Introduc{On to Java, Etc

Introducon to Java, etc.

August 2012 Connecng to the class server

• Class server : bio5495-work.wustl.edu • Username = ﬁrst inial last name for eg : aeinstein • Password = 123 for eg : aeinstein123 • Mac Users : Applicaons àUlies à Terminal ssh [email protected] • Windows Users : ssh client like PuTTy/ WinSCP Hostname = bio5495-work.wustl.edu

(Last year the class server was Warlord, incase you noce it in the notes, read as class server)

SSH and SFTP

• Login : use secure shell – ssh [email protected] • Transfer ﬁles : use secure ﬁle transfer protocol – sp [email protected] Quick Unix Overview

ls list files ls -l list files (long format) ls –a list all files (hidden too) man (command) help cd change directory mkdir make directory cp source folder copy source to folder mv source folder mover source to folder rm filename remove filename rmdir folder remove empty directory rm -rf folder remove directory and all its contents

Need more? Search ‘unix commands cheat sheet’ Sp commands

• cd folder: change current locaon to folder on the server • lcd folder :change current locaon to folder on the local machine • ls : list files in the current folder on the server • lls : list files in the current folder on the local machine • Once you are in the correct folders on both ends : – get file : download a file (accepts wildcards like "*") – put file : upload a file (accepts wildcards like "*") Java Development Environment

• IDE (Integrated Development Environment) – Eclipse • hp://www.eclipse.org/downloads/ • Download Eclipse Classic 3.7 • Tutorials available on our website – Netbeans – DrJava • Text Editor – Emacs – VIM • Get Eclipse and ssh clients • Create Helloworld.java in Eclipse public class HelloWorld { public static void main(String[] args) { System.out.println("Hello, World!"); } } Run program using: • Upload Helloworld.java on your account on the server using sp/puy • Stfp [email protected] • $ lls, lcd to the local folder conaning helloworld.java • $ put helloworld.java • Login via ssh • Compile and run the program on the Server $ javac HelloWorld.java (Java Program à Compiler à Java Bytecode) $ java HelloWorld (Java Bytecode à Java Virtual Machine à Output)

Comments - Comment your code!

// Single Line Comments

/* Multi Line Comments */ Object Oriented Programming

• Objects : States and Behavior • Classes : Blueprint for objects • Methods : Operaons class Bicycle { class BicycleDemo { public stac void main(String[] args) { int speed = 0; int gear = 1; // Create two diﬀerent Bicycle objects Bicycle bike1 = new Bicycle(); void changeGear(int newValue) { Bicycle bike2 = new Bicycle(); gear = newValue; } // Invoke methods on those objects

void speedUp(int increment) { bike1.speedUp(10); speed = speed + increment; bike1.changeGear(2); } bike1.printStates();

void applyBrakes(int decrement) { bike2.speedUp(15); speed = speed - decrement; bike2.changeGear(5); } bike2.printStates(); } void printStates() { } System.out.println(" speed:" + speed + " gear:" + gear); Speed : 10 Gear 2 } Speed : 15 Gear 5 } Methods

Every method in java must be deﬁned within some class. ( ) { } // Example method: main public static void main(String[] args) { System.out.println("Hello, World!"); } Method Parameters args contains an command-line arguments

Example: public class TestArgs { public static void main(String[] args) { System.out.println("First Argument: " + args[0]); System.out.println("Second Argument: " + args[1]); } }

If you run this: $ java TestArgs comp bio

First Argument: comp Second Argument: bio Class Example 1 - Math

Math.abs(x) Math.sin(x), Math.cos(x), Math.tan(x) Math.exp(x) // number e raised to the power x Math.log(x) // logarithm of x in the base e Math.pow(x, y) // x raised to y Math.floor(x) Math.random() Class Example 2 - Sequence public class Sequence { // class variables static int maxLength = 1000; // member variables private String name; private String seq; // member methods public Sequence reverseComplement() { ... } public Sequence getSubsequence(int_sta, int_end, boolean_pos) { ... } } Constructors

• Special block of code to inialize an object • Every class has a default constructor • Deﬁne your own constructor: // constructor public Sequence(String n, String s) { name = n; seq = s; } ... Sequence gene1 = new Sequence(“gene1", "ATCG"); Geers and Seers

• Declare variables of classes private • Private variables can only be used by the class where it is deﬁned public String getName() { return name; } public void setName( String newName ) { name = newName; } gene1.setName(“TP53”); Packages and Imports

Java classes can be grouped together in packages. • Example: Java.util To use a package’s classes inside a Java source ﬁle, import the classes from the package with animport declaraon: • import java.util.*; – import java.util.Random; – import java.util.Scanner; – import java.util.Vector; – import java.util.Collections; – import java.util.ArrayList; – import java.util.LinkedList; – import java.util.List; • import java.io.*; – import java.io.File; Control Structures while ( ) { } ... if ( ) { } else { } Control Structures, cont. do { } while ( );

... for ( ; ; ) { }

For eg : for (i = 0; i <5; i++) Arrays

• An array is a data structure consisng of a numbered list of items, where all the items are of the same type. • Example: – int[] list = new int[5]; – list is an array of ﬁve integers Important Notes about Arrays

int[] list = new int[5];

• The array “knows” how long it is (list.length) • The length of the array cannot be changed aer it has been Inialized • Array indexing starts with zero • Newly created arrays are automacally ﬁlled with zeros (numbers), false (boolean values), Unicode number zero (char), or null (objects) Mul-dimensional Arrays

There are no limit on the number of dimensions that an array type can have: int[][] A = new int[3][4]; for (int row = 0; row < 3; row++} { for (int column = 0; column < 4; column++) { A[row][column] = 1; } } ArrayLists

An ArrayList is like a regular array, however, the size can be increased at will

• java.util.ArrayList Example: – ArrayList seqs = new ArrayList(); – seqs.add(newSequence); – seqs.remove(sequence); – seqs.size(); – seqs.get(N); – seqs.set(N, sequence); – seqs.indexOf(sequence); Relaonal and Boolean Operators

A == B A != B A < B A > B A <= B A >= B A || B A && B !A Strings

String s1, s2; s1.equals(s2); s1.equalsIgnoreCase(s2); s1.length(); s1.charAt(N); s1.substring(N,M); s1.indexOf(s2); s1.compareTo(S2); s1.toUpperCase(); s1.trim(); Random Numbers import java.util.Random;

// Uses time in milliseconds as the seed Random r = new Random();

// Uses the provided seed for testing purposes Random r = new Random(long seed);

// All methods return a uniform distribution of values, // except nextGaussian(). Assume r is a Random object. int i = r.nextInt(int n) int i = r.nextInt() long l = r.nextLong() float f = r.nextFloat() double d = r.nextDouble() boolean b = r.nextBoolean() double d = r.nextGaussian() Common mistakes

• Naming the Class Differently from its File Name • Comparing Strings/Objects with == • Neglecng Import Statements • Null pointers • Accessing non-stac member variables from stac methods • Forgeng java is zero-indexed • Type mismatch/invalid cast • Case sensivity • Treang Strings as In/Out parameters Underflow/Overflow - How to Deal

• Problem: underflow – can occur when the true result of a floang point operaon is smaller in magnitude (that is, closer to zero) than the smallest value representable as a normal floang point number in the target datatype

• Soluon: calculate in log space – very small numbers can be represented Logarithm Review

y x = b à y = logbx Basic Rules of Logarithms:

1. logb(xy) = logbx + logby

2. logb(x/y) = logbx - logby n 3. logb(x ) = n*logbx 4. logbx = logax/logab • Be careful : if x = zero, try and set x to a very small value