[Biojava-l] Ontology and BioSQL

L.persistTerm(OntologySQL.java:5 54) ... 7 more Java Result: 1 When I check in the database, I find that the ontology has been created, and entries made in term for each of the terms, and also an entry has been made in term for the triple itself. So why the exception? Is it trying to insert

RE: [Biojava-l] Ontology and BioSQL

lready exists in the term table _before_ persistTriple is getting called. Why? How? Hmm. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipie

RE: [Biojava-l] Ontology and BioSQL

() from the start of the persistTriple() method in OntologySQL, as the action has already been done at this stage by the Ontology.TERM change event. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is

RE: [Biojava-l] Ontology and BioSQL

That'd be nice but unfortunately Oracle is case-sensitive. However I think I just got what was causing it, see my post of 5 seconds ago. I'm not sure why it hasn't broken for other people though. cheers, Richard Richard Holland Bioinformatics Specialist GIS

[Biojava-l] Fix to org.biojava.bio.seq.db.biosql.OntologySQL

ology obtained from an BioSQLSequenceDB object. The upload example I gave now works without a hitch. Does anyone want to verify this and update CVS if it works and doesn't break anything else? cheers, Richard Richard Holland Bioinformatics Specialist GIS exte

[Biojava-l] Ontology and BioSQL

ySQL.persistTerm(OntologySQL.java:5 54) ... 7 more Java Result: 1 When I check in the database, I find that the ontology has been created, and entries made in term for each of the terms, and also an entry has been made in term for the triple itself. So why the exception? Is it trying to insert th

[Biojava-l] Exception handling

what type it is likely to be, then behave nicely instead of killing the whole app. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended re

[Biojava-l] Exception not being caught.

I am getting an exception thrown by my code that never seems to get caught. I am not sure if this is because of BioJava or because of a lack of understanding of Exceptions on my part? The exception causes the program to grind to an immediate halt. My method throws the general Exception class, but t

RE: [Biojava-l] Exception not being caught.

BioException that people could catch easily? cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us

[Biojava-l] Blast SAX parser output

)); breader.setContentHandler(adapter); breader.parse(is); cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete it and

RE: [Biojava-l] can use biojava in JApplet?

interdependencies. Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose

RE: [Biojava-l] reading nib sequence files

It's a compressed binary format. I doubt BioJava would be able to read it without a lot of effort as the current parser framework is set up for text input only. Richard Holland Bioinformatics Specialist GIS extension 8199 - This ema

RE: [Biojava-l] reading nib sequence files

rn singleton Symbol objects if requested, by decoding the binary sequence on the fly, but you would no longer need to store the sequence using them. Is this worth considering for the big BioJava rewrite? Richard Holland Bioinformatics Specialist GIS extension 8199 ---

RE: [Biojava-l] reading nib sequence files

NIB files store one base per 4 bits, non-variable, giving a 50% compression rate and a maximum arity of 16 different base values per position. Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be

RE: [Biojava-l] reading nib sequence files

slowing down the create/update process too much either. Hence a custom fixed-width binary solution would be the first thing that comes to mind, but it may not be the only one. Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is

RE: [Biojava-l] reading nib sequence files

a good thing to work into the mechanism. Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not

[Biojava-l] PatternHunter parsing

Are there any BioJava or BioPerl modules for parsing PatternHunter output? It's very similar to Blast output, so if there isn't one already, would other people be interested in using one if I wrote one? cheers, Richard Richard Holland Bioinformatics Specialist GIS exte

[Biojava-l] RE: [BioSQL-l] release preparation

ther Bio* projects who use the simple schema though so we probably can't just drop it. Are there any objections? I have crossposted this to the BioJava list to make sure everyone who might be affected gets a say. cheers, Richard Richard Holland Bioinform

[Biojava-l] RE: [BioSQL-l] release preparation

aving table helpers in BioJava to check which version to use and therefore maintain backwards compatibility is a good one. It's slightly more work, but not too much to warrant a major panic attack. I'll let you know when biojava-live has been updated. cheers, Richard Richa

RE: [Biojava-l] setting up biojava and running a program for translate

Include the downloaded jar files on your classpath when running any programs using them. Otherwise you will get exactly the errors you mention below. Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be

[Biojava-l] BioJava/BioSQL on Oracle

would attempt to reference the triple by its unique ID before actually giving it one, which of course fails. This should now be fixed. cheers, Richard Richard Holland Bioinformatics Specialist Genome Institute of Singapore 60 Biopolis Street, #02-01 Genome, Singapore 138672 Tel: (65) 6478 8000

[Biojava-l] RE: [BioSQL-l] location in features

s already fixed your problem. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not

[Biojava-l] RE: [BioSQL-l] location in features

he feature object location to Location.empty. I have committed this change to biojava-live, so you will need to use CVS to check out a copy of biojava-live to see if this has solved your problem. For the copy of your code which I have here, it works fine. cheers, Richard Richard Holland Bioi

RE: [Biojava-l] Fasta File

http://www.biojava.org/docs/api/ cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please d

RE: [Biojava-l] Fasta File

My apologies - that should have been db.sequenceIterator() not db.getSequenceIterator()...! cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended

[Biojava-l] Term Synonyms

problems. cheers, Richard Richard Holland Bioinformatics Specialist Genome Institute of Singapore 60 Biopolis Street, #02-01 Genome, Singapore 138672 Tel: (65) 6478 8000 DID: (65) 6478 8199 Email: [EMAIL PROTECTED] - This email is confidential and may be

RE: [Biojava-l] How to read in an aligment and then start viterbi

od which shows (a) how you construct the alphabet, (b) creating the Hmm with it, (c) reading the alignment file, and (d) passing it to Viterbi. It doesn't have to be very complicated or intricate as long as it shows what you are doing and produces similar exceptions. cheers, Richard Ri

RE: [Biojava-l] nested features

l erasure). This probably won't fix it, but it's worth a try. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete

RE: [Biojava-l] BioException Error

spath contains nothing else (except other jar files your project requires, that is). cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, p

[Biojava-l] Change Proposal regarding References

d help from everyone out there in updating the file parsers to use this proposed mechanism. cheers, Richard Richard Holland Bioinformatics Specialist Genome Institute of Singapore 60 Biopolis Street, #02-01 Genome, Singapore 138672 Tel: (65) 6478 8000 DID: (65) 6478 8199 Email: [EMAIL PROTECT

RE: [Biojava-l] Change Proposal regarding References

#x27;identifier' and 'provider' fields in BibRef are optional and only for use when a PubMed/Medline etc. value has been specified in the original file. They will both be ignored by the BioSQL persistence layer if either are set to null. cheers, Richar

RE: [Biojava-l] Re: [Biojava-dev] Local binary execution

at 1.4.2 (from HP), likewise PPC (from IBM), whereas ia64 can run 1.5 apps using HP's JRE but no compiler yet exists for them. There may also be some open source purists out there who object when they can't use their favourite open source JDK any more... Richard Holland Bioinformatics

RE: [Biojava-l] Phrap output

s them and writes out the corresponding bits of file. You'd also have to decide how to represent the assembly once it is in memory. The interface org.biojava.seq.Assembly might be a good starting point. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199

[Biojava-l] RE: [BioSQL-l] _removeSequence

Perl-db already makes this assumption. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Ple

[Biojava-l] RE: [BioSQL-l] _removeSequence

ely I don't currently use the MySQL implementation myself so I can't help much. I hope someone on BioSQL-L knows a little more? Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If

RE: [BioSQL-l] Re: [Biojava-l] _removeSequence

There is also the BS-zap-all script in the BioSQL distribution which will wipe the whole lot for you in one go. :) Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the

[Biojava-l] RE: [BioSQL-l] update seqfeature

Actually, BioJava is not that clever. Yet. Martina's original observation is right, in that the correct way to do this would be to check the database to see if the altered seqfeature already existed, and if it did, to refer to that one instead. But this is not the way BioJava does things at pres

RE: [Biojava-l] Re: [BioSQL-l] _removeSequence

The revamped BioJava/BioSQL classes will expose the rank to the user for all tables which have ranks. cheers, Richard -Original Message- From: [EMAIL PROTECTED] on behalf of Simon Foote Sent: Wed 6/22/2005 12:15 AM To: Martina Cc: Hilmar Lapp; [EMAIL PROTECTED]; BioJava; [EM

RE: [Biojava-l] BLAST Parser for extracting all BLAST data?

BioJava's BLAST framework parses files and fires events for every piece of information it finds. The SeqSimilarityAdapter class is an example of how to catch these events and construct basic BLAST result objects (SimpleSeqSimilarityHit), however they are not comprehensive and do not record full

RE: [Biojava-l] Psi-Blast results

The standard BLAST parser in BioJava cannot understand PsiBLAST output as far as I'm aware. I haven't used PsiBLAST much so I don't know if you can change its output format, but if you can persuade it to output its results in NCBI BLAST format instead, then you might have more luck. BioPerl mos

RE: [Biojava-l] Implementing a Feature

The best thing to do is write your own class which extends SimpleFeature, or ignores SimpleFeature and just implements the Feature interface with all-new methods written from scratch, plus your new ones. If the extra methods are pretty generic, you could create a new interface which extends Fea

RE: [Biojava-l] New look for BJIA

ility. Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or dis

RE: [Biojava-l] New look for BJIA

Sneaky trick that might just work : make the code listing a numbered list, then use CSS to format it so that the numbers are nicely justified. When you copy-paste a numbered list the numbers don't get included! Richard Holland Bioinformatics Specialist GIS extension

RE: [Biojava-l] memory leak while reading nr.fasta

a random-access one. Can someone clarify if a lazy-loading parser/database implementation already exists for situations like this, or does one need to be written? cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email i

RE: [Biojava-l] Dealing with huge sequences (was: "memory leak whilereading nr.fasta")

t along, unless otherwise told not to, to prevent duplicate reads where multiple accesses take place. This however is fundamentally different to the way files are currently parsed in BioJava. Not sure how it would actually work in reality. Any takers? Richard Holland Bioinformatics Specialist GIS

RE: [Biojava-l] field names in term_synonym

atement should be moved to the database-specific DBHelper class (HypersonicDBHelper, MySQLDBHelper, OracleDBHelper, etc.), as is done with references to the 'seq' column of the 'biosequence' table for instance. Richard Holland Bioinformatics Specialist GIS extension 8199 -

RE: [Biojava-l] FASTA Parser problems

Could you send me the input file you are using as an attachment (directly, not via the mailing list as it will get removed), I can then run the script and compare input to output. Also, which BioJava version are you using? cheers, Richard Richard Holland Bioinformatics Specialist GIS extension

RE: [Biojava-l] Sequence and String

Internally the Sequence is stored not as a String but as an array of Symbol objects. Hence when you call seqString(), a new String is generated every time by appending the results of calling toString() on every Symbol object in the internal array. cheers, Richard -Original Message- Fr

RE: [Biojava-l] Add Symbols in a Sequence

SymbolLists are generally immutable. To edit one you have to apply Edits to it. See http://biojava.org/docs/bj_in_anger/edit.htm for details. cheers, Richard. Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is

RE: [Biojava-l] Blast xml parser question -- new to Biojava

/blastecho.htm cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any

RE: [Biojava-l] ZTR trace file parser?

ldly wrong). The ABI parser can be found at org.biojava.bio.program.abi.ABIFParser. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please

RE: [Biojava-l] Newbie Installation Question

aming or doing stuff behind the scenes to the jar files when you download them, try using Firefox (I haven't used IE for so long I can't remember how to fix that particular problem). cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 -

[Biojava-l] RE: [BioSQL-l] Special cases of protein data

uld such a required dependency be justified for the sake of correct parsing of multiple sources? cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intende

RE: [Biojava-l] is valid character

) System.out.println("Alphabet DOES contain token "+token); else System.out.println("Alphabet DOES NOT contain token "+token); cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is conf

RE: [Biojava-l] 3 questions and problems

s for myself. Is using just Protein a viable alternative? 3. Dunno, that's a question that sounds like something Mark might be able to answer. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential

RE: [Biojava-l] classpath

Also, check that your classpath only contains one reference to the jar file, not two or more, as having multiple references to copies in different locations has the same effect as not including it at all. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199

RE: [Biojava-l] Another problem with TaxonFactories

biojavax should circumvent this. have a look in the org.biojavax.bio packages in biojava-live for a sneak preview. Basically we have adopted the BioSQL conventions, and created a new NCBITaxon class to represent the table from the database. The code is written to work with Hibernate for database

[Biojava-l] BioJavaX ready for testing

is to make all this an official part of BioJava come the 1.5 release, whenever that may be. For now though it is very very much a testing-stage thing, not even an alpha release. Questions on a postcard to either Mark or myself. Feedback most welcome. cheers, Richard Richard Holland Bioi

RE: [Biojava-l] Extract accession number out of xml blast result

ll provide a direct pointer into your list to tell you which query accession you are currently working with. Likewise, you should know already what blast database you blasted against, so you shouldn't really need to get this information from the results. cheers, Rich

RE: [Biojava-l] install Biojava

your user profile that is run when you start a shell, or to the system profile that is run for everyone when they start a shell. Or, write a wrapper script for javac that sets the classpath each time before calling the real javac. cheers, Richard Richard Holland Bioinformatics Specialist GIS exte

RE: [Biojava-l] Error loading ontology terms

s, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, o

RE: [Biojava-l] Multiple questions

Hello Ola, > 1) Is it possible to search the Biojava-l archives without having to > manually browse by month? Not that I know of. Google is a pretty good alternative as it has indexed all the archive - just add +"biojava-l" to the beginning of your query. > 2) Is there a wrapper for SequenceIO.

RE: [Biojava-l] DAS questions

ring)i.next()); } Hopefully you will be able to find out whats going on by investigating the contents of this set. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privilege

RE: [Biojava-l] Multiple questions

// Iterate over the sequences while (seqs.hasNext()) { RichSequence rs = seqs.nextRichSequence(); // ... Do something with it here ... } cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - Thi

RE: [Biojava-l] sturcture.io

Combine into a single String separated with newline characters, then see java.io.StringReader - this provides a Reader, which you can then wrap in a BufferedReader. Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is

RE: [Biojava-l] modify structure

See the addChain(), addModel() and setConnections() methods in the Structure interface. For addChain() and addModel() also refer to the Chain and Model interfaces in the same package. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199

RE: [Biojava-l] cvs downlod install

ing the backslash. Try replacing it with a double backslash (\\) or a forward slash (/). cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, plea

RE: [Biojava-l] cvs ant build failure

the Matrix and SingularValueDecomposition classes. Andreas can you fix this please? cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, ple

RE: [Biojava-l] cvs ant build failure

*doh!* All working. Thanks, Andreas. Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy

RE: [Biojava-l] Sequence Iteration in BioJava(x)

n a SymbolList are 1-indexed, not 0-indexed. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediat

RE: [Biojava-l] Sequence Iteration in BioJava(x)

Mark's comments earlier make my sample code redundant. I had the two different window thingies confused. See his post for more details! cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 - This email is confidential an

RE: [Biojava-l] Gapping Sequence problems

I think you could try swapping the use of == for equals() when testing for equivalence to the gap symbol. It _should_ be the same literal object, but maybe not. equals() will work in both cases but == will not. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199