Debian java confusion

On my Debian laptop, I've been having several java apps hang up on me and need to be killed. Primarily, these have been UI apps, like MagicDraw and UI installers, Like Metro 1.4, which I needed for NHIN Connect.

Looking into this, I found two versions of java installed, the 1.5 Gnu Compiler for java, and the 1.6.0 JDK from sun.

/usr/lib/jvm$ ls
java-1.5.0-gcj-4.3-1.5.0.0 java-6-sun java-6-sun-1.6.0.12 java-gcj

So which am I running?

/usr/lib/jvm$ which java
/usr/bin/java

Which is a symbolic link to /etc/alternatives/java. Looking further, looks as though /etc/alternatives is pointing to a mix of 1.5gcj/1.6jdk. This is somewhat less than ideal.

/etc/alternatives$ ls -lgo ja* | grep gcj | cut -c34-
jar -> /usr/lib/jvm/java-gcj/jre/bin/jar
jar.1.gz -> /usr/lib/jvm/java-gcj/man/man1/jar.1.gz
java -> /usr/lib/jvm/java-gcj/jre/bin/java

jeff@oci1412:/etc/alternatives$ ls -lgo ja* | grep sun | cut -c34-
jarsigner -> /usr/lib/jvm/java-6-sun/bin/jarsigner
jarsigner.1.gz -> /usr/lib/jvm/java-6-sun/man/man1/jarsigner.1.gz
javac -> /usr/lib/jvm/java-6-sun/bin/javac
javac.1.gz -> /usr/lib/jvm/java-6-sun/man/man1/javac.1.gz
javadoc -> /usr/lib/jvm/java-6-sun/bin/javadoc
javadoc.1.gz -> /usr/lib/jvm/java-6-sun/man/man1/javadoc.1.gz
javah -> /usr/lib/jvm/java-6-sun/bin/javah
javah.1.gz -> /usr/lib/jvm/java-6-sun/man/man1/javah.1.gz
javap -> /usr/lib/jvm/java-6-sun/bin/javap
javap.1.gz -> /usr/lib/jvm/java-6-sun/man/man1/javap.1.gz
java-rmi.cgi -> /usr/lib/jvm/java-6-sun/bin/java-rmi.cgi
java_vm -> /usr/lib/jvm/java-6-sun/jre/bin/java_vm
javaws -> /usr/lib/jvm/java-6-sun/jre/bin/javaws
javaws.1.gz -> /usr/lib/jvm/java-6-sun/jre/man/man1/javaws.1.gz

Easy enough to (attempt to) fix:
/etc/alternatives$ sudo rm jar
/etc/alternatives$ sudo ln -s /usr/lib/jvm/java-6-sun/bin/jar ./jar
/etc/alternatives$ sudo rm java
/etc/alternatives$ sudo ln -s /usr/lib/jvm/java-6-sun/bin/java ./java
/etc/alternatives$ sudo rm jar.1.gz
/etc/alternatives$ sudo ln -s /usr/lib/jvm/java-6-sun/man/man1/jar.1.gz

And verify:
/etc/alternatives$ ls -lgo ja* | grep gcj | cut -c34-

Problem Solved!