Perl Java and Biojava

Contents: Preface. I. Perl for bioinformatics: 1. Perl control flow motif. 2. Basic operators lists and arrays file handling pattern matching. 3. Subroutines hashes and application in bioinformatics. II. Java, Bio java and Bio java packages: 4. Java for bioinformatics. 5. Java programming. 6. Object oriented programming. 7. Exception handling. 8. Event handling. 9. Interfaces and packages. 10. Multithreading in Java. 11. Applets and graphics. 12. Java database and connectivity. 13. Network programming with Java. 14. Bio java. Glossary of definitions used in Java. Bibliography. Index. One characteristic of Java is portability which means that computer programs written in the Java language must run similarly on any hardware/operating system platform. This is achieved by compiling the Java language code to an intermediate representation called Java bytecode, instead of directly to platform-specific machine code. Java bytecode instructions are analogous to machine code but they are intended to be interpreted by a virtual machine VM written specifically for the host hardware. End-users commonly use a Java Runtime Environment (JRE) installed on their own machine for standalone Java applications, or in a web browser for Java applets. Bio Java is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the Bio java project is to facilitate rapid application development for bioinformatics. (jacket).…