some ideas.
>
>One thing to remember is that you don't have to translate
>every part of a complex filter to SQL -- just do the easy/
>important bits, then use the FeatureFilter.accept methods
>to apply the parts of the filter your translater doesn't
>understand, and you should still get correct results with
>good performance.
>
>In the past, David Huen has talked about some more general
>solutions for FeatureFilter -> SQL translation, so he might
>want to add something here,
>
>     Thomas.
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l@biojava.org
>http://biojava.org/mailman/listinfo/biojava-l
>
>  
>


From eric_bellard at yahoo.com  Tue Jan 13 08:35:06 2004
From: eric_bellard at yahoo.com (Eric BELLARD)
Date: Tue Jan 13 08:41:55 2004
Subject: [Biojava-l] how to calculate consensus from a fasta file
Message-ID: <20040113133506.52143.qmail@web41509.mail.yahoo.com>

Hi,

I'd like to first thank you all for your great job on
this project.

I'm using biojava in a project to store some
sequencing result.

In my application the user upload sequences from a
fasta file, and I like to build an alignment from it.

With your project, I can easily parse the fasta file
and get all the sequences. 

Let's consider the sequences as lines.
I'd like to calculate the column consensus using dna
degenerate alphabet.

Does biojava implements a way to do this?

Thanks by advance.

Eric



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From mark.schreiber at group.novartis.com  Tue Jan 13 20:01:53 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Tue Jan 13 20:05:45 2004
Subject: [Biojava-l] how to calculate consensus from a fasta file
Message-ID: <OFDB16BDC0.AE3081D4-ON48256E1B.00054AE3-48256E1B.0005632A@EU.novartis.net>

Hi Eric -

I'm not sure if this will solve your problem but you could make an 
Alignment object from the sequences and then use the methods of 
DistributionTools to get a Distribution object for each position in the 
Alignment. These distributions will tell you the frequency of each base at 
each position in the Alignment which you could use to make a consensus. 
You can also use DistributionTools to calculate information or entropy at 
each position.

Alternatively you could generate a markov model that represents the 
alignment and probabilistically represents the consensus.

Hope this helps

Mark



Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
1 Science Park Road
#04-14 The Capricorn
Singapore 117528

phone +65 6722 2973
fax  +65 6722 2910





Eric BELLARD <eric_bellard@yahoo.com>
Sent by: biojava-l-bounces@portal.open-bio.org
01/13/2004 09:35 PM
Please respond to eric

 
        To:     biojava-l@biojava.org
        cc: 
        Subject:        [Biojava-l] how to calculate consensus from a fasta file


Hi,

I'd like to first thank you all for your great job on
this project.

I'm using biojava in a project to store some
sequencing result.

In my application the user upload sequences from a
fasta file, and I like to build an alignment from it.

With your project, I can easily parse the fasta file
and get all the sequences. 

Let's consider the sequences as lines.
I'd like to calculate the column consensus using dna
degenerate alphabet.

Does biojava implements a way to do this?

Thanks by advance.

Eric



__________________________________
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From eric_bellard at yahoo.com  Wed Jan 14 04:03:05 2004
From: eric_bellard at yahoo.com (Eric BELLARD)
Date: Wed Jan 14 04:09:53 2004
Subject: [Biojava-l] how to calculate consensus from a fasta file
In-Reply-To: <OFDB16BDC0.AE3081D4-ON48256E1B.00054AE3-48256E1B.0005632A@EU.novartis.net>
Message-ID: <20040114090306.57723.qmail@web41506.mail.yahoo.com>

Thanks for your response.

My problem is easier than you though.

I simpy have to calculate the ambiguity symbol for
each column.

My solution is:
- create a list whith a set of symbol for each column
- fill the set with each symbol of each sequence
- calculate the ambiguity symbols for each set of this
list

It works pretty well but if the sequences become too
long I imagine I'll use too much memory.

I'll try to find another solution using the alignment
object in the framework. At the moment I don't know
enough the framework to find solution of this kind
with it. I'll try...

Anyway thanks for your help.

Eric

--- mark.schreiber@group.novartis.com wrote:
> Hi Eric -
> 
> I'm not sure if this will solve your problem but you
> could make an 
> Alignment object from the sequences and then use the
> methods of 
> DistributionTools to get a Distribution object for
> each position in the 
> Alignment. These distributions will tell you the
> frequency of each base at 
> each position in the Alignment which you could use
> to make a consensus. 
> You can also use DistributionTools to calculate
> information or entropy at 
> each position.
> 
> Alternatively you could generate a markov model that
> represents the 
> alignment and probabilistically represents the
> consensus.
> 
> Hope this helps
> 
> Mark
> 
> 
> 
> Mark Schreiber
> Principal Scientist (Bioinformatics)
> 
> Novartis Institute for Tropical Diseases (NITD)
> 1 Science Park Road
> #04-14 The Capricorn
> Singapore 117528
> 
> phone +65 6722 2973
> fax  +65 6722 2910
> 
> 
> 
> 
> 
> Eric BELLARD <eric_bellard@yahoo.com>
> Sent by: biojava-l-bounces@portal.open-bio.org
> 01/13/2004 09:35 PM
> Please respond to eric
> 
>  
>         To:     biojava-l@biojava.org
>         cc: 
>         Subject:        [Biojava-l] how to calculate
> consensus from a fasta file
> 
> 
> Hi,
> 
> I'd like to first thank you all for your great job
> on
> this project.
> 
> I'm using biojava in a project to store some
> sequencing result.
> 
> In my application the user upload sequences from a
> fasta file, and I like to build an alignment from
> it.
> 
> With your project, I can easily parse the fasta file
> and get all the sequences. 
> 
> Let's consider the sequences as lines.
> I'd like to calculate the column consensus using dna
> degenerate alphabet.
> 
> Does biojava implements a way to do this?
> 
> Thanks by advance.
> 
> Eric
> 
> 
> 
> __________________________________
> Do you Yahoo!?
> Yahoo! Hotjobs: Enter the "Signing Bonus"
> Sweepstakes
> http://hotjobs.sweepstakes.yahoo.com/signingbonus
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 
> 
> 


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From benjamins at Biomax.de  Wed Jan 14 04:18:41 2004
From: benjamins at Biomax.de (Benjamin Schuster-Boeckler)
Date: Wed Jan 14 04:25:30 2004
Subject: [Biojava-l] Non-Deterministic behaviour of the FeatureFilter-Walker
	!?
Message-ID: <40050971.6070009@Biomax.de>

I witness a _very_ weird problem executing my code. I have a class 
called FilterHandler that implements org.biojava.utils.walker.Visitor 
and is used in conjunction with FilterUtils.visitFilter(). I added some 
debuging-output to the each handling method just to see what's  going 
on. So normally I get this:

------------------------------ snip ------------------------------
DEBUG das.ContigSequence - filter - And(And(ByType(orf) , 
Not(ByAncestor(ByClass(org.biojava.bio.seq.ComponentFeature)))) , 
Overlaps([1,1000000])), recurse=true
DEBUG das.FilterHandler - byType - orf
DEBUG das.FilterHandler - byClass - org.biojava.bio.seq.ComponentFeature
DEBUG das.FilterHandler - byAncestor - ByAncestor
DEBUG das.FilterHandler - not - Not
DEBUG das.FilterHandler - and - And
DEBUG das.FilterHandler - overlapsLocation - [1, 1000000]
DEBUG das.FilterHandler - and - And
------------------------------ snap ------------------------------

This is fine. The first line is simply filter.toString() before I pass 
the filter to the visitFilter method.
Now for some reason, and I can't tell when actually, I get that:

------------------------------ snip ------------------------------
DEBUG das.ContigSequence - filter - And(And(ByType(orf) , 
Not(ByAncestor(ByClass(org.biojava.bio.seq.ComponentFeature)))) , 
Overlaps([1,1000000])), recurse=true
WARN  das.FilterHandler - and - Seems like some Filter was not evaluated!
DEBUG das.FilterHandler - and - And
------------------------------ snap ------------------------------

The warning is of course my own code, it just triggers if And was called 
without any other filters evaluated beforehand. It seems like the filter 
is not beeing processed, just the outer 'and' but nothing else. Any clue 
how this can be? I don't seem to get any error messages, too. I'll 
attach the handler method at the end of the file.

Thanks in advance,

Benjamin

------------------------------ snip ------------------------------
public final class FilterHandler implements 
org.biojava.utils.walker.Visitor {

    private Logger logger; //the log4j-logger to write to
    private Stack query; //keep track of recent calls
    private List types; //in case we have ByType queries
    private Location boundaries;
    private boolean isComponentQuery;

    public FilterHandler() {
        this.logger = Logger.getLogger(FilterHandler.class); //tell 
logger the name of this class
        query = new Stack(); //the query is still empty"
        types = new Vector(); //no types to look for, yet...
        isComponentQuery = false; //we don't look for structural 
features, do we?
    }
   
    public void and( FeatureFilter.And ffa ) {
        try{
            query.pop();
            query.pop();
        } catch(EmptyStackException e) {
            logger.warn("Seems like some Filter was not evaluated!", e);
        }
        query.push("and");
        logger.debug("And");
    }

    public void or( FeatureFilter.Or ffo ) {
        try{
            query.pop();
            query.pop();
        } catch(EmptyStackException e) {
            logger.warn("Seems like some Filter was not evaluated!", e);
        }
        query.push("or");
        logger.debug("Or");
    }

    public void not( FeatureFilter.Not ffn ) {
        try {
            if((String)query.pop() == "byAncestor")
                if((String)query.pop() == "byClass")
                    if(isComponentQuery) isComponentQuery = false;
        } catch(EmptyStackException e) {
            logger.warn("This was not the usual case of 'not'!", e);
        }
        query.push("not");
        logger.debug("Not");
    }

    public void byAncestor( FeatureFilter.ByAncestor ffb ) {
        query.push("byAncestor");
        logger.debug("ByAncestor");
    }

    public void byClass( FeatureFilter.ByClass ffc ) {
        query.push("byClass");
        if(ffc.getTestClass().getName().indexOf("ComponentFeature")>=0) 
isComponentQuery = true;
        logger.debug(ffc.getTestClass().getName());
    }

    public void byType( FeatureFilter.ByType fft ) {
        query.push("byType");
        types.add(fft.getType());
        logger.debug(fft.getType());
    }

    public void overlapsLocation( FeatureFilter.OverlapsLocation ffo ) {
        query.push("overlapsLocation");
        boundaries = ffo.getLocation();
        logger.debug("["+ffo.getLocation().getMin()+", 
"+ffo.getLocation().getMax()+"]");
    }
------------------------------ snap ------------------------------

From eric_bellard at yahoo.com  Wed Jan 14 05:40:44 2004
From: eric_bellard at yahoo.com (Eric BELLARD)
Date: Wed Jan 14 05:47:31 2004
Subject: [Biojava-l] ClassCastException during ambiguity calcul
Message-ID: <20040114104044.13010.qmail@web41509.mail.yahoo.com>

Hi,

I'm calculating ambiguity of symbol sets and i've got
a class cast exception. I've managed to isolate the
bug. The following code triggers the exception:

		Set lc_set = new HashSet();

		SymbolList lc_sequence = DNATools.createDNA("AG");

		Iterator lc_i = lc_sequence.iterator();
		while (lc_i.hasNext()) {

			lc_set.add(lc_i.next());

		}

		lc_set.add(DNATools.getDNA().getGapSymbol());

		try {
			Symbol lc_symbol =
DNATools.getDNA().getAmbiguity(lc_set);
			System.out.println(lc_symbol.getName());
		} catch (IllegalSymbolException e) {
			throw e;
		}


If I don't add the gap symbol in the set I don't have
the exception.

Even an excpetion must be thrown during this code
execution, I don't think the class cast exception is
the good one.

Does someone have a clue? Is it a bug? Do you want me
to propose a fix?

I think I got good java skills but the worst
biological skill you've ever seen :-) 

Regards,

Eric

__________________________________
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From mark.schreiber at group.novartis.com  Wed Jan 14 20:54:58 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Wed Jan 14 20:58:50 2004
Subject: [Biojava-l] ClassCastException during ambiguity calcul
Message-ID: <OFDB6376F0.19A74B07-ON48256E1C.0009E04C-48256E1C.000A3EB4@EU.novartis.net>

Hi Eric -

I think the problem is caused by trying to determine the ambiguity for a 
set that contains the gap symbol. In reality there is no IUPAC ambiguity 
code for anything paired with a gap. An ambiguity is like saying either 
this nucleotide or this one (as in an ambiguous DNA sequence read). It 
can't really cover the concept of either this nucleotide or a gap

- Mark





Eric BELLARD <eric_bellard@yahoo.com>
Sent by: biojava-l-bounces@portal.open-bio.org
01/14/2004 06:40 PM
Please respond to eric

 
        To:     biojava-l@biojava.org
        cc: 
        Subject:        [Biojava-l] ClassCastException during ambiguity calcul


Hi,

I'm calculating ambiguity of symbol sets and i've got
a class cast exception. I've managed to isolate the
bug. The following code triggers the exception:

                                 Set lc_set = new HashSet();

                                 SymbolList lc_sequence = 
DNATools.createDNA("AG");

                                 Iterator lc_i = lc_sequence.iterator();
                                 while (lc_i.hasNext()) {

                                                 lc_set.add(lc_i.next());

                                 }

 lc_set.add(DNATools.getDNA().getGapSymbol());

                                 try {
                                                 Symbol lc_symbol =
DNATools.getDNA().getAmbiguity(lc_set);
 System.out.println(lc_symbol.getName());
                                 } catch (IllegalSymbolException e) {
                                                 throw e;
                                 }


If I don't add the gap symbol in the set I don't have
the exception.

Even an excpetion must be thrown during this code
execution, I don't think the class cast exception is
the good one.

Does someone have a clue? Is it a bug? Do you want me
to propose a fix?

I think I got good java skills but the worst
biological skill you've ever seen :-) 

Regards,

Eric

__________________________________
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From immunoguest at hotmail.com  Sun Jan 18 19:44:57 2004
From: immunoguest at hotmail.com (tai kwan do)
Date: Sun Jan 18 19:51:38 2004
Subject: [Biojava-l] Blast XML output question
Message-ID: <BAY7-F9521n6LWo4IPN000442c5@hotmail.com>

Hello,

I'm seeing a difference in the data being output by stand-alone blast and 
online blast.  The identities value are different between the xml output and 
the text output.  The other difference I see is in the query and hit 
sequences.  I've included below the outputs using the same input parameters, 
does anyone know why this is the case?

    gb|AE000111.1|AE000111 Escherichia coli K-12 MG1655 section 1 of 400 of 
the complete

          genome
         Length = 10596

Score =  589 bits (297), Expect = e-168
Identities = 315/324 (97%)
Strand = Plus / Plus


Query: 237 aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtg 296
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237 aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtg 296


Query: 297 cgggcnnnnnnnnncgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcgg 356
          |||||         ||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 297 cgggctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcgg 356


Query: 357 cggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaa 416
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 357 cggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaa 416


Query: 417 tgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacct 476
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 417 tgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacct 476


Query: 477 ggtggcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgc 536
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 477 ggtggcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgc 536


Query: 537 cgaacgtatttttgccgaactttt 560
          ||||||||||||||||||||||||
Sbjct: 537 cgaacgtatttttgccgaactttt 560


       <Hit>
         <Hit_num>1</Hit_num>
         <Hit_id>gi|1786181|gb|AE000111.1|AE000111</Hit_id>
         <Hit_def>Escherichia coli K-12 MG1655 section 1 of 400 of the 
complete genome</Hit_def>
         <Hit_accession>AE000111</Hit_accession>
         <Hit_len>10596</Hit_len>
         <Hit_hsps>
           <Hsp>
             <Hsp_num>1</Hsp_num>
             <Hsp_bit-score>589.253</Hsp_bit-score>
             <Hsp_score>297</Hsp_score>
             <Hsp_evalue>1.04898e-168</Hsp_evalue>
             <Hsp_query-from>237</Hsp_query-from>
             <Hsp_query-to>560</Hsp_query-to>
             <Hsp_hit-from>237</Hsp_hit-from>
             <Hsp_hit-to>560</Hsp_hit-to>
             <Hsp_query-frame>1</Hsp_query-frame>
             <Hsp_hit-frame>1</Hsp_hit-frame>
             <Hsp_identity>324</Hsp_identity>
             <Hsp_positive>324</Hsp_positive>
             <Hsp_align-len>324</Hsp_align-len>
             
<Hsp_qseq>AGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT</Hsp_qseq>
             
<Hsp_hseq>AGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT</Hsp_hseq>
             
<Hsp_midline>||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>
           </Hsp>
           <Hsp>

_________________________________________________________________
Rethink your business approach for the new year with the helpful tips here. 
http://special.msn.com/bcentral/prep04.armx

From tkirsten at izbi.uni-leipzig.de  Fri Jan 23 10:35:47 2004
From: tkirsten at izbi.uni-leipzig.de (Toralf Kirsten)
Date: Fri Jan 23 10:40:54 2004
Subject: [Biojava-l] GenBank XML File Parse Error
Message-ID: <40113F53.8020407@izbi.uni-leipzig.de>

Hi,
I have to extract data from the GenBank XML files.
For this purpose I use the biojava API. But I get a parser error.

java.lang.StringIndexOutOfBoundsException: String index out of range: 12
at java.lang.String.substring(String.java:1477)
at org.biojava.bio.seq.io.GenbankContext.processHeaderLine
(GenbankContext.java:621)
at org.biojava.bio.seq.io.GenbankContext.processLine
(GenbankContext.java:263)
at org.biojava.bio.seq.io.GenbankFormat.readSequence
(GenbankFormat.java:144)
at org.biojava.bio.seq.io.StreamReader.nextSequence
(StreamReader.java:100)

rethrown as org.biojava.bio.BioException: Could not read sequence
at
org.biojava.bio.seq.io.StreamReader.nextSequence
(StreamReader.java:103)
at de.izbi.gbm.logistics.GenBankBioJavaImporter.readFile
(GenBankBioJavaImporter.java:41)
at de.izbi.gbm.gui.GenBankBaseFrame.actionPerformed
(GenBankBaseFrame.java:134)
at javax.swing.AbstractButton.fireActionPerformed
(AbstractButton.java:1764)
at javax.swing.AbstractButton$ForwardActionEvents.actionPerformed
(AbstractButton.java:1817)
at javax.swing.DefaultButtonModel.fireActionPerformed
(DefaultButtonModel.java:419)
at javax.swing.DefaultButtonModel.setPressed
(DefaultButtonModel.java:257)
at javax.swing.AbstractButton.doClick(AbstractButton.java:289)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick
(BasicMenuItemUI.java:1109)
at javax.swing.plaf.basic.BasicMenuItemUI$MouseInputHandler.
mouseReleased(BasicMenuItemUI.java:943)
at java.awt.Component.processMouseEvent(Component.java:5093)
at java.awt.Component.processEvent(Component.java:4890)
at java.awt.Container.processEvent(Container.java:1566)
at java.awt.Component.dispatchEventImpl(Component.java:3598)
at java.awt.Container.dispatchEventImpl(Container.java:1623)
at java.awt.Component.dispatchEvent(Component.java:3439)
at java.awt.LightweightDispatcher.retargetMouseEvent
(Container.java:3450)
  at java.awt.LightweightDispatcher.processMouseEvent
(Container.java:3165)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3095)
at java.awt.Container.dispatchEventImpl(Container.java:1609)
at java.awt.Window.dispatchEventImpl(Window.java:1585)
at java.awt.Component.dispatchEvent(Component.java:3439)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:450)
at java.awt.EventDispatchThread.pumpOneEventForHierarchy
(EventDispatchThread.java:197)
at java.awt.EventDispatchThread.pumpEventsForHierarchy
(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:144)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:136)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:99)



The program is just simple. The user specifies path and file name by the
FileChooser component. Then I open the file and apply the Sequence and
Annotation classes as visible in the attached method taken from a extended
file class.

What I need are the sequence data of the GenBank entry (accession,
sequence etc.)
and also for its features (start, end position, subtype like t-RNA, cds
etc.)

Any hints are welcome.
Thanks Tori

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

public GenBankBioJavaImporter(String path, String fileName, Connection
genDbCon) {
    super();
    super.setPath(path);
    super.setFileName(fileName);
  }
public boolean readFile() {
    if (!super.createInputFile()) return(false);

    //read the GenBank File
    SequenceIterator sequences =
SeqIOTools.readGenbank(super.fileReaderHandler); // fileReaderHandler is
a BufferedReader

    //iterate through the sequences
    while(sequences.hasNext()) {
      try {

        Sequence seq = sequences.nextSequence();
        //do stuff with the sequence
        System.out.println("Info: "+seq.getName()+", "+seq.getURN()+",
"+seq.countFeatures());
        Annotation anno = seq.getAnnotation();
        //anno.getProperty()
      }
      catch (BioException ex) {
        //not in GenBank format
        ex.printStackTrace();
        super.closeInputFile();
        return(false);
      }catch (NoSuchElementException ex) {
        //request for more sequence when there isn't any
        ex.printStackTrace();
        super.closeInputFile();
        return(false);
      }
    }
    super.closeInputFile();
    return(true);
  }






From thomas at derkholm.net  Fri Jan 23 12:01:51 2004
From: thomas at derkholm.net (Thomas Down)
Date: Fri Jan 23 12:10:21 2004
Subject: [Biojava-l] GenBank XML File Parse Error
In-Reply-To: <40113F53.8020407@izbi.uni-leipzig.de>
References: <40113F53.8020407@izbi.uni-leipzig.de>
Message-ID: <20040123170151.GA5148@firechild>

Once upon a time, Toralf Kirsten wrote:
> Hi,
> I have to extract data from the GenBank XML files.
> For this purpose I use the biojava API. But I get a parser error.
> 
> java.lang.StringIndexOutOfBoundsException: String index out of range: 12
> at java.lang.String.substring(String.java:1477)
> at org.biojava.bio.seq.io.GenbankContext.processHeaderLine
> (GenbankContext.java:621)
> [snip]
> 
> 
> The program is just simple. The user specifies path and file name by the
> FileChooser component. Then I open the file and apply the Sequence and
> Annotation classes as visible in the attached method taken from a extended
> file class.
> 
> What I need are the sequence data of the GenBank entry (accession,
> sequence etc.)
> and also for its features (start, end position, subtype like t-RNA, cds
> etc.)

I'm afraid that BioJava doesn't currently support the XML version
of genbank records.  The Genbank parser you are using expects the
normal flatfile version of the genbank records -- do you have
access to these?

We should probably look at adding Genbank XML support to BioJava.
Does anyone know how widely it's used (I must admit I haven't met
it before).

    Thomas.
From tkirsten at izbi.uni-leipzig.de  Fri Jan 23 12:17:05 2004
From: tkirsten at izbi.uni-leipzig.de (Toralf Kirsten)
Date: Fri Jan 23 22:17:03 2004
Subject: [Biojava-l] GenBank XML File Parse Error
In-Reply-To: <20040123170151.GA5148@firechild>
References: <40113F53.8020407@izbi.uni-leipzig.de>
	<20040123170151.GA5148@firechild>
Message-ID: <40115711.5080000@izbi.uni-leipzig.de>

Thomas,
thanks for the your answer.
ASCII plain text or normal flat file as you said is downloadable from 
the NCBI web page.
So there is no problem to use it. But we would like to use XML file, due 
to each term is accessible at atomic level.
Thanks again.
Toralf

Thomas Down wrote:

>Once upon a time, Toralf Kirsten wrote:
>  
>
>>Hi,
>>I have to extract data from the GenBank XML files.
>>For this purpose I use the biojava API. But I get a parser error.
>>
>>java.lang.StringIndexOutOfBoundsException: String index out of range: 12
>>at java.lang.String.substring(String.java:1477)
>>at org.biojava.bio.seq.io.GenbankContext.processHeaderLine
>>(GenbankContext.java:621)
>>[snip]
>>
>>
>>The program is just simple. The user specifies path and file name by the
>>FileChooser component. Then I open the file and apply the Sequence and
>>Annotation classes as visible in the attached method taken from a extended
>>file class.
>>
>>What I need are the sequence data of the GenBank entry (accession,
>>sequence etc.)
>>and also for its features (start, end position, subtype like t-RNA, cds
>>etc.)
>>    
>>
>
>I'm afraid that BioJava doesn't currently support the XML version
>of genbank records.  The Genbank parser you are using expects the
>normal flatfile version of the genbank records -- do you have
>access to these?
>
>We should probably look at adding Genbank XML support to BioJava.
>Does anyone know how widely it's used (I must admit I haven't met
>it before).
>
>    Thomas.
>  
>
From tkirsten at izbi.uni-leipzig.de  Tue Jan 27 02:20:52 2004
From: tkirsten at izbi.uni-leipzig.de (Toralf Kirsten)
Date: Tue Jan 27 02:25:52 2004
Subject: [Biojava-l] GenBank Feature Extraction
Message-ID: <40161154.9050905@izbi.uni-leipzig.de>

Hi,
does anybody know how to extract the feature details, e.g. CDS /product 
/translation etc., from the GenBank flat file?
Any code example or hints which class/classes should be used are welcome.
Thanks, Toralf

From mark.schreiber at group.novartis.com  Tue Jan 27 03:06:21 2004
From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com)
Date: Tue Jan 27 03:09:43 2004
Subject: [Biojava-l] GenBank Feature Extraction
Message-ID: <OF00E84494.79407F82-ON48256E28.002C7A1C-48256E28.002C3C73@EU.novartis.net>

Hi -

Take a look at http://www.biojava.org/docs/bj_in_anger/filter.htm

- Mark





Toralf Kirsten <tkirsten@izbi.uni-leipzig.de>
Sent by: biojava-l-bounces@portal.open-bio.org
01/27/2004 03:20 PM

 
        To:     biojava-l@biojava.org
        cc: 
        Subject:        [Biojava-l] GenBank Feature Extraction


Hi,
does anybody know how to extract the feature details, e.g. CDS /product 
/translation etc., from the GenBank flat file?
Any code example or hints which class/classes should be used are welcome.
Thanks, Toralf

_______________________________________________
Biojava-l mailing list  -  Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l



From tkirsten at izbi.uni-leipzig.de  Tue Jan 27 11:10:41 2004
From: tkirsten at izbi.uni-leipzig.de (Toralf Kirsten)
Date: Tue Jan 27 11:15:49 2004
Subject: [Biojava-l] GenBank Feature Extraction
In-Reply-To: <OF00E84494.79407F82-ON48256E28.002C7A1C-48256E28.002C3C73@EU.novartis.net>
References: <OF00E84494.79407F82-ON48256E28.002C7A1C-48256E28.002C3C73@EU.novartis.net>
Message-ID: <40168D81.7000506@izbi.uni-leipzig.de>

Hi Mark,
thank you very much. It works. ;-)
Toralf

mark.schreiber@group.novartis.com wrote:

>Hi -
>
>Take a look at http://www.biojava.org/docs/bj_in_anger/filter.htm
>
>- Mark
>
>
>
>
>
>Toralf Kirsten <tkirsten@izbi.uni-leipzig.de>
>Sent by: biojava-l-bounces@portal.open-bio.org
>01/27/2004 03:20 PM
>
> 
>        To:     biojava-l@biojava.org
>        cc: 
>        Subject:        [Biojava-l] GenBank Feature Extraction
>
>
>Hi,
>does anybody know how to extract the feature details, e.g. CDS /product 
>/translation etc., from the GenBank flat file?
>Any code example or hints which class/classes should be used are welcome.
>Thanks, Toralf
>
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l@biojava.org
>http://biojava.org/mailman/listinfo/biojava-l
>
>
>  
>

From sherpa at coresoft.be  Tue Jan 27 13:55:39 2004
From: sherpa at coresoft.be (Frederik Decouttere)
Date: Tue Jan 27 14:02:08 2004
Subject: [Biojava-l] 2 problems found in org.biojava.bio.seq.db.biosql code
In-Reply-To: <40168D81.7000506@izbi.uni-leipzig.de>
Message-ID: <001501c3e507$286deb90$7f7ba8c0@SISKA>

Hi,

After doing some tests with the biojava - biosql code I think there are
2 (little) bugs in there:

- when persisting a Sequence which contains a Feature with
BetweenLocation this Location gets converted to a RangeLocation upon
retrieval

- when persisting a Sequence which contains (a) Feature(s) in 2
different biodatabases an exception is thrown in the ontology code part
of biojava

You can find an example for both cases below

Environment: biojava.jar build from cvs, hsqldb database + biosql
schema, jdk1.4

If someone with knowledge of the biosql persistence code finds some time
to have a look...
Dont think it's very hard to fix

Ciao
Frederik

######test
code##################################################################
import java.util.*;
import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.db.biosql.*;
import org.biojava.bio.seq.impl.*;
import org.biojava.bio.symbol.*;

public class BioSqlTest {
	
	String driver = "org.hsqldb.jdbcDriver" ;
	String user = "sa";
	String pass = "";
	String url = "jdbc:hsqldb:file:./database/biosqldb" ;

	public BioSqlTest() {
	}
	
	/**
	 * demonstrates the switch from between to range location after
persistence code
	 */
	public void generateFeaturePersistenceProblem() throws Exception
{
		BioSQLSequenceDB db1 = new BioSQLSequenceDB(driver, url,
user, pass
	
, "testbiosqldb_1", true);
		db1.addSequence(getSequence()) ;
		
		Sequence seq = db1.getSequence("test_seq") ;
		for (Iterator iter = seq.features(); iter.hasNext();) {
			StrandedFeature f = (StrandedFeature)
iter.next();
			Location loc = f.getLocation() ;
			
			/*
			 * ERROR: Location is now a RangeLocation and
not a BetweenLocation !
			 */
			
			if(loc instanceof BetweenLocation) {
				// ok
				System.out.println("[feature] location
is still a BetweenLocation: "
				+ loc.getClass().getName());
			}
			else {
				// problem
				System.out.println("[feature] location
is now an instance of: " 
							+
loc.getClass().getName());
			}
		}
	}
	
	public void generateOntolgyPersistenceProblem() throws Exception
{

		BioSQLSequenceDB db2 = new BioSQLSequenceDB(driver, url,
user, pass
	
, "testbiosqldb_2", true);
									
		/*
		 	EXCEPTION: the second addSequence will cause a
exception 
		 	in the ontology persistence code

			Caused by: java.sql.SQLException: Failed to
persist term: ATYPE from ontology: ontology: __biojava_guano with error:
-9 : 23000
				at
org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:5
06)
				at
org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:4
68)
				... 12 more
			Caused by: java.sql.SQLException: Violation of
unique index: SYS_IDX_SYS_CT_9_10 in statement [insert into term
(name, definition, ontology_id) values (?, ?, ?)]
				at
org.hsqldb.jdbcDriver.throwError(Unknown Source)
				at
org.hsqldb.jdbcPreparedStatement.executeUpdate(Unknown Source)
				at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delega
tingPreparedStatement.java:233)
				at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delega
tingPreparedStatement.java:233)
				at
org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:4
98)
				... 13 more
		 */
		
		db2.addSequence(getSequence()) ;
	}
	
	public static Sequence getSequence() throws Exception {
		SymbolList sl =
DNATools.createDNA("ACTGGTGTACCCCAATGGGAATATC") ;
		Sequence sequence = new SimpleSequence(sl, null,
"test_seq", null);
		sequence.createFeature(getFeature());
		return sequence ;
	}
	
	private static StrandedFeature.Template getFeature() throws
Exception {
		SimpleAnnotation annotation = new SimpleAnnotation();
		annotation.setProperty("Comment", "comment line");
		StrandedFeature.Template templ = new
StrandedFeature.Template();
		templ.annotation = annotation;
		templ.location = new BetweenLocation(new
RangeLocation(3,4));
		templ.strand = StrandedFeature.POSITIVE;
		templ.type = "ATYPE";
		templ.source = "ASRC";
		
		return templ ;
	}
	
	public static void main(String[] args) {
		BioSqlTest test = new BioSqlTest() ;
		try {
			test.generateFeaturePersistenceProblem() ;
		}
		catch(Throwable t) {
			t.printStackTrace();
		}

		try {
			//test.generateOntolgyPersistenceProblem() ;
		}
		catch(Throwable t) {
			t.printStackTrace();
		}
		finally {
			System.exit(0);
		}
	}
}

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From jan.wuerthner at uni-duesseldorf.de  Thu Jan 29 14:23:54 2004
From: jan.wuerthner at uni-duesseldorf.de (Jan =?iso-8859-15?q?W=FCrthner?=)
Date: Thu Jan 29 14:29:03 2004
Subject: [Biojava-l] creating a sequence...
Message-ID: <200401292023.54751.jan.wuerthner@uni-duesseldorf.de>


Hi,

I have written a BlastParser for xml based BLAST results, in order to 
reconstruct SeqSimilaritySearchResult instances from xml files returned by 
the NCBI for BLAST requests.

In constructing the searchresult, I use

SequenceBuilder sb = new SimpleSequenceBuilder();
SeqSimilaritySearchResult result
    = new SimpleSeqSimilaritySearchResult( sb.makeSequence(),
							  new DummySequenceDB("dummy"),
							  searchParameters,
							  hits,
							  new SimpleAnnotation(annotations));
where hits is a List of SeqSimilaritySearchHits and searchParameters and 
annotations are Maps.

The XML file still contains information about the query, like ID and length, 
but not the whole query sequence, e.g.:

  <BlastOutput_query-ID>gi|1698579|gb|U60438.1|MMU60438</BlastOutput_query-ID>
  <BlastOutput_query-def>Mus musculus serum amyloid A protein isoform 2 mRNA, 
complete cds</BlastOutput_query-def>
  <BlastOutput_query-len>576</BlastOutput_query-len>

Here is my question:

How can I adopt this information into the SimpleSeqSimilaritySearchResult? The 
sequence I obtain by

  sb.makeSequence()

of course does not contain anything. Is there a way to construct a sequence by 
the query-ID, query-def and query-len? (Especially the length is something I 
need!)

Thanks in advance
Jan


-- 
Jan W?rthner
Institute for Medical Microbiology
Building 22.21
Heinrich-Heine-University
Universit?tsstra?e 1
40225 Duesseldorf

Tel. +49 (0) 211 81 12461
URL: www.medmikro.uni-duesseldorf.de


From jan.wuerthner at uni-duesseldorf.de  Thu Jan 29 15:54:26 2004
From: jan.wuerthner at uni-duesseldorf.de (Jan =?iso-8859-15?q?W=FCrthner?=)
Date: Thu Jan 29 15:59:22 2004
Subject: [Biojava-l] creating a sequence...
In-Reply-To: <200401292023.54751.jan.wuerthner@uni-duesseldorf.de>
References: <200401292023.54751.jan.wuerthner@uni-duesseldorf.de>
Message-ID: <200401292154.26545.jan.wuerthner@uni-duesseldorf.de>


Sorry for answering the email myself...

after looking at it again, I think it is adequate to treat these three 
elements (query-ID, query-def and query-len) as annotations. There is no 
sense in assigning them to an unknown sequence, right?

I have implemented it this way and it works fine,
thanks anyway

kind regards
Jan


Am Thursday 29 January 2004 20:23 schrieb Jan W?rthner:
> Hi,
>
> I have written a BlastParser for xml based BLAST results, in order to
> reconstruct SeqSimilaritySearchResult instances from xml files returned by
> the NCBI for BLAST requests.
>
> In constructing the searchresult, I use
>
> SequenceBuilder sb = new SimpleSequenceBuilder();
> SeqSimilaritySearchResult result
>     = new SimpleSeqSimilaritySearchResult( sb.makeSequence(),
> 							  new DummySequenceDB("dummy"),
> 							  searchParameters,
> 							  hits,
> 							  new SimpleAnnotation(annotations));
> where hits is a List of SeqSimilaritySearchHits and searchParameters and
> annotations are Maps.
>
> The XML file still contains information about the query, like ID and
> length, but not the whole query sequence, e.g.:
>
>  
> <BlastOutput_query-ID>gi|1698579|gb|U60438.1|MMU60438</BlastOutput_query-ID
>> <BlastOutput_query-def>Mus musculus serum amyloid A protein isoform 2
> mRNA, complete cds</BlastOutput_query-def>
>   <BlastOutput_query-len>576</BlastOutput_query-len>
>
> Here is my question:
>
> How can I adopt this information into the SimpleSeqSimilaritySearchResult?
> The sequence I obtain by
>
>   sb.makeSequence()
>
> of course does not contain anything. Is there a way to construct a sequence
> by the query-ID, query-def and query-len? (Especially the length is
> something I need!)
>
> Thanks in advance
> Jan

-- 
Jan W?rthner
Institute for Medical Microbiology
Building 22.21
Heinrich-Heine-University
Universit?tsstra?e 1
40225 Duesseldorf

Tel. +49 (0) 211 81 12461
URL: www.medmikro.uni-duesseldorf.de