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add library to java, CLASSPATH, jar, linux

I've been browsering the Internet for a couple of hours and I am unable to find an answer to my question. The library I'm trying to add is JGraphT
I'm new to Java and I wanted to add a free graph library. I downloaded all .jar files and then the issues startet. What step by step should I do?
I found information about compiling with -cp or -classpath or addng .jar to CLASSPATH (I'm using Linux and I write my programms in gedit (obligatory for my studies) and compile it with terminal). But I wonder what should I do step by step?
What do I have so far:
I have downloaded multiple .jar and they all sit in one folder with
the xxx.java file I would like to compile
do I need to change CLASSPATH? How to do it? How should I compile and
run my program after changing CLASSPATH? The ordinary way(javac
xxx.java; java xxx) or should I change sth?
or maybe I don't need to change CLASSPATH just add -classpath while
compiling? If so, what should the compile anr run commend look
like?
Also I have already tried using -cp... I'm enclosing my lines in terminal. It compiled correctly, but when I tried to run it, I received strange errors. I'm sure the code is correct since it was given in the library as a way to test wether or not is it installed correctly.
wiktoria#wiktoria-1015PW:~/programowanie/grafy/java/testy$ javac -cp jgrapht-ext-0.9.1-uber.jar: HelloJGraphT.java
wiktoria#wiktoria-1015PW:~/programowanie/grafy/java/testy$ java -cp jgrapht-ext-0.9.1-uber.jar: HelloJGraphT
Exception in thread "main" java.lang.NoClassDefFoundError: HelloJGraphT (wrong name: org/jgrapht/demo/HelloJGraphT)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
wiktoria#wiktoria-1015PW:~/programowanie/grafy/java/testy$

Let's say your class belongs into the package net.example.graph. This means the real name of the class is net.example.graph.HelloJGraphT.
This also means you have a directory structure like this:
project_dir/net/example/graph
Go to the project_dir folder, then try this:
javac -cp <path to jgrapht JAR> net/example/graph/HelloJGraphT.java
java -cp <path to jgrapht JAR> net.example.graph.HelloJGraphT

How to use classpath in ubuntu terminal for executing java class?

I tried to execute CreateTextFileTest.class file with classpath in the terminal as the following:
java -classpath ..:"/home/fatih/NetBeansProjects/Unit17 - CreatingTextFile/src/unit17/unit17/creatingtextfile" CreateTextFileTest
My class files in this directory : /home/fatih/NetBeansProjects/Unit17 - CreatingTextFile/src/unit17/unit17/creatingtextfile .
I have 3 classes in the directory: AccountRecord.class , CreateTextFile.class, and CreateTextFileTest.class
But, when I executed the CreateTextFileTest from the terminal with the code above, an error occured like that:
Exception in thread "main" java.lang.NoClassDefFoundError: CreateTextFileTest (**wrong name**: unit17/creatingtextfile/CreateTextFileTest)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
As far as I understand because CreateTextFileTest.java uses two different classes, executing fails. How to handle this situation? How to run my java project? How to use classpath in this situation? Am I using wrongly?

The error message states that the package name declared in your compiled class doesn't match what the JVM was expecting given your classpath setup. The classpath should point to the directory from which your packages start, not the directory actually containing your .class files. Given your error message I believe that this should work:
java -classpath ..:"/home/fatih/NetBeansProjects/Unit17 - CreatingTextFile/src/unit17" unit17.creatingtextfile.CreateTextFileTest
Given the duplicate unit17 in your path I get the impression there's something else mixed up here. You'll get a better answer on Stack Overflow...

Java program executes in eclipse but not in terminal

I am using Eclipse with Eclipse Maven Plugin (m2e).
My java program compiles and run correctly from eclipse interface but I am unable to compile and run it from terminal.
My Eclipse Setting:
I am using two third party APIs, for which in eclipse build path I added
"/home/syed/workspace/FirstMaven/target/resources/fuse-jna-master/build/classes" (as external class folder)
"/home/syed/workspace/FirstMaven/target/resources/apache-jena-2.11.1/lib" (as external jars)
Package:
package org.organization.upesh.FirstMaven;
My Project path:
syed#ubuntu:~/workspace/FirstMaven$
Source Code Directory Path:
syed#ubuntu:~/workspace/FirstMaven/src/main/java/org/organization/upesh/FirstMaven$
Classes Directory:
syed#ubuntu:~/workspace/FirstMaven/target/classes/org/organization/upesh/FirstMaven$
When I try to execute myProgram via below command
syed#ubuntu:~/workspace/FirstMaven/target/classes$ java org.organization.upesh.FirstMaven.myProgram
it gives me these errors:
Exception in thread "main" java.lang.NoClassDefFoundError: net/fusejna/util/FuseFilesystemAdapterFull
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Caused by: java.lang.ClassNotFoundException: net.fusejna.util.FuseFilesystemAdapterFull
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
... 13 more
But my test program that do not use the third party API runs correctly via:
syed#ubuntu:~/workspace/FirstMaven/target/classes$ java org.organization.upesh.FirstMaven.test
I think myProgram is not executing because of the two APIs (class folder and jar folder) that I am using.
I have added path of class and jar folders of the APIs to /etc/environment (given below) and rested my computer, but still the same error
PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/syed/workspace/FirstMaven/target/resources/apache-jena-2.11.1/lib:/home/syed/workspace/FirstMaven/target/resources/fuse-jna-master/build/classes"
Please guide me how to run my program correctly

JVM does not get libraries from PATH. It uses special environment variable CLASSPATH that can contain a list of directories or jar files separated by colon on Unix or semicolon on Windows.
So, just define CLASSPATH and put references to all your libraries there.
Aleternatively (and IMHO better) use command line switch -classpath (or its alias -cp) when running java:
java -cp mylib1.jar:mylib2.jar com.mycompany.Main

Java program does not run and throws an error about classes

So I want to run my just compiled Start.class file that I compiled from Start.java. The problem is that it will throw this error:
java Start
Exception in thread "main" java.lang.NoClassDefFoundError: Start (wrong name: files/Start)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
I have written the program in Eclipse and I want to run it from a Terminal. What is the problem here?
New error:
java files.Start http://mirror.symnds.com/software/Apache/tomcat/tomcat-7/v7.0.53/bin/apache-tomcat-7.0.53.zip
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/io/IOUtils
at files.Start.main(Start.java:93)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.io.IOUtils
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
... 1 more

Please have a look at How to Compile and Run Java Code from a Command Line where you will get the information about the class path and how to add dependent jars in class path.
Here is the details from above link.
Task
Lets say we have a fairly standard java project that consists of three top level folders:
/bin - empty folder that will contain compiled .class files
/lib - contains third party .jar files
/src - contains .java source files`
Our task would be to compile and launch the project from its root folder. We will use Windows OS as example (on Unix systems the only difference would be path separation symbol - ":" instead of ";").
Compiling Java Code
The first step is compiling plain text .java sources into Java Virtual Machine byte code (.class files). This is done with javac utility that comes with JDK.
Assuming we are at the application root folder trying to compile Application.java file from com.example package that uses lib1.jar and lib2.jar libraries from lib folder to a destination bin folder, compilation command should have the following format:
javac -d bin -sourcepath src -cp lib/lib1.jar;lib/lib2.jar src/com/example/Application.java

Java: Issue running from command line

I'm writing a program in Eclipse, and running it from the command line. In an earlier version of the program, it took no arguements, and I could run it fine as > java foo. I've since added a couple of arguments, and need to run it as > java foo file1.txt file2.txt. When I run this, I get a java.lang.NoClassDefFoundError: error. Even when I include the classpath, i.e. > java foo file1.txt file2.txt -cp . it still doesn't work.
Could someone point me in the right direction?
EDIT
Here is the complete stack trace
Exception in thread "main" java.lang.NoClassDefFoundError: edu/cuny/pausePred/TemplateToCharTestVector (wrong name: edu/cuny/pausepred/TemplateToCharTestVector)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:791)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:480)

Write the full directory path then compile all classes
Write the full directory and run the class that contains the main() method

A common mistake for beginners in using Java is misunderstanding class names and the classpath.
A class name is a fully qualified thing which includes the package; the compiler lets you refer to a class using its base name, which is a convenience to keep programming sane. The actual name of your class is <package>.foo.
The classpath must include the root of any packages which you are using. So if your package for foo is edu.cuny.pausePred then the class name for foo is edu.cuny.pausePred.foo and the classpath must include the directory which contains edu, not the directory which contains foo.
You command line should be something like:
jave -cp the-directory-root-for-java-sources foo file1.txt file2.txt
noting that this assumes that the two data files are in the current directory.
As an aside, note that a class base name should be lead uppercase, so Foo, not foo.

Exception in thread "main" java.lang.NoClassDefFoundError:
edu/cuny/pausePred/TemplateToCharTestVector
(wrong name: edu/cuny/pausepred/TemplateToCharTestVector)
Paths in java are case-sensitive. pausepred is not the same as pausePred