Option 1: if the program shows an icon on left-side start bar when you open the program through terminal, then right click on that icon , and select " Lock to launcher" option.
Option 2: install GNOME Do. This little program shows up on login, and you type the name of any app that you wanna start.
Option 3: Classic menu.
In software center download Classic Ubuntu Menu. It's an equivalent of start menu in Windows XP, and lists almost all programs you installed on Ubuntu.
Option 4 : Configure File Manager in Edit-> Properties -> Behavior to "Run executable text files when they are opened. " That way, you can make a scrip to open this program in xterm or another terminal emulator.
So having changed file manager behavior, create a new text file on desktop , and open with your favourite text editor. For me that's nano, so i would type in terminal:
nano ~/Desktop/Shortcut_Script.sh
And in this script file put the following lines
#!/bin/bash
xterm -hold -e " /path/to/your/program/java -cp jts.jar:total.2013.jar -Xmx512M -XX:MaxPermSize=128M jclient.LoginFrame "
A small explanation here: this script basically calls xterm window, tells it to stay on (hold), and execute the commands enclosed by double quotes. From reading your question, I understand that you first need to navigate to the right folder, and then call the program, right ? So /path/to/your/program/ part should let you call that program in the right folder, while staying in the original start folder for xterm (which is your home/user folder). Now, if this does not work, and you do need to navigate to the folder, what you can do is this:
xterm -hold -e " cd /path/to/your/program/ ; java -cp jts.jar:total.2013.jar -Xmx512M -XX:MaxPermSize=128M jclient.LoginFrame "
Notice the semicolon. As you may know, it separates commands to bash. It will execute cd /path/to/your/folder first, and call the program second.