I just installed java according to this article, and java -version displays

java version "1.7.0_07"

Java(TM) SE Runtime Environment (build 1.7.0_07-b10)

Java HotSpot(TM) 64-Bit Server VM (build 23.3-b01, mixed mode)

update-alternatives --config java' returns this:

There are 2 choices for the alternative java (providing /usr/bin/java).



  Selection    Path                                  Priority   Status

------------------------------------------------------------

  0            /usr/bin/gij-4.6                       1046      auto mode

  1            /usr/bin/gij-4.6                       1046      manual mode

* 2            /usr/local/java/jdk1.7.0_07/bin/java   1         manual mode



Press enter to keep the current choice[*], or type selection number: 

with update-alternatives --config javac (or javaws) returning similarly.

however Java isn't listed in the default applications menu when I click on a .jar file and go to "open with application".

• I tried to install Java this way, and on the update-alternatives part of the command returned me:

  
  

  
  

  /etc/alternatives/[java,javac,javaws] is dangling, it will be updated with best choice

  
  

  
  



• I just confirmed that I can use Java, as java -jar file.jar does work.

  
  



• Just figured that I'd mention it, don't know why I didn't before, but when I right click on a .jar file, Java 7 run-time isn't even listed there, it seems that the file manager isn't recognizing it as a program, but it is there, and it does work...

  
  

CAUSE OF THE PROBLEM

After much experimenting, and research, I've found the cause of the problem - a missing .desktop file in /usr/share/applications. I've posted an answer that you can use to manually create an entry, but as stated it isn't recomended as I'm sure that there's a better way to do it.