Full Setup

Requirements

For recreating the environment that was used to write the provided software, you need Perl (Version 5.8.6), Java 2 Platform Standard Edition (Version 1.5.0 or 5.0), and a PostgreSQL database (Version 7.4.6).

Setup

Using the Perl Code and the Java Code recreate the environment as follows:

1. Database Requirements
2. Partitioning the Data
3. Clustering Sequences

Required Changes

In order to run the Perl scripts so that they access a database, the file 000databaseconnect.pl has to be adjusted. It contains the connection string for accessing the database.

In order to run the Java programs so that they access a database, the file PostgreSqlConnection.java has to be adjusted. It contains the connection string for accessing the database. This requires the recompilation of the PostgreSqlConnection.java file.

Compilation

For compiling the Java Code, the following command should be used:

javac -classpath .;./lib/colt.jar;./lib/commons-collections-3.1.jar;./lib/commons-collections-testframework-3.1.jar;./lib/concurrent.jar;
./lib/jung-1.7.2.jar;./lib/junit.jar;./lib/postgresql-8.0-311.jdbc3.jar;./lib/resolver.jar;./lib/xercesImpl.jar;./lib/xml-apis.jar
*.java .\gui\StandAlone.java

Execution

For executing any program of the Java Code, the following command should be used:

java -cp .;./lib/colt.jar;./lib/commons-collections-3.1.jar;./lib/commons-collections-testframework-3.1.jar;./lib/concurrent.jar;
./lib/jung-1.7.2.jar;./lib/junit.jar;./lib/postgresql-8.0-311.jdbc3.jar;./lib/resolver.jar;./lib/xercesImpl.jar;./lib/xml-apis.jar
-Xmx1024m <Java Class Name> <Parameters>