JAVA_HOME and PATH are set but java -version still shows the old one

While it looks like your setup is correct, there are a few things to check:

1. The output of env - specifically PATH.
2. command -v java tells you what?
3. Is there a java executable in $JAVA_HOME\bin and does it have the execute bit set? If not chmod a+x java it.

I trust you have source'd your .profile after adding/changing the JAVA_HOME and PATH?

Also, you can help yourself in future maintenance of your JDK installation by writing this instead:

export JAVA_HOME=/home/aqeel/development/jdk/jdk1.6.0_35
export PATH=$JAVA_HOME/bin:$PATH

Then you only need to update one env variable when you setup the JDK installation.

Finally, you may need to run hash -r to clear the Bash program cache. Other shells may need a similar command.

Cheers,

update-java-alternatives

The java executable is not found with your JAVA_HOME, it only depends on your PATH.

update-java-alternatives is a good way to manage it for the entire system is through:

update-java-alternatives -l

Sample output:

java-7-oracle 1 /usr/lib/jvm/java-7-oracle
java-8-oracle 2 /usr/lib/jvm/java-8-oracle

Choose one of the alternatives:

sudo update-java-alternatives -s java-7-oracle

Like update-alternatives, it works through symlink management. The advantage is that is manages symlinks to all the Java utilities at once: javac, java, javap, etc.

I am yet to see a JAVA_HOME effect on the JDK. So far, I have only seen it used in third-party tools, e.g. Maven.