[Joelib-devel] errors

[Ambrish R. <che...@ya...>]

Hi
there is a problem in compiling 
can anyone help 
the error is 
reader = new SimpleReader(input, inType);
Does anyone knows the solution....
Please reply back immediately
Thanks
Ambrish


"Joerg K. Wegner" <we...@in...> wrote:
Hi Ambrish,

1. please use the mailing list, such things are interesting for all 
users. I forward it automatically, hope you don't mind.

> 4. i have put all the necessary jar files in JOELib\lib.
> but when i run Test.java i get errors like
> package joelib.molecule does not exist import joelib.molecule.JOEAtom;
> package joelib.data does not exist import joelib.data.JOEPairData;
> and similar errors.
The compiler does not find the sources and/or the build directory or the 
joelib.jar. Do you have set also JOELIBDIR?
2. Installation is the most critical step. I strongly recommend to use 
'cygwin' instead of the DOS prompt. Unfortunately this is tricky to 
install. Then you can work with the shell scripts build.sh.

Sorry, i might have no quick fix for this problem, so i tell you 
possible solutions and you can decide which one might be the fastest:

2.1. Use the joelib.jar-file (only if you don't need the interface 
classes, like CDK, Java3D, Ghemical, ...)

2.2. Use Windows with BAT-files. Problem: The classpath must be checked 
by hand, that it includes all required .jar files and directories. 
Please check if you have set:
JAVA_HOME
ANT_HOME
JOELIBDIR

2.3. Use Windows/Cygwin or Linux, then you can use the shell scripts SH. 
They will find all required jar files in the lib directory 
automatically. So, this is much easier than fixing them by hand. If you 
are a Windows user, installing Cygwin might be a problem, because the 
installation menu is not optimal.
Please check if you have set:
JAVA_HOME
ANT_HOME
JOELIBDIR

2.4. Install ANT and add it to your PATH environment. If this was done 
you can use: 'joelib/ant/ant compile'. That's what is done, by the 
build.sh anyway. Then you must not set JOELIBDIR, because only the shell 
scripts require this environment option.

> I am soory to bother you so much but i need ur help immediately as i have to complete my project before 10th December.
> Can you please tell me in detail how to start using and copiling all the packages....
> Looking forrward for an early reply.
> Ambrish
> Bioinformatics Centre
Sorry, for this late reply.

Kind regards, Joerg
> 
> 
> "Joerg K. Wegner" wrote:
> Hi Ambrish,
> 
> 1. LOG4J requires its property file in the classpath. If you use the 
> source code distribution (strongly recommended) this will be copied 
> automatically to
> joelib/build/log4j.properties
> 
> 2. Seems that there are the required libraries missing which are located 
> under joelib/lib/log4j.jar
> 
> Please check carefully if the properties and the libraries are part of 
> your classpath.
> You can resolve such things dynamically via ANT or the included shell 
> scripts. For Windows and your own potential application you must check 
> such things 'by hand'.
> 
> Kind regards, Joerg
> 
> 
> 
>>hi
>>thanx for the prompt reply.....
>>i am having problem s like
>>1.package org.apache.log4j does not exist import org.apache.log4j.Category;
>>2. private static Category logger = Category.getInstance(
>>
>>I tried to configure log4j but still the problem persists. i also searched for the solution but got some hits like This class has been deprecated and replaced by the Logger subclass
>>should i replace that in my program.
>>
>>
>>
>>
>>
>>"Joerg K. Wegner" wrote:
>>Hi Ambrish,
>>
>>
>>
>>>i am a new user to JOELib but am not able to make out how to get started with the package....
>>>Can somebody write to me in detail how to start and if i want to write a program using this package where will i have to store the program i.e whether in same directory?
>>
>>I recommend to start with all examples in joelib/src/joelib/test
>>Have a look at them and try to understand them, then you will know the 
>>basic functionalities.
>>
>>
>>
>>>Also i am getting problem with setting with JOELib enviornment.
>>
>>That's to sloppy fomulated.
>>What are your problems: Java, ANT, eclipse, properties files, 
>>protonation model, atom typer, ...
>>
>>Kind regards, Joerg
> 
> 
> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
(E. Hemingway)

Never mistake action for meaningful action.
(Hugo Kubinyi,2004)



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