[Biojava-l] Once more time
jon portuondo murguiondo
jon portuondo murguiondo <jon.portuondo01@campus.upf.es>
Fri, 27 Dec 2002 17:50:32
Mensaje con FORMATO mime.
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Hi! I have tried all the options you proposed me, and none worked at all. SOS!
I read the tutorial, very interesting.
http://java.sun.com/docs/books/tutorial/java/interpack/packages.html
I tried to put the .class in this directory
(relative to my CLASSPATH)
:/org/biojava/bio/program/PdbToXMLConverter.class
But it does'nt solve the problem.
If I put the .class in the directory where I run the
program, the error is the same.
On the other hand, if the .class is ONLY in the
package directory (the org/biojava....), I mean if I
remove the .class from the current directory, the
problem is:
[jon@diana ~]$ java PdbToXMLConverter 1FS1.pdb
Exception in thread "main"
java.lang.NoClassDefFoundError: PdbToXMLConverter
[jon@diana ~]$
In this configuration, if I type:
[jon@diana program]$ java org.biojava.bio.program.PdbToXMLConverter /home/jon/1FS1.pdb
Exception in thread "main" java.lang.NoSuchMethodError: main
I tried removing the package line "package
org.biojava.bio.program" of the .java, but the error was the same than the previous one.
This is my extra-large CLASSPATH:
CLASSPATH=/home/jon:/home/jon/java/llibreries/biojava-20020823.jar:/home/jon/java/llibreries/xerces.jar:/home/jon/java/llibreries/bytecode-0.91.jar:/home/jon/java/llibreries/jakarta-regexp.jar:/home/jon/java/llibreries/xml.jar:/usr/java/j2re1.4.1_01/lib/javaplugin.jar/home/jon/java/biojava-live/src.
I suppose there are too much directories in the CLASSPATH but I'm trying all possibilities I can imagine.
I have downloaded the source of the library biojava-20020823 (that is in a .tar.gz file in that direction: http://biojava.org/download/source/
Inside this document I don't find the package java.lang...
If I compile the PdbToXmlConverter.java that is inside biojava-20020823.tar.gz, the problem is exactly the same that the previous one(I say that because you can download that file and try to make it run).
I remember you I work in Linux with j2re1.4.1_01 and j2sdk1.
.4.1_01.
The questions are:
Where is java.lang package?
Is that in the biojava-20020823.jar library?
Could be any problem with the version number?
HOW CAN I SOLVE THE PROBLEM?
Thanks for all!
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From: =?iso-8859-1?q?Matthew=20Pocock?= <matthew_pocock@yahoo.co.uk>
Subject: Re: [Biojava-l] It's me once again
To: jon portuondo murguiondo <jon.portuondo01@campus.upf.es>,
biojava-l@biojava.org
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Date: Tue, 10 Dec 2002 17:16:01 +0000 (GMT)
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Hi,
Try reading through this tutorial. It should help fill
the gaps.
http://java.sun.com/docs/books/tutorial/java/interpack/packages.html
> I tried to put the .class in this directory
> (relative to my CLASSPATH)
> :/org/biojava/bio/program/PdbToXMLConverter.class
> But it does'nt solve the problem.
> If I put the .class in the directory where I run the
> program, the error is the same.
> On the other hand, if the .class is ONLY in the
> package directory (the org/biojava....), I mean if I
> remove the .class from the current directory, the
> problem is:
>
> [jon@diana ~]$ java PdbToXMLConverter 1FS1.pdb
> Exception in thread "main"
> java.lang.NoClassDefFoundError: PdbToXMLConverter
> [jon@diana ~]$
In this configuration, you would need to type:
java org.biojava.bio.program.PdbToXMLConverter
lFSl.pdb
Notice that the package prefix to the class matches
the package of the classes package & it's location.
>
> I tried removing the package line "package
> org.biojava.bio.program" but the following error
> ocurred while compiling:
>
> [jon@diana ~]$ javac PdbToXMLConverter2.java
> PdbToXMLConverter2.java:69: invalid method
> declaration; return type required
> public PdbToXMLConverter(String poInput) {
> ^
> 1 error
This is because you have renamed the class to
PdbToXMLConverter2, but have not renamed the
constructor to match the class name. Rename this
constructor to match the class name and try again.
Make sure that you use
java PdbToXMLConverter2 lFSl.pdb
OH. The name of a java class and of it's file must
match if it is a public class. So, if you have a class
called Foo, it must be in a file called Foo.java and
will produce a class file Foo.class and will have a
constructor called Foo() and you would run its main
method as java Foo <args>..
If it is in package bar, then the class is bar.Foo,
and it will be in a file bar/Foo.java and will produce
a class file bar/Foo.class and if it has a main method
you run it as java bar.Foo <args>.
Best,
Matthew
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