T1 Java programming for bioinformatics

T1 Java programming for bioinformatics - BIOC1805 Elements...

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BIOC1805 Elements of Bioinformatics Java programming for bioinformatics Instructor: Junwen John Wang Department of Biochemistry 22-Jan-09
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The instructor ± Name: Dr. Junwen John Wang ± Office: 3/F, Laboratory Block, room 78 ± Email: [email protected] , phone: 2819-2809 ± Website: http://www.hku.hk/biochem/research/jjwang/pi_jjwang. html 2
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Lecture information ± Time: ± 10:40~12:30am, every other Wednesday, between 21/1/2009~15/4/09 ± Location: ± CALLab – Computer Aided Learning Center, LG1/F, William Mong Block ± Prerequisites: ± CSIS1117 Computer Programming I or equivalent ± Evaluation: ± One project ± Textbook: ± Thinking in Java by Bruce Eckel, downloadable from http://mindview.net/Books/TIJ/DownloadSites 3
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Temporary schedules Date Topic 21-Jan Introduction, netbeans, primitives, string, objects 11-Feb Java IO, API, data structures, serialization, thread, exceptions 18-Feb Java Swing, animation, Model-View-Controller, design patterns 18-Mar JSP/Servlets, html/xhtml/XML/CSS 01-Apr Javascript, AJAX 15-Apr Java packages for bioinformatics, WEKA, BioJAVA 4
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Introduction to java
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What You Need ± Have your own computer ± Download and install netbeans with Java ± http://java.sun.com/j2se/1.5.0/download-netbeans.html ± Alternatively, download and install Eclipse ± http://www.eclipse.org/downloads/ ± By the way: the JDK, netbeans and Eclipse are free 6
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Vocabulary I ± JRE, Java Runtime Environment ± This is the software that allows you to run Java programs on your computer ± JDK, Java Development Kit (previously called SDK, System Development Kit) ± The software that allows you to create and run Java programs on your computer ± When you install the SDK, you get a JRE along with it ± IDE, Integrated Development Environment ± A tool, such as Eclipse, that makes it easier to write programs 7
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What is Java? ± Java is a programming language: a language that you can learn to write, and the computer can be made to understand ± Java is currently a very popular language ± Java is a large, powerful language ± but it is not simple! ± Compared to C++, Java is elegant 8
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Structure of a Java program ± A program, or project, consists of one or more packages ± Package = directory = folder ± A package contains one or more classes ± A class contains one or more fields and methods ± A method contains declarations and statements ± Classes and methods may also contain comments ± We’ll begin by looking at the “insides” of methods 9 • packages • classes • fields • methods • declarations • statements Project:
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Some Java data types ± In Java, the four most important primitive (simple) types are: ± int variables hold integer values ± double variables hold floating-point numbers, that is, numbers containing a decimal point ± boolean variables hold a true or false value ± char variables hold single characters ± Another important type is the String ± A String is an Object, not a primitive type ± A String is composed of zero or more chars 10
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This note was uploaded on 07/29/2010 for the course BIOC BIOC1805 taught by Professor Dr.brianwong during the Summer '09 term at HKU.

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T1 Java programming for bioinformatics - BIOC1805 Elements...

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