/2003 12:56 a.m.
To: [EMAIL PROTECTED]
Cc:
Subject: [Biojava-l] Question about Swiss-Prot parsing
Hello,
I am parsing some Swiss-Prot files with Biojava 1.3 and need to put the
contents into Sequence Collections. It does
Hello,
I am parsing some Swiss-Prot files with Biojava 1.3 and need to put the
contents into Sequence Collections. It does not crash but there are two
problems:
1. Each annotation is shown as the tag, followed by a colon and then the
content, so for example AC :Q9L867. Other parsers seem to be
I'd go and put all of it in, no reason that RNA should be treated
differently from DNA there.
Francois
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]] On Behalf Of Thomas Down
Sent: 5 fevrier, 2003 12:32
To: Keith James
Cc: [EMAIL PROTECTED]
Subject: Re: [Bioj
On Wed, Feb 05, 2003 at 03:52:03PM +, Keith James wrote:
>
> I got bitten by this too, when porting some of the code. If you look
> in biojava-live/resources/org/biojava/bio/symbol/AlphabetManager.xml
> you will see that the default RNA alphabet contains only
> agcu-~. i.e. no ambiguity symbols
> "dion" == dion whitehead <[EMAIL PROTECTED]> writes:
dion> Hello, I am having a frustrating time with attempting to
dion> read in rna sequences. They contain the 'N' symbol which is
dion> a standard ambiguity symbol, but the code trips up on this
dion> every time, saying its
Hello,
I am having a frustrating time with attempting to read in rna sequences.
They contain the 'N' symbol which is a standard ambiguity symbol, but the
code trips up on this every time, saying its not a recognized symbol in the
alphabet. Do I have to specify it myself?
Thanks, and keep up th
Hi,
There is a class called Tools in the symbol package,
which is one of the demos. If you go to
demos/symbol/Tools.java you will see the relevant
code. We should have realy explicitly imported this
class. Sory for the confusion caused.
Matthew
--- ??? <[EMAIL PROTECTED]> wrote: > Hi:
>
>
Hi:
Iam a newbie here. I try to learn from demos example. My question is the
first line immediately after main function in demos/seq/TestTranslation.java
SymbolList randomSeq = symbol.Tools.createSymbolList(30);
Obviously it randomly create a symbol list with length 30. But there is n
On Fri, Sep 20, 2002 at 03:18:07PM +0200, Stein Aerts wrote:
>
> I've had these questions since I started using Biojava a year ago, and I
> still can't get it right:
>
> 1. How can I take a certain part of an annotated sequence (let's say from bp
> 500 to 750), make a new sequence from this part
I've had these questions since I started using Biojava a year ago, and I
still can't get it right:
1. How can I take a certain part of an annotated sequence (let's say from bp
500 to 750), make a new sequence from this part, while retaining all
annotations of the piece, in new coordinates? So a
AIL PROTECTED]> on 09/11/2002 05:30:46 PM
To:"Patrick McConnell" <[EMAIL PROTECTED]>
cc:[EMAIL PROTECTED]
Subject:Re: [Biojava-l] Question about BioJava DASClient classes
>>>>> "Patrick" == Patrick McConnell <[EMAIL PROTECTED]> writes:
> "Patrick" == Patrick McConnell <[EMAIL PROTECTED]> writes:
Patrick> Incidentally, it breaks on fasta34t10d3 - the error is:
Patrick> org.biojava.utils.ParserException: Fasta parser failed to
Patrick> recognise line type Parsing line: 37 ; pg_open-ext: -10
Patrick> -2
Alrig
on 09/11/2002 01:36:59 PM
To:"Patrick McConnell" <[EMAIL PROTECTED]>
cc:[EMAIL PROTECTED]
Subject:Re: [Biojava-l] Question about BioJava DASClient classes
>>>>> "Patrick" == Patrick McConnell <[EMAIL PROTECTED]> writes:
Patrick>
> "Patrick" == Patrick McConnell <[EMAIL PROTECTED]> writes:
Patrick> I am getting a NullPointerException running Fasta2XML in
Patrick> demos/eventbasedparsing on a test fasta run using -m 10
Patrick> output. I have pasted the output/stack trace at the end.
Patrick> Any idea
I am getting a NullPointerException running Fasta2XML in
demos/eventbasedparsing on a test fasta run using -m 10 output. I have
pasted the output/stack trace at the end.
Any ideas?
Thanks,
-Patrick
http://www.biojava.org";>
pg_cgap: 46
pg_gap-pen: -16 -4
pg_ktup: 6
pg
On Fri, Sep 06, 2002 at 09:57:18AM +0200, Jansen wrote:
> Hi,
> currently I am trying to understand how the BioJava DASClient classes and
> their methods (e.g. ReferenceServer.getReferenceServers(),
> DASSequence.filter(), ...) map to the related http-requests. Does anybody
> know some details abo
Hi,
currently I am trying to understand how the BioJava DASClient classes and
their methods (e.g. ReferenceServer.getReferenceServers(),
DASSequence.filter(), ...) map to the related http-requests. Does anybody
know some details about that?
Thanks
Thorsten
___
Hello everybody,
Do we have implementation of Smith-Waterman local
alignment algorithm in the current version of BioJava?
Thanks,
Alexander Churbanov
__
Do You Yahoo!?
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http://fifawor
variables.
Best Regards,
Wook-Shin Han
-Original Message-
From: David Huen [mailto:[EMAIL PROTECTED]]
Sent: Thursday, April 18, 2002 3:46 PM
To: Wook-Shin Han
Cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] Question
On Thu, 18 Apr 2002, Wook-Shin Han wrote:
> Dear Sir,
>
&g
On Thu, 18 Apr 2002, Wook-Shin Han wrote:
> Dear Sir,
>
> I have installed biojava 1.2 in my pc.
>
> However, I found the following error when I execute a program using
> biojava.
> (No compilation error found)
>
> java.lang.NoClassDefFoundError: org/bio
Dear Sir,
I have installed biojava 1.2 in my pc.
However, I found the following error when I execute a program using
biojava.
(No compilation error found)
java.lang.NoClassDefFoundError: org/biojava/bio/symbol/SymbolList
Exception in thread "main"
Absol
Hello,
I got a problem with parsing Blast-result raport. When parsing the raport
with BlastLikeSAXParser and my own written handler-class I get the queries
after "Query="-string in endElement-method by finding them among all the
text wich is produced in "Header"-part's "RawOutput-part". This work
I removed the default constructor. It really shouldn't be there. I think the user
should explicitly state the isotope type. I also fixed a bug in the Protease
class that was causing me difficulties parsing
org/biojava/bio/proteomics/ProteaseManager.xml.
I don't know how it could have parsed corre
> "Sanjeev" == Sanjeev S Bajwa <[EMAIL PROTECTED]> writes:
Sanjeev> Hello, I have recently downloaded BioJava, and I am
Sanjeev> trying to use the getMass method the MassCalc class. I am
Sanjeev> using the constructor and method that does not require
Sanjeev> the isotopicType
Hello,
I have recently downloaded BioJava, and I am trying to use the getMass
method the MassCalc class. I am using the constructor and method that does
not require the isotopicType parameter. Every time I try to run the program
I wrote it gives me a runtime error:
Exception in th
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