# Marine Biology Simulation

### Information on compiling and running the Marine Biology Simulation using TextPad:

This file assumes that you have already downloaded and installed TextPad, and used it to compile simple programs.

The easiest way to compile and run the Marine Biology Simulation program, copy the `compMBS.bat` and `runMBS.bat` files (for "Compile MBS" and "Run MBS") from the `DOSandWindows` folder to the `JavaMBS\Code` folder. If your system cannot find the javac and java commands (if they are not in a folder in your `PATH` environment variable), edit the two batch files and fully specify where javac.exe and java.exe can be found. You can then run `compMBS` directly in a DOS or Command Prompt window (you must move to the `Code` directory first), or run it from within Textpad by choosing Tools -> Run. (You can open a file in the `Code` directory first to make sure you're in the right directory.) Type in

      compMBS

as the Command, and leave the Parameters and Initial folder fields blank. Click on OK. The command will compile all the Java source files in the current directory (`Code`). You can also compile the files individually (see below), but then you need to keep track of which source files have been modified.

To run the Marine Biology Simulation program, choose Tools -> Run again, but this time type

      runMBS

as the Command and one of the following class names in the Parameters field:

        MBSGUI            program with full graphical user interface
                            (from beginning of Chapter 1)
        SimpleMBSDemo1    simple demo program (end of Chapter 1)
        SimpleMBSDemo2    second demo program (end of Chapter 1)

If you do not specify the target, `runMBS` will use `MBSGUI`.

When you go to open an environment data file, the file chooser window should come up in the `Code` folder, where the program is running. You will need to go up to the `JavaMBS` folder and then down to the `DataFiles` folder to find the initial configuration files.

For Chapter 3 (and later chapters), if you are using the `Fish.java` file from the `DynamicPopulation` folder rather than modifying the file in the `Code` folder (see `FishModsForChap3.txt` in the `Code` folder for more details), copy the `compDPop.bat` file from the `DOSandWindows` folder to the `JavaMBS\Code` folder. Correct the full path name for the javac command as you did in `compMBS.bat` (if necessary). Run `compDPop` from the `Code` folder. (You can open a file in the `Code` folder to make sure you're in the right folder.) This command will compile the `Fish` class in the `DynamicPopulation` folder and then copy the compiled class file to the `Code` folder. Then run the Marine Biology Simulation as usual.

### Compiling Java Source Files Individually

To compile source files individually from within TextPad, you will first need to set your "classpath" to find the jar files containing the black box and graphical user interface classes.

One way to do this is to set the classpath within the TextPad preferences. Go to Configure -> Preferences and click on "Compile Java" under the Tools topic. The input field for Parameters: should say "$File". Modify this field so that it has

       -classpath .;.\mbsbb.jar;.\mbsgui.jar $File

Then click on OK. You can modify the Parameters for "Run Java Application" by inserting the same classpath information before $BaseName. [Warning: The disadvantage of this technique is that you will now be using this classpath whenever you compile or run Java files within TextPad, at least until you change the preferences again. This should not create problems for you, though, unless you compile other programs that use the same class names as the MBS black box and GUI code.]

You can also set the CLASSPATH environment variable through AUTOEXEC.BAT or through the control panel. In either case, first check whether CLASSPATH is already defined.

      - Yes:  prepend     .;.\mbsbb.jar;.\mbsgui.jar;
      - No:   set it to   .;.\mbsbb.jar;.\mbsgui.jar

[Warning: The disadvantage of this technique is that you will now be using this classpath whenever you compile a Java file. This should not create problems for you, though, unless you compile other programs that use the same class names as the MBS black box and GUI code.]

Once you have set your classpath, you can compile individual Java source files using the Compile Java option in the Tools menu.