Fixed in CVS now
- Mark
"Heather Kent" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
03/02/2006 05:15 AM
To: [email protected]
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] problems with SubIntegerAlphabet
Hi
MAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
03/02/2006 05:15 AM
To: [email protected]
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject:[Biojava-l] problems with SubIntegerAlphabet
Hi,
i'm currently having a problem with the
IntegerAlphabet.SubIn
Hi,
i'm currently having a problem with the
IntegerAlphabet.SubIntegerAlphabetclass. When i make a call to the
seqstring() method from
AbstractSymbolList i get an error, No such element Exception "parser not
supported by Integer Alphabet yet" in the getTokenization method of my
SubIntegerAlphab
Hi,
[EMAIL PROTECTED] wrote:
I followed the instructions on how to install BioJava and the jar files. I tried the code 'How
can I make a motif into a regular expression' and get the error message that the compiler
cannot locate the package java.util.regex. Where should this package be located sin
I followed the instructions on how to install BioJava and the jar files. I tried the
code 'How
can I make a motif into a regular expression' and get the error message that the
compiler
cannot locate the package java.util.regex. Where should this package be located since
I
don't seem to have i
Millis.
>
> -Original Message-
> From: Schreiber, Mark
> [mailto:[EMAIL PROTECTED]
> Sent: Thursday, August 07, 2003 5:44 PM
> To: David Millis; [EMAIL PROTECTED]
> Subject: RE: [Biojava-l] problems installing biojava
> on Windows 2000
>
> Hi -
>
> Your
5:10 AM
To: 'Schreiber, Mark'
Cc: [EMAIL PROTECTED]
Subject: RE: [Biojava-l] problems installing biojava on Windows 2000
Mark -
Thanks for your response to my message.
I am using the netBeans 3.5 IDE for editing and compiling Java files. I
have found that if I mount the biojava-1.30-jdk14.ja
Hi,
I construct a profile HMM with randomized uniform distributions. I then train
the model and, regardless of the training set I use, it ends up looking like
this:
- a 0.999 probability to go from one delete state to the next
- roughly a uniform emission distribution for emission states (insert
From: Schreiber, Mark [mailto:[EMAIL PROTECTED]
Sent: Thursday, August 07, 2003 5:44 PM
To: David Millis; [EMAIL PROTECTED]
Subject: RE: [Biojava-l] problems installing biojava on Windows 2000
Hi -
Your class path looks OK but you can check that it has actually been set
by running set command wi
less you will also need the
Jakarta-Regexp jar on your path.
- Mark
-Original Message-
From: David Millis [mailto:[EMAIL PROTECTED]
Sent: Friday, 8 August 2003 6:04 a.m.
To: [EMAIL PROTECTED]
Subject: [Biojava-l] problems installing biojava on Windows 2000
Hello,
I am new to using
Hello,
I am new to using biojava. I am trying to install biojava on a PC running
Windows 2000 Professional. I am using Java 2 SDK version 1.4.2. I have
downloaded the files in the "binaries" directory in the download area of the
biojava server to the directory "C:\biojava" on my computer. I have
Hi,
I can't get the SearchProfile demo to work and I have tried various input
files. Is there a sample file available that will work so I can test if
something else is wrong?
Thanks,
Henry Romijn
Quoting [EMAIL PROTECTED]:
> Hi,
>
> I have tried to run the SearchProfile demo with something
Hi,
I have tried to run the SearchProfile demo with something simple like:
>a
MGNA
>b
MGNA
>c
MGNA
>d
MGNA
I use the ProfileHMM constructor that has a string as one of its parameters
(instead of the deprecated one). There appear to be no problems in creating
and initializing the ProfileHMM obj
> sure you don't have any older copies on your CLASSPATH or in
> the Java extensions directory (${JAVA_HOME}/jre/lib/ext/ on Unix,
> can't remember the exact name on OSX).
This was the problem..i got an old bytecode.jar in ext dir...working fine
now.
Thanks
Aroul.
__
Hi,
I have the same problem as well...
on linux, java 1.4.0_01-b03 build.
Aroul.
On Fri, 23 May 2003, Sylvain Foisy wrote:
> Hi to all,
>
> I have been having problems compiling biojava-live for that past few days
> now. My ant output is like this:
>
> compile:
> [javac] Compiling 48 sou
Once upon a time, Sylvain Foisy wrote:
> Hi to all,
>
> I have been having problems compiling biojava-live for that past few days
> now. My ant output is like this:
>
> compile:
> [javac] Compiling 48 source files to
> /Users/foisys/biojava-live/ant-build/classes/main
> [javac]
> /Users/
Hi to all,
I have been having problems compiling biojava-live for that past few days
now. My ant output is like this:
compile:
[javac] Compiling 48 source files to
/Users/foisys/biojava-live/ant-build/classes/main
[javac]
/Users/foisys/biojava-live/ant-build/src/main/org/biojava/bio/dp/t
Hi to all,
I have been having problems compiling biojava-live for that past few days
now. My ant output is like this:
compile:
[javac] Compiling 48 source files to
/Users/foisys/biojava-live/ant-build/classes/main
[javac]
/Users/foisys/biojava-live/ant-build/src/main/org/biojava/bio/dp/t
Hi,
I am parsing in RNA sequence data. One of the positions has a 'R' which
stands for the ambiguity symbol A or G. However, the RNA alphabet does
not have this as a token for anything (I did a quick test, and the
ambiguity token for A or G is N). So the genbank reader falls over when
it gets t
Hi,
I want to scan portions of sequences for motifs. I am trying to modify the
annotation for the sequence so that each time a motif is found, I get a new
annotation of the form "Motif x"+original annotation. It works when I print
it on the terminal with System.out but when I try to save the seque
Alexander Churbanov wrote:
Hello Matthew or Thomas,
I just use SAX BLAST parser to parse a massive of
BLAST output. Unfortunately this package does a really
poor job in a batch mode. It runs out of memory
because of the recursive self-calls which adversely
affects the heap.
I know that
Hello Matthew or Thomas,
I just use SAX BLAST parser to parse a massive of
BLAST output. Unfortunately this package does a really
poor job in a batch mode. It runs out of memory
because of the recursive self-calls which adversely
affects the heap.
I know that you have borrowed this from a
Hi Sylvain,
You could try:
cvs update -Pd
This will attempt to pull in any new directories and
prune out any empty directories. If that doesn't fix
the problem, get back in touch. I tend to habitually
use this rather than the plain "cvs update" just in
case.
Matthew
--- [EMAIL PROTECTED], "Ph
On Thu, Nov 07, 2002 at 09:42:01AM -0500, [EMAIL PROTECTED] wrote:
> Hi,
>
> I have some difficulties compiling biojava-live for the past couples of
> days, both on my Linux WS at work and my PowerMac G4 at home. On both
> machines, ant gives me the same warnings:
>
> [javac] /Users/foisys/bioj
--- Original Message -
From: <[EMAIL PROTECTED]>; "Ph. D." <[EMAIL PROTECTED]>
To: <[EMAIL PROTECTED]>
Sent: Thursday, November 07, 2002 9:42 AM
Subject: [Biojava-l] Problems in compiling biojava-live
> Hi,
>
> I have some difficulties compiling biojava-live
Hi,
I have some difficulties compiling biojava-live for the past couples of
days, both on my Linux WS at work and my PowerMac G4 at home. On both
machines, ant gives me the same warnings:
[javac] /Users/foisys/biojava-live/ant-
build/src/main/org/biojava/bio/seq/io/GAMEFormat.java:37: package
On Tue, Mar 05, 2002 at 12:42:36PM +0200, Eli Reuveni wrote:
>
> I tried to installed the library of biojava but had some errors
> in class "AlphabetManager" where some packages didn't found:
>
> "AlphabetManager.java": Error #: 704 : cannot access directory org\w3c\dom
> at line 30, column 1
>
On Tue, 5 Mar 2002, Eli Reuveni wrote:
>
>
> Hi I am a student for Bioinformatics studies
> and now in tha phase of choosing a software to use
> in building a web based application for manipulating genes
> and archive.
> I tried to installed the library of biojava but had some errors
> in class
Hi I am a student for Bioinformatics studies
and now in tha phase of choosing a software to use
in building a web based application for manipulating genes
and archive.
I tried to installed the library of biojava but had some errors
in class "AlphabetManager" where some packages didn't found:
"A
On Mon, Nov 12, 2001 at 12:39:50PM -0500, Andy Hunsucker wrote:
> Yes, this class is outside the heirarchy. When I compile the program, it
> gives a "cannot resolve symbol" error on the line in which I instantiate the
> variable to use in the program. For instance:
>
> RNA gc = new RNA();
>
>
Thanks for your help, I got it figured out.
- Original Message -
From: "David Huen" <[EMAIL PROTECTED]>
To: "Andy Hunsucker" <[EMAIL PROTECTED]>
Cc: <[EMAIL PROTECTED]>
Sent: Monday, November 12, 2001 2:50 AM
Subject: Re: [Biojava-l] problems gett
t
commands from the "RNA" class, it works fine.
Any other ideas?
Thanks for your help.
- Original Message -
From: "David Huen" <[EMAIL PROTECTED]>
To: "Andy Hunsucker" <[EMAIL PROTECTED]>
Cc: <[EMAIL PROTECTED]>
Sent: Monday, November
On Mon, 12 Nov 2001, Andy Hunsucker wrote:
> I'm having some problems with a program I'm writing. I've got all
> the biojava code written in a seperate class from my main program. I
Do I correctly assume that this class is outside of the biojava source
hierarchy as well?
> keep getting "cann
I'm having some problems with a program I'm
writing. I've got all the biojava code written in a seperate class from my
main program. I keep getting "cannot resolve symbol" errors whenever I try
to call that class's constructor. I've traced the problem to the fact that
my system will not r
Hi,
What JAVAC are you using, I seem to be able to build this fine.
Mark
On Mon, 29 Oct 2001, Howard Ungar wrote:
> I am having problems compling 4 of the files in the CVS archives. I
> was trying to get the latest version of certain other files when I ran
> into this.
>
> C:\java\biojava-l
I am having problems compling 4 of the files in the CVS archives. I
was trying to get the latest version of certain other files when I ran
into this.
C:\java\biojava-live>ant
Searching for build.xml ...
Buildfile: C:\java\biojava-live\build.xml
init:
prepare:
prepare-src:
compile:
[javac
> "Ron" == Ron Kuhn <[EMAIL PROTECTED]> writes:
Ron> BioJAVA, I submitted 2 problems (including fixes) to the
Ron> BIOJava Bug Tracking Web Interface. Without these fixes,
Ron> users will receive exceptions while trying to parse the
Ron> current Genbank and Swissprot files. I
BioJAVA,
I submitted 2 problems (including fixes) to the BIOJava Bug Tracking Web
Interface. Without these fixes, users will receive exceptions while trying
to parse the current Genbank and Swissprot files. I just wanted to make sure
these fixes make it into the next release. I don't know how oft
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