This document provides instructions to run BlockMatch on Windows XP system.

Our intent here is to show the user how to run BlockMatch without worrying
about setting paths, etc.

Step 1:
Click on the Start menu item on the left corner of your screen, then click on Run
on the pop-up menu, and then type in cmd so that you are in the DOS
environment.

Step 2:
Suppose you are now in the directory C:\Documents and Settings\johnsmith
(assuming your user name is johnsmith). Use the cd command to change to the C
directory as follows:
C:\Documents and Settings\johnsmith>cd ..
C:\Documents and Settings>cd ..
C:\>

Step 3:
Then use the mkdir command to create a new directory, called BlockMatch,
under the C drive as follows:
C:\>mkdir BlockMatch

Enter the BlockMatch directory by typing the cd command as follows:

C:\>cd BlockMatch
Now you are in the BlockMatch directory.

Step 4:
Go to the download webpage and use QUICK DOWNLOAD to download the
BlockMatch.jar file into your BlockMatch directory. Notice that when this file is
saved in your BlockMatch directory, it is called BlockMatch.zip. Use the move
command to change the file name to BlockMatch.jar as follows:
C:\BlockMatch>move BlockMatch.zip BlockMatch.jar

Some browsers allow you to save the file with the name BlockMatch.jar, for
which case skip executing the above renaming command.

Also, download additional files codeTable.Properties, ScoreMat.Structure and

sample input files (IRE.STO and RF00037.seed) into your BlockMatch directory.
To see all files available in your BlockMatch directory, you can use the dir
command as following:
C:\BlockMatch>dir

Step 5:
Then go to the documentation webpage to download Java. When you are led to
the java.sun.com webpage, you see Get the JDK download. Click on it and you
will be led to a webpage in which you are asked to select a platform. Select
Windows. Then you will be led to a new webpage where you see different files.
Download Windows Online Installation and save it in your BlockMatch
directory. Then Run the download file to install Java.
Since Java is now installed in your BlockMatch directory, there is no need to set
up any path.

Step 6:
Now, You can run the software using following command:
C:\BlockMatch>java –jar BlockMatch.jar -q IRE.STO –d RF00037.seed

This will display output on screen and it also generates default output file
“junk.out” in your BlockMatch directory. To see the contents, use the type or
more command as following:
C:\BlockMatch>more junk.out
Alternatively you can go to Windows and open the file to see its contents.

Finally use the exit command to terminate the DOS session and return to
Windows.